Familial aggregation of MATRICS Consensus Cognitive Battery scores in a large sample of outpatients with schizophrenia and their unaffected relatives.

PubMed

Mucci, A; Galderisi, S; Green, M F; Nuechterlein, K; Rucci, P; Gibertoni, D; Rossi, A; Rocca, P; Bertolino, A; Bucci, P; Hellemann, G; Spisto, M; Palumbo, D; Aguglia, E; Amodeo, G; Amore, M; Bellomo, A; Brugnoli, R; Carpiniello, B; Dell'Osso, L; Di Fabio, F; di Giannantonio, M; Di Lorenzo, G; Marchesi, C; Monteleone, P; Montemagni, C; Oldani, L; Romano, R; Roncone, R; Stratta, P; Tenconi, E; Vita, A; Zeppegno, P; Maj, M

2018-06-01

The increased use of the MATRICS Consensus Cognitive Battery (MCCB) to investigate cognitive dysfunctions in schizophrenia fostered interest in its sensitivity in the context of family studies. As various measures of the same cognitive domains may have different power to distinguish between unaffected relatives of patients and controls, the relative sensitivity of MCCB tests for relative-control differences has to be established. We compared MCCB scores of 852 outpatients with schizophrenia (SCZ) with those of 342 unaffected relatives (REL) and a normative Italian sample of 774 healthy subjects (HCS). We examined familial aggregation of cognitive impairment by investigating within-family prediction of MCCB scores based on probands' scores. Multivariate analysis of variance was used to analyze group differences in adjusted MCCB scores. Weighted least-squares analysis was used to investigate whether probands' MCCB scores predicted REL neurocognitive performance. SCZ were significantly impaired on all MCCB domains. REL had intermediate scores between SCZ and HCS, showing a similar pattern of impairment, except for social cognition. Proband's scores significantly predicted REL MCCB scores on all domains except for visual learning. In a large sample of stable patients with schizophrenia, living in the community, and in their unaffected relatives, MCCB demonstrated sensitivity to cognitive deficits in both groups. Our findings of significant within-family prediction of MCCB scores might reflect disease-related genetic or environmental factors.

Use of job-exposure matrices to estimate occupational exposure to pesticides: A review.

PubMed

Carles, Camille; Bouvier, Ghislaine; Lebailly, Pierre; Baldi, Isabelle

2017-03-01

The health effects of pesticides have been extensively studied in epidemiology, mainly in agricultural populations. However, pesticide exposure assessment remains a key methodological issue for epidemiological studies. Besides self-reported information, expert assessment or metrology, job-exposure matrices still appear to be an interesting tool. We reviewed all existing matrices assessing occupational exposure to pesticides in epidemiological studies and described the exposure parameters they included. We identified two types of matrices, (i) generic ones that are generally used in case-control studies and document broad categories of pesticides in a large range of jobs, and (ii) specific matrices, developed for use in agricultural cohorts, that generally provide exposure metrics at the active ingredient level. The various applications of these matrices in epidemiological studies have proven that they are valuable tools to assess pesticide exposure. Specific matrices are particularly promising for use in agricultural cohorts. However, results obtained with matrices have rarely been compared with those obtained with other tools. In addition, the external validity of the given estimates has not been adequately discussed. Yet, matrices would help in reducing misclassification and in quantifying cumulated exposures, to improve knowledge about the chronic health effects of pesticides.

What is the effect of matrices on cartilage repair? A systematic review.

PubMed

Wylie, James D; Hartley, Melissa K; Kapron, Ashley L; Aoki, Stephen K; Maak, Travis G

2015-05-01

Articular cartilage has minimal endogenous ability to undergo repair. Multiple chondral restoration strategies have been attempted with varied results. The purpose of our review was to determine: (1) Does articular chondrocyte transplantation or matrix-assisted articular chondrocyte transplantation provide better patient-reported outcomes scores, MRI morphologic measurements, or histologic quality of repair tissue compared with microfracture in prospective comparative studies of articular cartilage repair; and (2) which available matrices for matrix-assisted articular chondrocyte transplantation show the best patient-reported outcomes scores, MRI morphologic measurements, or histologic quality of repair tissue? We conducted a systematic review of PubMed, CINAHL, and MEDLINE from March 2004 to February 2014 using keywords determined to be important for articular cartilage repair, including "cartilage", "chondral", "cell source", "chondrocyte", "matrix", "augment", "articular", "joint", "repair", "treatment", "regeneration", and "restoration" to find articles related to cell-based articular cartilage repair of the knee. The articles were reviewed by two authors (JDW, MKH), our study exclusion criteria were applied, and articles were determined to be relevant (or not) to the research questions. The Methodological Index for Nonrandomized Studies (MINORS) scale was used to judge the quality of nonrandomized manuscripts used in this review and the Jadad score was used to judge the quality of randomized trials. Seventeen articles were reviewed for the first research question and 83 articles were reviewed in the second research question from 301 articles identified in the original systematic search. The average MINORS score was 9.9 (62%) for noncomparative studies and 16.1 (67%) for comparative studies. The average Jadad score was 2.3 for the randomized studies. Articular chondrocyte transplantation shows better patient-reported outcomes at 5 years in patients without chronic symptoms preoperatively compared with microfracture (p = 0.026). Matrix-assisted articular chondrocyte transplantation consistently showed improved patient-reported functional outcomes compared with microfracture (p values ranging from < 0.001 to 0.029). Hyalograft C(®) (Anika Therapeutics Inc, Bedford, MA, USA) and Chondro-gide(®) (Genzyme Biosurgery, Kastrup, Denmark) are the matrices with the most published evidence in the literature, but no studies comparing different matrices met our inclusion criteria, because the literature consists only of uncontrolled case series. Matrix-assisted articular chondrocyte transplantation leads to better patient-reported outcomes in cartilage repair compared with microfracture; however, future prospective research is needed comparing different matrices to determine which products optimize cartilage repair. Level IV, therapeutic study.

Optimal neighborhood indexing for protein similarity search.

PubMed

Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

2008-12-16

Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

Optimal neighborhood indexing for protein similarity search

PubMed Central

Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

2008-01-01

Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. Results The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website . Conclusion We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction. PMID:19087280

Proteoform-specific protein binding of small molecules in complex matrices

USDA-ARS?s Scientific Manuscript database

Characterizing the specific binding between protein targets and small molecules is critically important for drug discovery. Conventional assays require isolation and purification of small molecules from complex matrices through multistep chromatographic fractionation, which may alter their original ...

Dimensionality Assessment for Dichotomously Scored Items Using Multidimensional Scaling.

ERIC Educational Resources Information Center

Jones, Patricia B.; And Others

In order to determine the effectiveness of multidimensional scaling (MDS) in recovering the dimensionality of a set of dichotomously-scored items, data were simulated in one, two, and three dimensions for a variety of correlations with the underlying latent trait. Similarity matrices were constructed from these data using three margin-sensitive…

Linking the Congenital Heart Surgery Databases of the Society of Thoracic Surgeons and the Congenital Heart Surgeons’ Society: Part 1—Rationale and Methodology

PubMed Central

Jacobs, Jeffrey P.; Pasquali, Sara K.; Austin, Erle; Gaynor, J. William; Backer, Carl; Hirsch-Romano, Jennifer C.; Williams, William G.; Caldarone, Christopher A.; McCrindle, Brian W.; Graham, Karen E.; Dokholyan, Rachel S.; Shook, Gregory J.; Poteat, Jennifer; Baxi, Maulik V.; Karamlou, Tara; Blackstone, Eugene H.; Mavroudis, Constantine; Mayer, John E.; Jonas, Richard A.; Jacobs, Marshall L.

2014-01-01

Purpose The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) is the largest Registry in the world of patients who have undergone congenital and pediatric cardiac surgical operations. The Congenital Heart Surgeons’ Society Database (CHSS-D) is an Academic Database designed for specialized detailed analyses of specific congenital cardiac malformations and related treatment strategies. The goal of this project was to create a link between the STS-CHSD and the CHSS-D in order to facilitate studies not possible using either individual database alone and to help identify patients who are potentially eligible for enrollment in CHSS studies. Methods Centers were classified on the basis of participation in the STS-CHSD, the CHSS-D, or both. Five matrices, based on CHSS inclusionary criteria and STS-CHSD codes, were created to facilitate the automated identification of patients in the STS-CHSD who meet eligibility criteria for the five active CHSS studies. The matrices were evaluated with a manual adjudication process and were iteratively refined. The sensitivity and specificity of the original matrices and the refined matrices were assessed. Results In January 2012, a total of 100 centers participated in the STS-CHSD and 74 centers participated in the CHSS. A total of 70 centers participate in both and 40 of these 70 agreed to participate in this linkage project. The manual adjudication process and the refinement of the matrices resulted in an increase in the sensitivity of the matrices from 93% to 100% and an increase in the specificity of the matrices from 94% to 98%. Conclusion Matrices were created to facilitate the automated identification of patients potentially eligible for the five active CHSS studies using the STS-CHSD. These matrices have a sensitivity of 100% and a specificity of 98%. In addition to facilitating identification of patients potentially eligible for enrollment in CHSS studies, these matrices will allow (1) estimation of the denominator of patients potentially eligible for CHSS studies and (2) comparison of eligible and enrolled patients to potentially eligible and not enrolled patients to assess the generalizability of CHSS studies. PMID:24668974

Detecting reliable cognitive change in individual patients with the MATRICS Consensus Cognitive Battery.

PubMed

Gray, Bradley E; McMahon, Robert P; Green, Michael F; Seidman, Larry J; Mesholam-Gately, Raquelle I; Kern, Robert S; Nuechterlein, Keith H; Keefe, Richard S; Gold, James M

2014-10-01

Clinicians often need to evaluate the treatment response of an individual person and to know that observed change is true improvement or worsening beyond usual week-to-week changes. This paper gives clinicians tools to evaluate individual changes on the MATRICS Consensus Cognitive Battery (MCCB). We compare three different approaches: a descriptive analysis of MCCB test-retest performance with no intervention, a reliable change index (RCI) approach controlling for average practice effects, and a regression approach. Data were gathered as part of the MATRICS PASS study (Nuechterlein et al., 2008). A total of 159 people with schizophrenia completed the MCCB at baseline and 4weeks later. Data were analyzed using an RCI and a regression formula establishing confidence intervals. The RCI and regression approaches agree within one point when baseline values are close to the sample mean. However, the regression approach offers more accurate limits for expected change at the tails of the distribution of baseline scores. Although both approaches have their merits, the regression approach provides the most accurate measure of significant change across the full range of scores. As the RCI does not account for regression to the mean and has confidence limits that remain constant across baseline scores, the RCI approach effectively gives narrower confidence limits around an inaccurately predicted average change value. Further, despite the high test-retest reliability of the MCCB, a change in an individual's score must be relatively large to be confident that it is beyond normal month-to-month variation. Copyright © 2014 Elsevier B.V. All rights reserved.

Some Results on Mean Square Error for Factor Score Prediction

ERIC Educational Resources Information Center

Krijnen, Wim P.

2006-01-01

For the confirmatory factor model a series of inequalities is given with respect to the mean square error (MSE) of three main factor score predictors. The eigenvalues of these MSE matrices are a monotonic function of the eigenvalues of the matrix gamma[subscript rho] = theta[superscript 1/2] lambda[subscript rho] 'psi[subscript rho] [superscript…

Qualitative Analysis of the Performance of Introverts and Extraverts on Standard Progressive Matrices

ERIC Educational Resources Information Center

Mohan, Vidhu; Kumar, Dalip

1976-01-01

Does measurement of intelligence through a concolidated score imply that two or more subjects obtaining the same score are also undergoing the same mental process? Introverts are supposed to opt for accuracy and extraverts for speed. Attempts to investigate the qualitative differences between extraverts and introverts on an intelligence test.…

In Spite of Indeterminacy Many Common Factor Score Estimates Yield an Identical Reproduced Covariance Matrix

ERIC Educational Resources Information Center

Beauducel, Andre

2007-01-01

It was investigated whether commonly used factor score estimates lead to the same reproduced covariance matrix of observed variables. This was achieved by means of Schonemann and Steiger's (1976) regression component analysis, since it is possible to compute the reproduced covariance matrices of the regression components corresponding to different…

Commutative semigroups of real and complex matrices. [with use of the jordan form

NASA Technical Reports Server (NTRS)

Brown, D. R.

1974-01-01

The computation of divergence is studied. Covariance matrices to be analyzed admit a common diagonalization, or even triangulation. Sufficient conditions are given for such phenomena to take place, the arguments cover both real and complex matrices, and are not restricted to Hermotian or other special forms. Specifically, it is shown to be sufficient that the matrices in question commute in order to admit a common triangulation. Several results hold in the case that the matrices in question form a closed and bounded set, rather than only in the finite case.

Reference Curves for Field Tests of Musculoskeletal Fitness in U.S. Children and Adolescents: The 2012 NHANES National Youth Fitness Survey.

PubMed

Laurson, Kelly R; Saint-Maurice, Pedro F; Welk, Gregory J; Eisenmann, Joey C

2017-08-01

Laurson, KR, Saint-Maurice, PF, Welk, GJ, and Eisenmann, JC. Reference curves for field tests of musculoskeletal fitness in U.S. children and adolescents: The 2012 NHANES National Youth Fitness Survey. J Strength Cond Res 31(8): 2075-2082, 2017-The purpose of the study was to describe current levels of musculoskeletal fitness (MSF) in U.S. youth by creating nationally representative age-specific and sex-specific growth curves for handgrip strength (including relative and allometrically scaled handgrip), modified pull-ups, and the plank test. Participants in the National Youth Fitness Survey (n = 1,453) were tested on MSF, aerobic capacity (via submaximal treadmill test), and body composition (body mass index [BMI], waist circumference, and skinfolds). Using LMS regression, age-specific and sex-specific smoothed percentile curves of MSF were created and existing percentiles were used to assign age-specific and sex-specific z-scores for aerobic capacity and body composition. Correlation matrices were created to assess the relationships between z-scores on MSF, aerobic capacity, and body composition. At younger ages (3-10 years), boys scored higher than girls for handgrip strength and modified pull-ups, but not for the plank. By ages 13-15, differences between the boys and girls curves were more pronounced, with boys scoring higher on all tests. Correlations between tests of MSF and aerobic capacity were positive and low-to-moderate in strength. Correlations between tests of MSF and body composition were negative, excluding absolute handgrip strength, which was inversely related to other MSF tests and aerobic capacity but positively associated with body composition. The growth curves herein can be used as normative reference values or a starting point for creating health-related criterion reference standards for these tests. Comparisons with prior national surveys of physical fitness indicate that some components of MSF have likely decreased in the United States over time.

Arrowheaded enhanced multivariance products representation for matrices (AEMPRM): Specifically focusing on infinite matrices and converting arrowheadedness to tridiagonality

NASA Astrophysics Data System (ADS)

Özdemir, Gizem; Demiralp, Metin

2015-12-01

In this work, Enhanced Multivariance Products Representation (EMPR) approach which is a Demiralp-and-his- group extension to the Sobol's High Dimensional Model Representation (HDMR) has been used as the basic tool. Their discrete form have also been developed and used in practice by Demiralp and his group in addition to some other authors for the decomposition of the arrays like vectors, matrices, or multiway arrays. This work specifically focuses on the decomposition of infinite matrices involving denumerable infinitely many rows and columns. To this end the target matrix is first decomposed to the sum of certain outer products and then each outer product is treated by Tridiagonal Matrix Enhanced Multivariance Products Representation (TMEMPR) which has been developed by Demiralp and his group. The result is a three-matrix- factor-product whose kernel (the middle factor) is an arrowheaded matrix while the pre and post factors are invertable matrices decomposed of the support vectors of TMEMPR. This new method is called as Arrowheaded Enhanced Multivariance Products Representation for Matrices. The general purpose is approximation of denumerably infinite matrices with the new method.

A Study on the Application of the Extended Matrices Based on TRIZ in Constructing a Collaborative Model of Enterprise Network

NASA Astrophysics Data System (ADS)

Yang, Yan; Shao, Yunfei; Tang, Xiaowo

Based on mass related literature on enterprise network, the key influence factors are reduced to Trust, Control, Relationship and Interaction. Meanwhile, the specific contradiction matrices, judgment matrices and strategy collections based on TRIZ are constructed which make the connotation of contradiction matrices in TRIZ extended. Finally they are applied to the construction of the collaborative model on enterprise network based on Multi Agent System (MAS).

Confirming the cognition of rising scores: Fox and Mitchum (2013) predicts violations of measurement invariance in series completion between age-matched cohorts.

PubMed

Fox, Mark C; Mitchum, Ainsley L

2014-01-01

The trend of rising scores on intelligence tests raises important questions about the comparability of variation within and between time periods. Descriptions of the processes that mediate selection of item responses provide meaningful psychological criteria upon which to base such comparisons. In a recent paper, Fox and Mitchum presented and tested a cognitive theory of rising scores on analogical and inductive reasoning tests that is specific enough to make novel predictions about cohort differences in patterns of item responses for tests such as the Raven's Matrices. In this paper we extend the same proposal in two important ways by (1) testing it against a dataset that enables the effects of cohort to be isolated from those of age, and (2) applying it to two other inductive reasoning tests that exhibit large Flynn effects: Letter Series and Word Series. Following specification and testing of a confirmatory item response model, predicted violations of measurement invariance are observed between two age-matched cohorts that are separated by only 20 years, as members of the later cohort are found to map objects at higher levels of abstraction than members of the earlier cohort who possess the same overall level of ability. Results have implications for the Flynn effect and cognitive aging while underscoring the value of establishing psychological criteria for equating members of distinct groups who achieve the same scores.

Bayes linear covariance matrix adjustment

NASA Astrophysics Data System (ADS)

Wilkinson, Darren J.

1995-12-01

In this thesis, a Bayes linear methodology for the adjustment of covariance matrices is presented and discussed. A geometric framework for quantifying uncertainties about covariance matrices is set up, and an inner-product for spaces of random matrices is motivated and constructed. The inner-product on this space captures aspects of our beliefs about the relationship between covariance matrices of interest to us, providing a structure rich enough for us to adjust beliefs about unknown matrices in the light of data such as sample covariance matrices, exploiting second-order exchangeability and related specifications to obtain representations allowing analysis. Adjustment is associated with orthogonal projection, and illustrated with examples of adjustments for some common problems. The problem of adjusting the covariance matrices underlying exchangeable random vectors is tackled and discussed. Learning about the covariance matrices associated with multivariate time series dynamic linear models is shown to be amenable to a similar approach. Diagnostics for matrix adjustments are also discussed.

Dose reduction of risperidone and olanzapine can improve cognitive function and negative symptoms in stable schizophrenic patients: A single-blinded, 52-week, randomized controlled study.

PubMed

Zhou, Yanling; Li, Guannan; Li, Dan; Cui, Hongmei; Ning, Yuping

2018-05-01

The long-term effects of dose reduction of atypical antipsychotics on cognitive function and symptomatology in stable patients with schizophrenia remain unclear. We sought to determine the change in cognitive function and symptomatology after reducing risperidone or olanzapine dosage in stable schizophrenic patients. Seventy-five stabilized schizophrenic patients prescribed risperidone (≥4 mg/day) or olanzapine (≥10 mg/day) were randomly divided into a dose-reduction group ( n=37) and a maintenance group ( n=38). For the dose-reduction group, the dose of antipsychotics was reduced by 50%; for the maintenance group, the dose remained unchanged throughout the whole study. The Positive and Negative Syndrome Scale, Negative Symptom Assessment-16, Rating Scale for Extrapyramidal Side Effects, and Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) Consensus Cognitive Battery were measured at baseline, 12, 28, and 52 weeks. Linear mixed models were performed to compare the Positive and Negative Syndrome Scale, Negative Symptom Assessment-16, Rating Scale for Extrapyramidal Side Effects and MATRICS Consensus Cognitive Battery scores between groups. The linear mixed model showed significant time by group interactions on the Positive and Negative Syndrome Scale negative symptoms, Negative Symptom Assessment-16, Rating Scale for Extrapyramidal Side Effects, speed of processing, attention/vigilance, working memory and total score of MATRICS Consensus Cognitive Battery (all p<0.05). Post hoc analyses showed significant improvement in Positive and Negative Syndrome Scale negative subscale, Negative Symptom Assessment-16, Rating Scale for Extrapyramidal Side Effects, speed of processing, working memory and total score of MATRICS Consensus Cognitive Battery for the dose reduction group compared with those for the maintenance group (all p<0.05). This study indicated that a risperidone or olanzapine dose reduction of 50% may not lead to more severe symptomatology but can improve speed of processing, working memory and negative symptoms in patients with stabilized schizophrenia.

The method of similar operators in the study of the spectra of the adjacency matrices of graphs

NASA Astrophysics Data System (ADS)

Kozlukov, Serge

2018-03-01

The method of similar operators [1, 2, 3] is used to investigate spectral properties of a certain class of matrices in the context of graphs [4, 5]. Specifically, we consider the adjacency matrix of an “almost-complete graph”. Then we generalize the result to allow the matrices obtained as combinations of the Kronecker products [6, 7] and the small-norm perturbations. We derive the estimates of the spectra and the eigenvectors of such matrices.

How to Get Really Smart: Modeling Retest and Training Effects in Ability Testing using Computer-Generated Figural Matrix Items

ERIC Educational Resources Information Center

Freund, Philipp Alexander; Holling, Heinz

2011-01-01

The interpretation of retest scores is problematic because they are potentially affected by measurement and predictive bias, which impact construct validity, and because their size differs as a function of various factors. This paper investigates the construct stability of scores on a figural matrices test and models retest effects at the level of…

Exploring Possible Neural Mechanisms of Intelligence Differences Using Processing Speed and Working Memory Tasks: An fMRI Study

ERIC Educational Resources Information Center

Waiter, Gordon D.; Deary, Ian J.; Staff, Roger T.; Murray, Alison D.; Fox, Helen C.; Starr, John M.; Whalley, Lawrence J.

2009-01-01

To explore the possible neural foundations of individual differences in intelligence test scores, we examined the associations between Raven's Matrices scores and two tasks that were administered in a functional magnetic resonance imaging (fMRI) setting. The two tasks were an n-back working memory (N = 37) task and inspection time (N = 47). The…

MALDI matrices for low molecular weight compounds: an endless story?

PubMed

Calvano, Cosima Damiana; Monopoli, Antonio; Cataldi, Tommaso R I; Palmisano, Francesco

2018-04-23

Since its introduction in the 1980s, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has gained a prominent role in the analysis of high molecular weight biomolecules such as proteins, peptides, oligonucleotides, and polysaccharides. Its application to low molecular weight compounds has remained for long time challenging due to the spectral interferences produced by conventional organic matrices in the low m/z window. To overcome this problem, specific sample preparation such as analyte/matrix derivatization, addition of dopants, or sophisticated deposition technique especially useful for imaging experiments, have been proposed. Alternative approaches based on second generation (rationally designed) organic matrices, ionic liquids, and inorganic matrices, including metallic nanoparticles, have been the object of intense and continuous research efforts. Definite evidences are now provided that MALDI MS represents a powerful and invaluable analytical tool also for small molecules, including their quantification, thus opening new, exciting applications in metabolomics and imaging mass spectrometry. This review is intended to offer a concise critical overview of the most recent achievements about MALDI matrices capable of specifically address the challenging issue of small molecules analysis. Graphical abstract An ideal Book of matrices for MALDI MS of small molecules.

ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES.

PubMed

Fan, Jianqing; Rigollet, Philippe; Wang, Weichen

High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other ℓ r norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous results on functional estimation, the minimax rates exhibit an elbow phenomenon. Our results are further illustrated in simulated data as well as an empirical study of data arising in financial econometrics.

ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES

PubMed Central

Fan, Jianqing; Rigollet, Philippe; Wang, Weichen

2016-01-01

High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other ℓr norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous results on functional estimation, the minimax rates exhibit an elbow phenomenon. Our results are further illustrated in simulated data as well as an empirical study of data arising in financial econometrics. PMID:26806986

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

PubMed

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data.

PubMed

Kundu, Kousik; Costa, Fabrizio; Huber, Michael; Reth, Michael; Backofen, Rolf

2013-01-01

Src homology 2 (SH2) domains are the largest family of the peptide-recognition modules (PRMs) that bind to phosphotyrosine containing peptides. Knowledge about binding partners of SH2-domains is key for a deeper understanding of different cellular processes. Given the high binding specificity of SH2, in-silico ligand peptide prediction is of great interest. Currently however, only a few approaches have been published for the prediction of SH2-peptide interactions. Their main shortcomings range from limited coverage, to restrictive modeling assumptions (they are mainly based on position specific scoring matrices and do not take into consideration complex amino acids inter-dependencies) and high computational complexity. We propose a simple yet effective machine learning approach for a large set of known human SH2 domains. We used comprehensive data from micro-array and peptide-array experiments on 51 human SH2 domains. In order to deal with the high data imbalance problem and the high signal-to-noise ration, we casted the problem in a semi-supervised setting. We report competitive predictive performance w.r.t. state-of-the-art. Specifically we obtain 0.83 AUC ROC and 0.93 AUC PR in comparison to 0.71 AUC ROC and 0.87 AUC PR previously achieved by the position specific scoring matrices (PSSMs) based SMALI approach. Our work provides three main contributions. First, we showed that better models can be obtained when the information on the non-interacting peptides (negative examples) is also used. Second, we improve performance when considering high order correlations between the ligand positions employing regularization techniques to effectively avoid overfitting issues. Third, we developed an approach to tackle the data imbalance problem using a semi-supervised strategy. Finally, we performed a genome-wide prediction of human SH2-peptide binding, uncovering several findings of biological relevance. We make our models and genome-wide predictions, for all the 51 SH2-domains, freely available to the scientific community under the following URLs: http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/SH2PepInt.tar.gz and http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/Genome-wide-predictions.tar.gz, respectively.

Quantum-inspired algorithm for estimating the permanent of positive semidefinite matrices

NASA Astrophysics Data System (ADS)

Chakhmakhchyan, L.; Cerf, N. J.; Garcia-Patron, R.

2017-08-01

We construct a quantum-inspired classical algorithm for computing the permanent of Hermitian positive semidefinite matrices by exploiting a connection between these mathematical structures and the boson sampling model. Specifically, the permanent of a Hermitian positive semidefinite matrix can be expressed in terms of the expected value of a random variable, which stands for a specific photon-counting probability when measuring a linear-optically evolved random multimode coherent state. Our algorithm then approximates the matrix permanent from the corresponding sample mean and is shown to run in polynomial time for various sets of Hermitian positive semidefinite matrices, achieving a precision that improves over known techniques. This work illustrates how quantum optics may benefit algorithm development.

Surveying the quantum group symmetries of integrable open spin chains

NASA Astrophysics Data System (ADS)

Nepomechie, Rafael I.; Retore, Ana L.

2018-05-01

Using anisotropic R-matrices associated with affine Lie algebras g ˆ (specifically, A2n(2), A2n-1 (2) , Bn(1), Cn(1), Dn(1)) and suitable corresponding K-matrices, we construct families of integrable open quantum spin chains of finite length, whose transfer matrices are invariant under the quantum group corresponding to removing one node from the Dynkin diagram of g ˆ . We show that these transfer matrices also have a duality symmetry (for the cases Cn(1) and Dn(1)) and additional Z2 symmetries that map complex representations to their conjugates (for the cases A2n-1 (2) , Bn(1) and Dn(1)). A key simplification is achieved by working in a certain "unitary" gauge, in which only the unbroken symmetry generators appear. The proofs of these symmetries rely on some new properties of the R-matrices. We use these symmetries to explain the degeneracies of the transfer matrices.

Improving comprehension in adolescents with severe receptive language impairments: a randomized control trial of intervention for coordinating conjunctions.

PubMed

Ebbels, Susan H; Marić, Nataša; Murphy, Aoife; Turner, Gail

2014-01-01

Little evidence exists for the effectiveness of therapy for children with receptive language difficulties, particularly those whose difficulties are severe and persistent. To establish the effectiveness of explicit speech and language therapy with visual support for secondary school-aged children with language impairments focusing on comprehension of coordinating conjunctions in a randomized control trial with an assessor blind to group status. Fourteen participants (aged 11;3-16;1) with severe RELI (mean standard scores: CELF4 ELS = 48, CELF4 RLS = 53 and TROG-2 = 57), but higher non-verbal (Matrices = 83) and visual perceptual skills (Test of Visual Perceptual Skills (TVPS) = 86) were randomly assigned to two groups: therapy versus waiting controls. In Phase 1, the therapy group received eight 30-min individual sessions of explicit teaching with visual support (Shape Coding) with their usual SLT. In Phase 2, the waiting controls received the same therapy. The participants' comprehension was tested pre-, post-Phase 1 and post-Phase 2 therapy on (1) a specific test of the targeted conjunctions, (2) the TROG-2 and (3) a test of passives. After Phase 1, the therapy group showed significantly more progress than the waiting controls on the targeted conjunctions (d = 1.6) and overall TROG-2 standard score (d = 1.4). The two groups did not differ on the passives test. After Phase 2, the waiting controls made similar progress to those in the original therapy group, who maintained their previous progress. Neither group showed progress on passives. When the two groups were combined, significant progress was found on the specific conjunctions (d = 1.3) and TROG-2 raw (d = 1.1) and standard scores (d = 0.9). Correlations showed no measures taken (including Matrices and TVPS) correlated significantly with progress on the targeted conjunctions or the TROG-2. Four hours of Shape Coding therapy led to significant gains on comprehension of coordinating conjunctions which were maintained after 4 months. Given the significant progress at a group level and the lack of reliable predictors of progress, this approach could be offered to other children with similar difficulties to the participants. However, the intervention was delivered one-to-one by speech and language therapists, thus the effectiveness of this therapy method with other methods of delivery remains to be evaluated. © 2013 Royal College of Speech and Language Therapists.

Prediction of subcellular localization of eukaryotic proteins using position-specific profiles and neural network with weighted inputs.

PubMed

Zou, Lingyun; Wang, Zhengzhi; Huang, Jiaomin

2007-12-01

Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles (PSP) have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific Iterative-Basic Local Alignment Search Tool (PSI-BLAST) has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and 1st-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network (PSP-WNN). The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.

Rapid concentration and sensitive detection of hookworm ova from wastewater matrices using a real-time PCR method.

PubMed

Gyawali, P; Sidhu, J P S; Ahmed, W; Jagals, P; Toze, S

2015-12-01

The risk of human hookworm infections from land application of wastewater matrices could be high in regions with high hookworm prevalence. A rapid, sensitive and specific hookworm detection method from wastewater matrices is required in order to assess human health risks. Currently available methods used to identify hookworm ova to the species level are time consuming and lack accuracy. In this study, a real-time PCR method was developed for the rapid, sensitive and specific detection of canine hookworm (Ancylostoma caninum) ova from wastewater matrices. A. caninum was chosen because of its morphological similarity to the human hookworm (Ancylostoma duodenale and Necator americanus). The newly developed PCR method has high detection sensitivity with the ability to detect less than one A. caninum ova from 1 L of secondary treated wastewater at the mean threshold cycle (CT) values ranging from 30.1 to 34.3. The method is also able to detect four A. caninum ova from 1 L of raw wastewater and from ∼4 g of treated sludge with mean CT values ranging from 35.6 to 39.8 and 39.8 to 39.9, respectively. The better detection sensitivity obtained for secondary treated wastewater compared to raw wastewater and sludge samples could be attributed to sample turbidity. The proposed method appears to be rapid, sensitive and specific compared to traditional methods and has potential to aid in the public health risk assessment associated with land application of wastewater matrices. Furthermore, the method can be adapted to detect other helminth ova of interest from wastewater matrices. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Analytical Applications Of High-Resolution Molecular Fluorescence Spectroscopy In Low Temperature Solid Matrices

NASA Astrophysics Data System (ADS)

Hofstraat, Johannes W.; van Zeijl, W. J.; Smedes, F.; Ariese, Freek; Gooijer, Cees; Velthorst, Nel H.; Locher, R.; Renn, Alois; Wild, Urs P.

1989-05-01

High-resolution fluorescence spectroscopy may be used to obtain highly specific, vibrationally resolved spectral signatures of molecules. Two techniques are presented that both make use of low temperature, solid matrices. In Shpol'skii spectroscopy highly resolved spectra are obtained by employing n-alkanes as solvents that form neat crystalline matrices at low temperatures in which the guest molecules occupy well defined substitutional sites. Fluorescence line-narrowing spectroscopy is based on the application of selective (mostly laser-) excitation of the guest molecules. Principles and analytical applications of both techniques will be discussed. Specific attention will be paid to the determination of pyrene in bird meat by means of Shpol'skii spectroscopy and to the possibilities of applying two-dimensional fluorescence line-narrowing spectroscopy.

Commercial lateral flow devices for rapid detection of peanut (Arachis hypogaea) and hazelnut (Corylus avellana) cross-contamination in the industrial production of cookies.

PubMed

Röder, Martin; Vieths, Stefan; Holzhauser, Thomas

2009-09-01

Lateral flow devices (LFDs) are qualitative immunochromatographic tests for the rapid and specific detection of target analytes. We investigated commercially available LFDs for their ability to detect potentially allergenic peanut and hazelnut in raw cookie dough and chocolate, two important food matrices in the industrial production of cookies. Each three commercial LFDs for the detection of hazelnut and peanut were performed according to the manufacturers' instructions. All LFDs had comparably satisfactory specificity that was investigated with a variety of characteristic foods and food ingredients used in the production of cookies. In concordance with hazelnut-specific enzyme-linked immunosorbent assays (ELISAs), walnut was the most cross-reactive food for hazelnut-specific LFD. The sensitivity was verified in raw cookie doughs and chocolates that were either spiked with peanut or hazelnut between 1 and 25 mg/kg, respectively. Two hazelnut-specific LFDs detected hazelnut at a level of 3.5 mg/kg in both matrices, whereas the third LFD detected hazelnut at a level of 3.9 mg/kg in dough and 12.5 mg/kg in chocolate. Two peanut-specific LFDs detected peanut at a level of 1 mg/kg in both matrices. The third LFD detected peanut at a level of 14.2 mg/kg in chocolate and 4 mg/kg in dough. In conclusion, specific and sensitive LFD were identified for each hazelnut and peanut, having a level of sensitivity that is comparable to commercial ELISA for the investigated matrices. Such sensitive, specific, and rapid tests are useful analytical tools for allergen screening and sanitation in the industrial manufacture of foods.

A knowledge-based theory of rising scores on "culture-free" tests.

PubMed

Fox, Mark C; Mitchum, Ainsley L

2013-08-01

Secular gains in intelligence test scores have perplexed researchers since they were documented by Flynn (1984, 1987). Gains are most pronounced on abstract, so-called culture-free tests, prompting Flynn (2007) to attribute them to problem-solving skills availed by scientifically advanced cultures. We propose that recent-born individuals have adopted an approach to analogy that enables them to infer higher level relations requiring roles that are not intrinsic to the objects that constitute initial representations of items. This proposal is translated into item-specific predictions about differences between cohorts in pass rates and item-response patterns on the Raven's Matrices (Flynn, 1987), a seemingly culture-free test that registers the largest Flynn effect. Consistent with predictions, archival data reveal that individuals born around 1940 are less able to map objects at higher levels of relational abstraction than individuals born around 1990. Polytomous Rasch models verify predicted violations of measurement invariance, as raw scores are found to underestimate the number of analogical rules inferred by members of the earlier cohort relative to members of the later cohort who achieve the same overall score. The work provides a plausible cognitive account of the Flynn effect, furthers understanding of the cognition of matrix reasoning, and underscores the need to consider how test-takers select item responses. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

PubMed

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

Psychometric characteristics of the MATRICS Consensus Cognitive Battery in a large pooled cohort of stable schizophrenia patients.

PubMed

Georgiades, Anastasia; Davis, Vicki G; Atkins, Alexandra S; Khan, Anzalee; Walker, Trina W; Loebel, Antony; Haig, George; Hilt, Dana C; Dunayevich, Eduardo; Umbricht, Daniel; Sand, Michael; Keefe, Richard S E

2017-12-01

The MATRICS Consensus Cognitive Battery (MCCB) was developed to assess cognitive treatment effects in schizophrenia clinical trials, and is considered the FDA gold standard outcome measure for that purpose. The aim of the present study was to establish pre-treatment psychometric characteristics of the MCCB in a large pooled sample. The dataset included 2616 stable schizophrenia patients enrolled in 15 different clinical trials between 2007 and 2016 within the United States (94%) and Canada (6%). The MCCB was administered twice prior to the initiation of treatment in 1908 patients. Test-retest reliability and practice effects of the cognitive composite score, the neurocognitive composite score, which excludes the domain Social Cognition, and the subtests/domains were examined using Intra-Class Correlations (ICC) and Cohen's d. Simulated regression models explored which domains explained the greatest portion of variance in composite scores. Test-retest reliability was high (ICC=0.88) for both composite scores. Practice effects were small for the cognitive (d=0.15) and neurocognitive (d=0.17) composites. Simulated bootstrap regression analyses revealed that 3 of the 7 domains explained 86% of the variance for both composite scores. The domains that entered most frequently in the top 3 positions of the regression models were Speed of Processing, Working Memory, and Visual Learning. Findings provide definitive psychometric characteristics and a benchmark comparison for clinical trials using the MCCB. The test-retest reliability of the MCCB composite scores is considered excellent and the learning effects are small, fulfilling two of the key criteria for outcome measures in cognition clinical trials. Copyright © 2017 Elsevier B.V. All rights reserved.

Embedding strategies for effective use of information from multiple sequence alignments.

PubMed Central

Henikoff, S.; Henikoff, J. G.

1997-01-01

We describe a new strategy for utilizing multiple sequence alignment information to detect distant relationships in searches of sequence databases. A single sequence representing a protein family is enriched by replacing conserved regions with position-specific scoring matrices (PSSMs) or consensus residues derived from multiple alignments of family members. In comprehensive tests of these and other family representations, PSSM-embedded queries produced the best results overall when used with a special version of the Smith-Waterman searching algorithm. Moreover, embedding consensus residues instead of PSSMs improved performance with readily available single sequence query searching programs, such as BLAST and FASTA. Embedding PSSMs or consensus residues into a representative sequence improves searching performance by extracting multiple alignment information from motif regions while retaining single sequence information where alignment is uncertain. PMID:9070452

Assessment of composite motif discovery methods.

PubMed

Klepper, Kjetil; Sandve, Geir K; Abul, Osman; Johansen, Jostein; Drablos, Finn

2008-02-26

Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery - discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a suitable variety of challenges to most methods for module discovery.

Protein fold recognition using geometric kernel data fusion.

PubMed

Zakeri, Pooya; Jeuris, Ben; Vandebril, Raf; Moreau, Yves

2014-07-01

Various approaches based on features extracted from protein sequences and often machine learning methods have been used in the prediction of protein folds. Finding an efficient technique for integrating these different protein features has received increasing attention. In particular, kernel methods are an interesting class of techniques for integrating heterogeneous data. Various methods have been proposed to fuse multiple kernels. Most techniques for multiple kernel learning focus on learning a convex linear combination of base kernels. In addition to the limitation of linear combinations, working with such approaches could cause a loss of potentially useful information. We design several techniques to combine kernel matrices by taking more involved, geometry inspired means of these matrices instead of convex linear combinations. We consider various sequence-based protein features including information extracted directly from position-specific scoring matrices and local sequence alignment. We evaluate our methods for classification on the SCOP PDB-40D benchmark dataset for protein fold recognition. The best overall accuracy on the protein fold recognition test set obtained by our methods is ∼ 86.7%. This is an improvement over the results of the best existing approach. Moreover, our computational model has been developed by incorporating the functional domain composition of proteins through a hybridization model. It is observed that by using our proposed hybridization model, the protein fold recognition accuracy is further improved to 89.30%. Furthermore, we investigate the performance of our approach on the protein remote homology detection problem by fusing multiple string kernels. The MATLAB code used for our proposed geometric kernel fusion frameworks are publicly available at http://people.cs.kuleuven.be/∼raf.vandebril/homepage/software/geomean.php?menu=5/. © The Author 2014. Published by Oxford University Press.

The Graphic Representation of Structure in Similarity/Dissimilarity Matrices: Alternative Methods.

ERIC Educational Resources Information Center

Rudnitsky, Alan N.

Three approaches to the graphic representation of similarity and dissimilarity matrices are compared and contrasted. Specifically, Kruskal's multidimensional scaling, Johnson's hierarchical clustering, and Waern's graphing techniques are employed to depict, in two dimensions, data representing the structure of a set of botanical concepts. Each of…

Determination of phytate in high molecular weight, charged organic matrices by two-dimensional size exclusion-ion chromatography

USDA-ARS?s Scientific Manuscript database

A two-dimensional chromatography method for analyzing anionic targets (specifically phytate) in complex matrices is described. Prior to quantification by anion exchange chromatography, the sample matrix was prepared by size exclusion chromatography, which removed the majority of matrix complexities....

From Exploratory Talk to Abstract Reasoning: A Case for Far Transfer?

ERIC Educational Resources Information Center

Webb, Paul; Whitlow, J. W., Jr.; Venter, Danie

2017-01-01

Research has shown improvements in science, mathematics, and language scores when classroom discussion is employed in school-level science and mathematics classes. Studies have also shown statistically and practically significant gains in children's reasoning abilities as measured by the Raven's Standard Progressive Matrices test when employing…

Reply to Colom and Abad (2006)

ERIC Educational Resources Information Center

Mackintosh, N. J.

2007-01-01

Mackintosh and Bennett [Mackintosh, N. J., Bennett, E. S. (2005). What do Raven's Matrices measure? An analysis in terms of sex differences. "Intelligence, 33," 663-674] reported that male students obtained higher scores than females on Raven's items that required for their solution addition/subtraction or distribution of two rules, but…

An Exploring Model of Intelligence and Personality in Different Culture

ERIC Educational Resources Information Center

Wu, Yufeng; Qian, Guoying

2005-01-01

Middle school subjects of 13-21 years (from 4 nationalities) were used for studying the relationship between progressive cognition and personality characteristics by Raven's Standard Progressive Matrices and Eysenk's Personality Questionnaire. The results showed: (1) the correlation and stepwise regression were completely identical: P score was…

A non-verbal technique for the assessment of general intellectual ability in selection of aviation personnel.

DOT National Transportation Integrated Search

1971-06-01

A study was conducted in which performance on a non-verbal problem- solving task was correlated with the Otis Quick Scoring Mental Ability Test and the Raven Progressive Matrices Test. The problem-solving task, called 'code- lock' required the subjec...

An Assessment of the Dimensionality of SAT-Mathematical.

ERIC Educational Resources Information Center

Lawrence, Ida M.; Dorans, Neil J.

Six editions of Scholastic Aptitude Test-Mathematical (SAT-M) were factor analyzed using confirmatory and exploratory methods. Confirmatory factor analyses (using the LISREL VI program) were conducted on correlation matrices among item parcels--sums of scores on a small subset of items. Item parcels were constructed to yield correlation matrices…

Spelling and Learning Style in Children.

ERIC Educational Resources Information Center

Riding, R. J.; Tempest, J.

1986-01-01

Seventy-two 11-year-old students were tested on 32 dictated words containing two levels of both visual and phonemic complexity. Students were grouped within sexes on their extraversion scores on the Junior Eysenck Personality Inventory and quotients on the Raven's Matrices. Spelling performance was found to interact significantly with level of…

Core-shell alginate-ghatti gum modified montmorillonite composite matrices for stomach-specific flurbiprofen delivery.

PubMed

Bera, Hriday; Ippagunta, Sohitha Reddy; Kumar, Sanoj; Vangala, Pavani

2017-07-01

Novel alginate-arabic gum (AG) gel membrane coated alginate-ghatti gum (GG) modified montmorillonite (MMT) composite matrices were developed for intragastric flurbiprofen (FLU) delivery by combining floating and mucoadhesion mechanisms. The clay-biopolymer composite matrices containing FLU as core were accomplished by ionic-gelation technique. Effects of polymer-blend (alginate:GG) ratios and crosslinker (CaCl 2 ) concentrations on drug entrapment efficiency (DEE, %) and cumulative drug release after 8h (Q 8h , %) were studied to optimize the core matrices by a 3 2 factorial design. The optimized matrices (F-O) demonstrated DEE of 91.69±1.43% and Q 8h of 74.96±1.56% with minimum errors in prediction. The alginate-AG gel membrane enveloped optimized matrices (F-O, coated) exhibited superior buoyancy, better ex vivo mucoadhesion and slower drug release rate. The drug release profile of FLU-loaded uncoated and coated optimized matrices was best fitted in Korsmeyer-Peppas model with anomalous diffusion and case-II transport driven mechanism, respectively. The uncoated and coated matrices containing FLU were also characterized for drug-excipients compatibility, drug crystallinity, thermal behaviour and surface morphology. Thus, the newly developed alginate-AG gel membrane coated alginate-GG modified MMT composite matrices are appropriate for intragastric delivery of FLU over an extended period of time with improved therapeutic benefits. Copyright © 2017 Elsevier B.V. All rights reserved.

The level and nature of autistic intelligence II: what about Asperger syndrome?

PubMed

Soulières, Isabelle; Dawson, Michelle; Gernsbacher, Morton Ann; Mottron, Laurent

2011-01-01

A distinctively uneven profile of intelligence is a feature of the autistic spectrum. Within the spectrum, Asperger individuals differ from autistics in their early speech development and in being less likely to be characterized by visuospatial peaks. While different specific strengths characterize different autistic spectrum subgroups, all such peaks of ability have been interpreted as deficits: isolated, aberrant, and irreconcilable with real human intelligence. This view has recently been challenged by findings of autistic strengths in performance on Raven's Progressive Matrices (RPM), an important marker of general and fluid intelligence. We investigated whether these findings extend to Asperger syndrome, an autistic spectrum subgroup characterized by verbal peaks of ability, and whether the cognitive mechanisms underlying autistic and Asperger RPM performance differ. Thirty-two Asperger adults displayed a significant advantage on RPM over Wechsler Full-Scale and Performance scores relative to their typical controls, while in 25 Asperger children an RPM advantage was found over Wechsler Performance scores only. As previously found with autistics, Asperger children and adults achieved RPM scores at a level reflecting their Wechsler peaks of ability. Therefore, strengths in RPM performance span the autistic spectrum and imply a common mechanism advantageously applied to different facets of cognition. Autistic spectrum intelligence is atypical, but also genuine, general, and underestimated.

The Level and Nature of Autistic Intelligence II: What about Asperger Syndrome?

PubMed Central

Soulières, Isabelle; Dawson, Michelle; Gernsbacher, Morton Ann; Mottron, Laurent

2011-01-01

A distinctively uneven profile of intelligence is a feature of the autistic spectrum. Within the spectrum, Asperger individuals differ from autistics in their early speech development and in being less likely to be characterized by visuospatial peaks. While different specific strengths characterize different autistic spectrum subgroups, all such peaks of ability have been interpreted as deficits: isolated, aberrant, and irreconcilable with real human intelligence. This view has recently been challenged by findings of autistic strengths in performance on Raven's Progressive Matrices (RPM), an important marker of general and fluid intelligence. We investigated whether these findings extend to Asperger syndrome, an autistic spectrum subgroup characterized by verbal peaks of ability, and whether the cognitive mechanisms underlying autistic and Asperger RPM performance differ. Thirty-two Asperger adults displayed a significant advantage on RPM over Wechsler Full-Scale and Performance scores relative to their typical controls, while in 25 Asperger children an RPM advantage was found over Wechsler Performance scores only. As previously found with autistics, Asperger children and adults achieved RPM scores at a level reflecting their Wechsler peaks of ability. Therefore, strengths in RPM performance span the autistic spectrum and imply a common mechanism advantageously applied to different facets of cognition. Autistic spectrum intelligence is atypical, but also genuine, general, and underestimated. PMID:21991394

Optical matrix-matrix multiplication method demonstrated by the use of a multifocus hololens

NASA Technical Reports Server (NTRS)

Liu, H. K.; Liang, Y.-Z.

1984-01-01

A method of optical matrix-matrix multiplication is presented. The feasibility of the method is also experimentally demonstrated by the use of a dichromated-gelatin multifocus holographic lens (hololens). With the specific values of matrices chosen, the average percentage error between the theoretical and experimental data of the elements of the output matrix of the multiplication of some specific pairs of 3 x 3 matrices is 0.4 percent, which corresponds to an 8-bit accuracy.

Transition Matrices: A Tool to Assess Student Learning and Improve Instruction

NASA Astrophysics Data System (ADS)

Morris, Gary A.; Walter, Paul; Skees, Spencer; Schwartz, Samantha

2017-03-01

This paper introduces a new spreadsheet tool for adoption by high school or college-level physics teachers who use common assessments in a pre-instruction/post-instruction mode to diagnose student learning and teaching effectiveness. The spreadsheet creates a simple matrix that identifies the percentage of students who select each possible pre-/post-test answer combination on each question of the diagnostic exam. Leveraging analysis of the quality of the incorrect answer choices, one can order the answer choices from worst to best (i.e., correct), resulting in "transition matrices" that can provide deeper insight into student learning and the success or failure of the pedagogical approach than traditional analyses that employ dichotomous scoring.

Example-Based Learning: Exploring the Use of Matrices and Problem Variability

ERIC Educational Resources Information Center

Hancock-Niemic, Mary A.; Lin, Lijia; Atkinson, Robert K.; Renkl, Alexander; Wittwer, Joerg

2016-01-01

The purpose of the study was to investigate the efficacy of using faded worked examples presented in matrices with problem structure variability to enhance learners' ability to recognize the underlying structure of the problems. Specifically, this study compared the effects of matrix-format versus linear-format faded worked examples combined with…

"Cognitive Diagnosis and Q-Matrices in Language Assessment": A Commentary

ERIC Educational Resources Information Center

Alderson, J. Charles

2010-01-01

This commentary appraises the 2009 special issue of "Language Assessment Quarterly" on "Cognitive Diagnosis and Q-matrices in Language Assessment." Despite a number of weaknesses, specifically in attempting inappropriately to retrofit a suite of proficiency tests to diagnostic purposes, the special issue is seen as a landmark in the development of…

Tensor discriminant color space for face recognition.

PubMed

Wang, Su-Jing; Yang, Jian; Zhang, Na; Zhou, Chun-Guang

2011-09-01

Recent research efforts reveal that color may provide useful information for face recognition. For different visual tasks, the choice of a color space is generally different. How can a color space be sought for the specific face recognition problem? To address this problem, this paper represents a color image as a third-order tensor and presents the tensor discriminant color space (TDCS) model. The model can keep the underlying spatial structure of color images. With the definition of n-mode between-class scatter matrices and within-class scatter matrices, TDCS constructs an iterative procedure to obtain one color space transformation matrix and two discriminant projection matrices by maximizing the ratio of these two scatter matrices. The experiments are conducted on two color face databases, AR and Georgia Tech face databases, and the results show that both the performance and the efficiency of the proposed method are better than those of the state-of-the-art color image discriminant model, which involve one color space transformation matrix and one discriminant projection matrix, specifically in a complicated face database with various pose variations.

The use of genomic coancestry matrices in the optimisation of contributions to maintain genetic diversity at specific regions of the genome.

PubMed

Gómez-Romano, Fernando; Villanueva, Beatriz; Fernández, Jesús; Woolliams, John A; Pong-Wong, Ricardo

2016-01-13

Optimal contribution methods have proved to be very efficient for controlling the rates at which coancestry and inbreeding increase and therefore, for maintaining genetic diversity. These methods have usually relied on pedigree information for estimating genetic relationships between animals. However, with the large amount of genomic information now available such as high-density single nucleotide polymorphism (SNP) chips that contain thousands of SNPs, it becomes possible to calculate more accurate estimates of relationships and to target specific regions in the genome where there is a particular interest in maximising genetic diversity. The objective of this study was to investigate the effectiveness of using genomic coancestry matrices for: (1) minimising the loss of genetic variability at specific genomic regions while restricting the overall loss in the rest of the genome; or (2) maximising the overall genetic diversity while restricting the loss of diversity at specific genomic regions. Our study shows that the use of genomic coancestry was very successful at minimising the loss of diversity and outperformed the use of pedigree-based coancestry (genetic diversity even increased in some scenarios). The results also show that genomic information allows a targeted optimisation to maintain diversity at specific genomic regions, whether they are linked or not. The level of variability maintained increased when the targeted regions were closely linked. However, such targeted management leads to an important loss of diversity in the rest of the genome and, thus, it is necessary to take further actions to constrain this loss. Optimal contribution methods also proved to be effective at restricting the loss of diversity in the rest of the genome, although the resulting rate of coancestry was higher than the constraint imposed. The use of genomic matrices when optimising contributions permits the control of genetic diversity and inbreeding at specific regions of the genome through the minimisation of partial genomic coancestry matrices. The formula used to predict coancestry in the next generation produces biased results and therefore it is necessary to refine the theory of genetic contributions when genomic matrices are used to optimise contributions.

Rendezvous with IQ: Metacognition in Real-Life Situations

ERIC Educational Resources Information Center

Al-Hilawani, Yasser A.

2018-01-01

The purpose of this study was to examine the relationship between metacognition as measured in real-life situations and IQ scores as reflected by performance on the Raven Standard Progressive Matrices Scale. It is also intended in this study to report on whether or not there were significant differences in performance on the metacognitive…

Intelligence and Metacognition as Predictors of Foreign Language Achievement: A Structural Equation Modeling Approach

ERIC Educational Resources Information Center

Pishghadam, Reza; Khajavy, Gholam Hassan

2013-01-01

This study examined the role of metacognition and intelligence in foreign language achievement on a sample of 143 Iranian English as a Foreign Language (EFL) learners. Participants completed Raven's Advanced Progressive Matrices as a measure of intelligence, and Metacognitive Awareness Inventory as a measure of metacognition. Learners' scores at…

Dysgenic Fertility, Intelligence and Family Size in Libya

ERIC Educational Resources Information Center

Al-Shahomee, Alsedig Abdalgadr; Lynn, Richard; Abdalla, Saleh El-ghmary

2013-01-01

The Standard Progressive Matrices (SPM) was administered to a sample of 592 16 year old school students in Libya. There was a small negative correlation of -0.14 between SPM scores and the number of siblings, indicating only marginal dysgenic fertility. Supplementary material giving the data is given online. (Contains 1 table.)

Relationships between Visual and Auditory Perceptual Skills and Comprehension in Students with Learning Disabilities.

ERIC Educational Resources Information Center

Weaver, Phyllis A.; Rosner, Jerome

1979-01-01

Scores of 25 learning disabled students (aged 9 to 13) were compared on five tests: a visual-perceptual test (Coloured Progressive Matrices); an auditory-perceptual test (Auditory Motor Placement); a listening and reading comprehension test (Durrell Listening-Reading Series); and a word recognition test (Word Recognition subtest, Diagnostic…

A Study on Academic Achievement and Personality of Secondary School Students

ERIC Educational Resources Information Center

Suvarna, V. D.; Ganesha Bhata, H. S.

2016-01-01

This study is concerned with the Academic Achievement and Personality of 300 students of secondary schools of Mandya city. The Raven's Standard Progress Matrices was used to obtain the Academic Scores and Eysenk Personality Inventory was used to collect data regarding their Personality. Result reflects that there is negligible positive…

A Note on the Incremental Validity of Aggregate Predictors.

ERIC Educational Resources Information Center

Day, H. D.; Marshall, David

Three computer simulations were conducted to show that very high aggregate predictive validity coefficients can occur when the across-case variability in absolute score stability occurring in both the predictor and criterion matrices is quite small. In light of the increase in internal consistency reliability achieved by the method of aggregation…

Meta-Analytic Structural Equation Modeling: A Two-Stage Approach

ERIC Educational Resources Information Center

Cheung, Mike W. L.; Chan, Wai

2005-01-01

To synthesize studies that use structural equation modeling (SEM), researchers usually use Pearson correlations (univariate r), Fisher z scores (univariate z), or generalized least squares (GLS) to combine the correlation matrices. The pooled correlation matrix is then analyzed by the use of SEM. Questionable inferences may occur for these ad hoc…

Intelligence and Creativity: Over the Threshold Together?

ERIC Educational Resources Information Center

Welter, Marisete Maria; Jaarsveld, Saskia; van Leeuwen, Cees; Lachmann, Thomas

2016-01-01

Threshold theory predicts a positive correlation between IQ and creativity scores up to an IQ level of 120 and no correlation above this threshold. Primary school children were tested at beginning (N = 98) and ending (N = 70) of the school year. Participants performed the standard progressive matrices (SPM) and the Test of Creative…

A longitudinal twin study of the direction of effects between ADHD symptoms and IQ.

PubMed

Rommel, Anna Sophie; Rijsdijk, Frühling; Greven, Corina U; Asherson, Philip; Kuntsi, Jonna

2015-01-01

While the negative association between ADHD symptoms and IQ is well documented, our knowledge about the direction and aetiology of this association is limited. Here, we examine the association of ADHD symptoms with verbal and performance IQ longitudinally in a population-based sample of twins. In a population-based sample of 4,771 twin pairs, DSM-IV ADHD symptoms were obtained from the Conners' Parent Rating Scale-Revised. Verbal (vocabulary) and performance (Raven's Progressive Matrices) IQ were assessed online. ADHD symptom ratings and IQ scores were obtained at ages 12, 14 and 16 years. Making use of the genetic sensitivity and time-ordered nature of our data, we use a cross-lagged model to examine the direction of effects, while modelling the aetiologies of the association between ADHD symptoms with vocabulary and Raven's scores over time. Although time-specific aetiological influences emerged for each trait at ages 14 and 16 years, the aetiological factors involved in the association between ADHD symptoms and IQ were stable over time. ADHD symptoms and IQ scores significantly predicted each other over time. ADHD symptoms at age 12 years were a significantly stronger predictor of vocabulary and Raven's scores at age 14 years than vice versa, whereas no differential predictive effects emerged from age 14 to 16 years. The results suggest that ADHD symptoms may put adolescents at risk for decreased IQ scores. Persistent genetic influences seem to underlie the association of ADHD symptoms and IQ over time. Early intervention is likely to be key to reducing ADHD symptoms and the associated risk for lower IQ.

Gender Differences in Figural Matrices: The Moderating Role of Item Design Features

ERIC Educational Resources Information Center

Arendasy, Martin E.; Sommer, Markus

2012-01-01

There is a heated debate on whether observed gender differences in some figural matrices in adults can be attributed to gender differences in inductive reasoning/G[subscript f] or differential item functioning and/or test bias. Based on previous studies we hypothesized that three specific item design features moderate the effect size of the gender…

Optical detection of parasitic protozoa in sol-gel matrices

NASA Astrophysics Data System (ADS)

Livage, Jacques; Barreau, J. Y.; Da Costa, J. M.; Desportes, I.

1994-10-01

Whole cell parasitic protozoa have been entrapped within sol-gel porous silica matrices. Stationary phase promastigote cells of Leishmania donovani infantum are mixed with a silica sol before gelation occurs. They remain trapped within the growing oxide network and their cellular organization appears to be well preserved. Moreover protozoa retain their antigenic properties in the porous gel. They are still able to detect parasite specific antibodies in serum samples from infected patients via an enzyme linked immunosorbent assay (ELISA). Antigen- antibody associations occurring in the gel are optically detected via the reactions of a peroxidase conjugate with ortho-phenylenediamine leading to the formation of a yellow coloration. A clear-cut difference in optical density is measured between positive and negative sera. Such an entrapment of antigenic species into porous sol-gel matrices avoids the main problems due to non specific binding and could be advantageously used in diagnostic kits.

Profiling and quantitative evaluation of three Nickel-Coated magnetic matrices for purification of recombinant proteins: lelpful hints for the optimized nanomagnetisable matrix preparation

PubMed Central

2011-01-01

Background Several materials are available in the market that work on the principle of protein magnetic fishing by their histidine (His) tags. Little information is available on their performance and it is often quoted that greatly improved purification of histidine-tagged proteins from crude extracts could be achieved. While some commercial magnetic matrices could be used successfully for purification of several His-tagged proteins, there are some which have been proved to operate just for a few extent of His-tagged proteins. Here, we address quantitative evaluation of three commercially available Nickel nanomagnetic beads for purification of two His-tagged proteins expressed in Escherichia coli and present helpful hints for optimized purification of such proteins and preparation of nanomagnetisable matrices. Results Marked differences in the performance of nanomagnetic matrices, principally on the basis of their specific binding capacity, recovery profile, the amount of imidazole needed for protein elution and the extent of target protein loss and purity were obtained. Based on the aforesaid criteria, one of these materials featured the best purification results (SiMAG/N-NTA/Nickel) for both proteins at the concentration of 4 mg/ml, while the other two (SiMAC-Nickel and SiMAG/CS-NTA/Nickel) did not work well with respect to specific binding capacity and recovery profile. Conclusions Taken together, functionality of different types of nanomagnetic matrices vary considerably. This variability may not only be dependent upon the structure and surface chemistry of the matrix which in turn determine the affinity of interaction, but, is also influenced to a lesser extent by the physical properties of the protein itself. Although the results of the present study may not be fully applied for all nanomagnetic matrices, but provide a framework which could be used to profiling and quantitative evaluation of other magnetisable matrices and also provide helpful hints for those researchers facing same challenge. PMID:21824404

Assessing Fit of Item Response Models Using the Information Matrix Test

ERIC Educational Resources Information Center

Ranger, Jochen; Kuhn, Jorg-Tobias

2012-01-01

The information matrix can equivalently be determined via the expectation of the Hessian matrix or the expectation of the outer product of the score vector. The identity of these two matrices, however, is only valid in case of a correctly specified model. Therefore, differences between the two versions of the observed information matrix indicate…

Dimensionality of Data Matrices with Applications to Gene Expression Profiles

ERIC Educational Resources Information Center

Feng, Xingdong

2009-01-01

Probe-level microarray data are usually stored in matrices. Take a given probe set (gene), for example, each row of the matrix corresponds to an array, and each column corresponds to a probe. Often, people summarize each array by the gene expression level. Is one number sufficient to summarize a whole probe set for a specific gene in an array?…

Enhanced Ex Vivo Expansion of Human Hematopoietic Progenitors on Native and Spin Coated Acellular Matrices Prepared from Bone Marrow Stromal Cells

PubMed Central

Wasnik, Samiksha; Kantipudi, Suma; Kirkland, Mark A.; Pande, Gopal

2016-01-01

The extracellular microenvironment in bone marrow (BM) is known to regulate the growth and differentiation of hematopoietic stem and progenitor cells (HSPC). We have developed cell-free matrices from a BM stromal cell line (HS-5), which can be used as substrates either in native form or as tissue engineered coatings, for the enhanced ex vivo expansion of umbilical cord blood (UCB) derived HSPC. The physicochemical properties (surface roughness, thickness, and uniformity) of native and spin coated acellular matrices (ACM) were studied using scanning and atomic force microscopy (SEM and AFM). Lineage-specific expansion of HSPC, grown on these substrates, was evaluated by immunophenotypic (flow cytometry) and functional (colony forming) assays. Our results show that the most efficient expansion of lineage-specific HSPC occurred on spin coated ACM. Our method provides an improved protocol for ex vivo HSPC expansion and it offers a system to study the in vivo roles of specific molecules in the hematopoietic niche that influence HSPC expansion. PMID:26981135

Determination of Inorganic Arsenic in a Wide Range of Food Matrices using Hydride Generation - Atomic Absorption Spectrometry.

PubMed

de la Calle, Maria B; Devesa, Vicenta; Fiamegos, Yiannis; Vélez, Dinoraz

2017-09-01

The European Food Safety Authority (EFSA) underlined in its Scientific Opinion on Arsenic in Food that in order to support a sound exposure assessment to inorganic arsenic through diet, information about distribution of arsenic species in various food types must be generated. A method, previously validated in a collaborative trial, has been applied to determine inorganic arsenic in a wide variety of food matrices, covering grains, mushrooms and food of marine origin (31 samples in total). The method is based on detection by flow injection-hydride generation-atomic absorption spectrometry of the iAs selectively extracted into chloroform after digestion of the proteins with concentrated HCl. The method is characterized by a limit of quantification of 10 µg/kg dry weight, which allowed quantification of inorganic arsenic in a large amount of food matrices. Information is provided about performance scores given to results obtained with this method and which were reported by different laboratories in several proficiency tests. The percentage of satisfactory results obtained with the discussed method is higher than that of the results obtained with other analytical approaches.

Is there an Asian idiom of distress? Somatic symptoms in female Japanese and Korean students.

PubMed

Saint Arnault, Denise; Kim, Oksoo

2008-02-01

The term 'idiom of distress' is used to describe culturally specific experiences of suffering. Most of these studies have been conducted with small groups, making comparison of symptom profiles difficult. Female undergraduate and graduate students in Japan (n = 50) and Korea (n = 61) completed the Beck Depression Inventory (BDI) and 7-day daily reports of their experiences of 46 somatic symptoms. Between-culture comparisons revealed that BDI scores did not differ; however, the Korean women had significantly higher somatic distress means than the Japanese women. Despite the higher Korean distress mean, regression analysis showed that somatic distress explained 30% of the variance of BDI score for the Japanese but only 22% of the variance for the Koreans. Within-culture comparisons showed that both high-BDI Japanese and Koreans had 19 somatic distress symptoms with significantly higher means than their low-BDI counterparts; 11 somatic symptoms were shared by the two groups. Multidimensional scaling matrices were used to compare symptom proximities and revealed cultural differences. The problems with using broad racial categories in clinical research, the clinical significance of these findings, and the implications for psychiatric nursing assessment and practice are discussed.

Is there an Asian idiom of distress? Somatic Symptoms in Female Japanese and Korean Students

PubMed Central

Arnault, Denise Saint; Kim, Oksoo

2007-01-01

The term “idiom of distress” is used to describe culturally-specific experiences of suffering. Most of these studies have been conducted with small groups, making comparison of symptom profiles difficult. Female undergraduate and graduate students in Japan (N=50) and Korea (N=61) completed Beck Depression Inventory (BDI) and seven-day dairy reports of their experiences of 46 somatic symptoms. Between-culture comparisons revealed that BDI scores did not differ; however, Korean women had significantly higher somatic distress means than the Japanese women. Despite the higher Korean distress mean, regression analysis showed that somatic distress explained 30% of the variance of BDI score for the Japanese, but only 22% of the variance for the Koreans. Within-culture comparisons showed that both the High BDI Japanese and Koreans had 19 somatic distress symptoms with significantly higher means than their Low BDI counterparts; eleven somatic symptoms were shared by the two groups. Multidimensional Scaling matrices were used to compare symptom proximities and revealed cultural differences. The problems with using broad racial categories in clinical research, the clinical significance of these findings, and implications for psychiatric nursing assessment and practice are discussed. PMID:18207054

Sleep spindles and intelligence in early childhood-developmental and trait-dependent aspects.

PubMed

Ujma, Péter P; Sándor, Piroska; Szakadát, Sára; Gombos, Ferenc; Bódizs, Róbert

2016-12-01

Sleep spindles act as a powerful marker of individual differences in cognitive ability. Sleep spindle parameters correlate with both age-related changes in cognitive abilities and with the age-independent concept of IQ. While some studies have specifically demonstrated the relationship between sleep spindles and intelligence in young children, our previous work in older subjects revealed sex differences in the sleep spindle correlates of IQ, which was never investigated in small children before. We investigated the relationship between age, Raven Colored Progressive Matrices (CPM) scores and sleep spindles in 28 young children (age 4-8 years, 15 girls). We specifically investigated sex differences in the psychometric correlates of sleep spindles. We also aimed to separate the correlates of sleep spindles that are because of age-related maturation from other effects that reflect an age-independent relationship between sleep spindles and general intelligence. Our results revealed a modest positive correlation between fast spindle amplitude and age. Raven CPM scores positively correlated with both slow and fast spindle amplitude, but this effect remained a tendency in males and vanished after correcting for the effects of age. Age-corrected correlations between Raven CPM scores and both slow and fast spindle amplitude were only significant in females. Overall, our results show that in male children sleep spindles are a maturational marker, but in female children they indicate trait-like intelligence, in line with previous studies in adolescent and adult subjects. Thalamocortical white matter connectivity may be the underlying mechanism behind both higher spindle amplitude and higher intelligence in female, but not male subjects. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Detection of Botulinum Neurotoxin Serotype A, B, and F Proteolytic Activity in Complex Matrices with Picomolar to Femtomolar Sensitivity

PubMed Central

Dunning, F. Mark; Ruge, Daniel R.; Piazza, Timothy M.; Stanker, Larry H.; Zeytin, Füsûn N.

2012-01-01

Rapid, high-throughput assays that detect and quantify botulinum neurotoxin (BoNT) activity in diverse matrices are required for environmental, clinical, pharmaceutical, and food testing. The current standard, the mouse bioassay, is sensitive but is low in throughput and precision. In this study, we present three biochemical assays for the detection and quantification of BoNT serotype A, B, and F proteolytic activities in complex matrices that offer picomolar to femtomolar sensitivity with small assay volumes and total assay times of less than 24 h. These assays consist of magnetic beads conjugated with BoNT serotype-specific antibodies that are used to purify BoNT from complex matrices before the quantification of bound BoNT proteolytic activity using the previously described BoTest reporter substrates. The matrices tested include human serum, whole milk, carrot juice, and baby food, as well as buffers containing common pharmaceutical excipients. The limits of detection were below 1 pM for BoNT/A and BoNT/F and below 10 pM for BoNT/B in most tested matrices using 200-μl samples and as low as 10 fM for BoNT/A with an increased sample volume. Together, these data describe rapid, robust, and high-throughput assays for BoNT detection that are compatible with a wide range of matrices. PMID:22923410

EMQIT: a machine learning approach for energy based PWM matrix quality improvement.

PubMed

Smolinska, Karolina; Pacholczyk, Marcin

2017-08-01

Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high-throughput methods such as, e.g., ChiP-seq the need to provide unbiased models of binding events has been made apparent. We present EMQIT a modification to the approach introduced by Alamanova et al. and later implemented as 3DTF server. We observed that tuning of Boltzmann factor weights, used for conversion of calculated energies to nucleotide probabilities, has a significant impact on the quality of the associated PWM matrix. Consequently, we proposed to use receiver operator characteristics curves and the 10-fold cross-validation to learn best weights using experimentally verified data from TRANSFAC database. We applied our method to data available for various TFs. We verified the efficiency of detecting TF binding sites by the 3DTF matrices improved with our technique using experimental data from the TRANSFAC database. The comparison showed a significant similarity and comparable performance between the improved and the experimental matrices (TRANSFAC). Improved 3DTF matrices achieved significantly higher AUC values than the original 3DTF matrices (at least by 0.1) and, at the same time, detected notably more experimentally verified TFBSs. The resulting new improved PWM matrices for analyzed factors show similarity to TRANSFAC matrices. Matrices had comparable predictive capabilities. Moreover, improved PWMs achieve better results than matrices downloaded from 3DTF server. Presented approach is general and applicable to any energy-based matrices. EMQIT is available online at http://biosolvers.polsl.pl:3838/emqit . This article was reviewed by Oliviero Carugo, Marek Kimmel and István Simon.

An Increase of Intelligence in Saudi Arabia, 1977-2010

ERIC Educational Resources Information Center

Batterjee, Adel A.; Khaleefa, Omar; Ali, Khalil; Lynn, Richard

2013-01-01

Normative data for 8-15 year olds for the Standard Progressive Matrices in Saudi Arabia were obtained in 1977 and 2010. The 2010 sample obtained higher average scores than the 1977 sample by 0.78d, equivalent to 11.7 IQ points. This represents a gain of 3.55 IQ points a decade over the 33 year period. (Contains 1 table.)

ADPROCLUS: a graphical user interface for fitting additive profile clustering models to object by variable data matrices.

PubMed

Wilderjans, Tom F; Ceulemans, Eva; Van Mechelen, Iven; Depril, Dirk

2011-03-01

In many areas of psychology, one is interested in disclosing the underlying structural mechanisms that generated an object by variable data set. Often, based on theoretical or empirical arguments, it may be expected that these underlying mechanisms imply that the objects are grouped into clusters that are allowed to overlap (i.e., an object may belong to more than one cluster). In such cases, analyzing the data with Mirkin's additive profile clustering model may be appropriate. In this model: (1) each object may belong to no, one or several clusters, (2) there is a specific variable profile associated with each cluster, and (3) the scores of the objects on the variables can be reconstructed by adding the cluster-specific variable profiles of the clusters the object in question belongs to. Until now, however, no software program has been publicly available to perform an additive profile clustering analysis. For this purpose, in this article, the ADPROCLUS program, steered by a graphical user interface, is presented. We further illustrate its use by means of the analysis of a patient by symptom data matrix.

Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks.

PubMed

Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

2018-06-13

Deep learning has been increasingly used to solve a number of problems with state-of-the-art performance in a wide variety of fields. In biology, deep learning can be applied to reduce feature extraction time and achieve high levels of performance. In our present work, we apply deep learning via two-dimensional convolutional neural networks and position-specific scoring matrices to classify Rab protein molecules, which are main regulators in membrane trafficking for transferring proteins and other macromolecules throughout the cell. The functional loss of specific Rab molecular functions has been implicated in a variety of human diseases, e.g., choroideremia, intellectual disabilities, cancer. Therefore, creating a precise model for classifying Rabs is crucial in helping biologists understand the molecular functions of Rabs and design drug targets according to such specific human disease information. We constructed a robust deep neural network for classifying Rabs that achieved an accuracy of 99%, 99.5%, 96.3%, and 97.6% for each of four specific molecular functions. Our approach demonstrates superior performance to traditional artificial neural networks. Therefore, from our proposed study, we provide both an effective tool for classifying Rab proteins and a basis for further research that can improve the performance of biological modeling using deep neural networks. Copyright © 2018 Elsevier Inc. All rights reserved.

A mathematical model of medial consonant identification by cochlear implant users.

PubMed

Svirsky, Mario A; Sagi, Elad; Meyer, Ted A; Kaiser, Adam R; Teoh, Su Wooi

2011-04-01

The multidimensional phoneme identification model is applied to consonant confusion matrices obtained from 28 postlingually deafened cochlear implant users. This model predicts consonant matrices based on these subjects' ability to discriminate a set of postulated spectral, temporal, and amplitude speech cues as presented to them by their device. The model produced confusion matrices that matched many aspects of individual subjects' consonant matrices, including information transfer for the voicing, manner, and place features, despite individual differences in age at implantation, implant experience, device and stimulation strategy used, as well as overall consonant identification level. The model was able to match the general pattern of errors between consonants, but not the full complexity of all consonant errors made by each individual. The present study represents an important first step in developing a model that can be used to test specific hypotheses about the mechanisms cochlear implant users employ to understand speech.

A mathematical model of medial consonant identification by cochlear implant users

PubMed Central

Svirsky, Mario A.; Sagi, Elad; Meyer, Ted A.; Kaiser, Adam R.; Teoh, Su Wooi

2011-01-01

The multidimensional phoneme identification model is applied to consonant confusion matrices obtained from 28 postlingually deafened cochlear implant users. This model predicts consonant matrices based on these subjects’ ability to discriminate a set of postulated spectral, temporal, and amplitude speech cues as presented to them by their device. The model produced confusion matrices that matched many aspects of individual subjects’ consonant matrices, including information transfer for the voicing, manner, and place features, despite individual differences in age at implantation, implant experience, device and stimulation strategy used, as well as overall consonant identification level. The model was able to match the general pattern of errors between consonants, but not the full complexity of all consonant errors made by each individual. The present study represents an important first step in developing a model that can be used to test specific hypotheses about the mechanisms cochlear implant users employ to understand speech. PMID:21476674

Tandem sulfur chemiluminescence and flame ionization detection with planar microfluidic devices for the characterization of sulfur compounds in hydrocarbon matrices.

PubMed

Luong, J; Gras, R; Shellie, R A; Cortes, H J

2013-07-05

The detection of sulfur compounds in different hydrocarbon matrices, from light hydrocarbon feedstocks to medium synthetic crude oil feeds provides meaningful information for optimization of refining processes as well as demonstration of compliance with petroleum product specifications. With the incorporation of planar microfluidic devices in a novel chromatographic configuration, sulfur compounds from hydrogen sulfide to alkyl dibenzothiophenes and heavier distributions of sulfur compounds over a wide range of matrices spanning across a boiling point range of more than 650°C can be characterized, using one single analytical configuration in less than 25min. In tandem with a sulfur chemiluminescence detector for sulfur analysis is a flame ionization detector. The flame ionization detector can be used to establish the boiling point range of the sulfur compounds in various hydrocarbon fractions for elemental specific simulated distillation analysis as well as profiling the hydrocarbon matrices for process optimization. Repeatability of less than 3% RSD (n=20) over a range of 0.5-1000 parts per million (v/v) was obtained with a limit of detection of 50 parts per billion and a linear range of 0.5-1000 parts per million with a correlation co-efficient of 0.998. Copyright © 2013 Elsevier B.V. All rights reserved.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

PubMed

Dang, Cuong Cao; Lefort, Vincent; Le, Vinh Sy; Le, Quang Si; Gascuel, Olivier

2011-10-01

Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. http://www.atgc-montpellier.fr/ReplacementMatrix/ olivier.gascuel@lirmm.fr Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Biclustering sparse binary genomic data.

PubMed

van Uitert, Miranda; Meuleman, Wouter; Wessels, Lodewyk

2008-12-01

Genomic datasets often consist of large, binary, sparse data matrices. In such a dataset, one is often interested in finding contiguous blocks that (mostly) contain ones. This is a biclustering problem, and while many algorithms have been proposed to deal with gene expression data, only two algorithms have been proposed that specifically deal with binary matrices. None of the gene expression biclustering algorithms can handle the large number of zeros in sparse binary matrices. The two proposed binary algorithms failed to produce meaningful results. In this article, we present a new algorithm that is able to extract biclusters from sparse, binary datasets. A powerful feature is that biclusters with different numbers of rows and columns can be detected, varying from many rows to few columns and few rows to many columns. It allows the user to guide the search towards biclusters of specific dimensions. When applying our algorithm to an input matrix derived from TRANSFAC, we find transcription factors with distinctly dissimilar binding motifs, but a clear set of common targets that are significantly enriched for GO categories.

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.

PubMed

Sharan, Malvika; Förstner, Konrad U; Eulalio, Ana; Vogel, Jörg

2017-06-20

RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Amino Acid Properties Conserved in Molecular Evolution

PubMed Central

Rudnicki, Witold R.; Mroczek, Teresa; Cudek, Paweł

2014-01-01

That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts – one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications. PMID:24967708

How Well Can Young People with Asperger's Disorder Recognize Threat and Learn about Affect in Faces?: A Pilot Study

ERIC Educational Resources Information Center

Miyahara, Motohide; Ruffman, Ted; Fujita, Chikako; Tsujii, Masatsugu

2010-01-01

The abilities to identify threat and learn about affect in facial photographs were compared between a non-autistic university student group (NUS), a matched Asperger's group (MAS) on the Standard Progressive Matrices (SPM), and an unmatched Asperger's group (UAS) who scored lower on the SPM. Participants were given pairs of faces and asked which…

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

PubMed

Quinn, Terrance; Sinkala, Zachariah

2014-01-01

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

Statistical analysis of DOE EML QAP data from 1982 to 1998.

PubMed

Mizanur Rahman, G M; Isenhour, T L; Larget, B; Greenlaw, P D

2001-01-01

The historical database from the Environmental Measurements Laboratory's Quality Assessment Program from 1982 to 1998 has been analyzed to determine control limits for future performance evaluations of the different laboratories contracted to the U.S. Department of Energy. Seventy-three radionuclides in four different matrices (air filter, soil, vegetation, and water) were analyzed. The evaluation criteria were established based on a z-score calculation.

Differences in Achievement Motivation and Academic and Social Self-Concept in Gifted Students of Higher Education

ERIC Educational Resources Information Center

Sierra, María Dolores Valadez; Cuervo, Angel Alberto Valdés; Amezaga, Teodoro Rafael Wendlandt; Sánchez, Ana Carolina Reyes; Guzmán, Rogelio Zambrano; Agraz, Juan Pedro Navarro

2015-01-01

The purpose of this study is to identify groups of gifted university students that differ in their self-concept and achievement motivation. For this, 80 students who achieved scores of the 95th percentile or higher in the Raven's Progressive Matrices test were selected. Two groups were identified in terms of their social self-concept and the…

Q-mode versus R-mode principal component analysis for linear discriminant analysis (LDA)

NASA Astrophysics Data System (ADS)

Lee, Loong Chuen; Liong, Choong-Yeun; Jemain, Abdul Aziz

2017-05-01

Many literature apply Principal Component Analysis (PCA) as either preliminary visualization or variable con-struction methods or both. Focus of PCA can be on the samples (R-mode PCA) or variables (Q-mode PCA). Traditionally, R-mode PCA has been the usual approach to reduce high-dimensionality data before the application of Linear Discriminant Analysis (LDA), to solve classification problems. Output from PCA composed of two new matrices known as loadings and scores matrices. Each matrix can then be used to produce a plot, i.e. loadings plot aids identification of important variables whereas scores plot presents spatial distribution of samples on new axes that are also known as Principal Components (PCs). Fundamentally, the scores matrix always be the input variables for building classification model. A recent paper uses Q-mode PCA but the focus of analysis was not on the variables but instead on the samples. As a result, the authors have exchanged the use of both loadings and scores plots in which clustering of samples was studied using loadings plot whereas scores plot has been used to identify important manifest variables. Therefore, the aim of this study is to statistically validate the proposed practice. Evaluation is based on performance of external error obtained from LDA models according to number of PCs. On top of that, bootstrapping was also conducted to evaluate the external error of each of the LDA models. Results show that LDA models produced by PCs from R-mode PCA give logical performance and the matched external error are also unbiased whereas the ones produced with Q-mode PCA show the opposites. With that, we concluded that PCs produced from Q-mode is not statistically stable and thus should not be applied to problems of classifying samples, but variables. We hope this paper will provide some insights on the disputable issues.

Agricultural matrices affect ground ant assemblage composition inside forest fragments

PubMed Central

Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was ‘generalist’ both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an ‘ocean of crops’. PMID:29791493

Agricultural matrices affect ground ant assemblage composition inside forest fragments.

PubMed

Assis, Diego Santana; Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Barrios-Rojas, Katty Elena; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was 'generalist' both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an 'ocean of crops'.

Payload/orbiter contamination control requirement study, volume 2, exhibit A

NASA Technical Reports Server (NTRS)

Bareiss, L. E.; Hooper, V. W.; Rantanen, R. O.; Ress, E. B.

1974-01-01

The computer printout data generated during the Payload/Orbiter Contamination Control Requirement Study are presented. The computer listings of the input surface data matrices, the viewfactor data matrices, and the geometric relationship data matrices for the three orbiter/spacelab configurations analyzed in this study are given. These configurations have been broken up into the geometrical surfaces and nodes necessary to define the principal critical surfaces whether they are contaminant sources, experimental surfaces, or operational surfaces. A numbering scheme was established based upon nodal numbers that relates the various spacelab surfaces to a specific surface material or function. This numbering system was developed for the spacelab configurations such that future extension to a surface mapping capability could be developed as required.

How Does Attention Relate to the Ability-Specific and Position-Specific Components of Reasoning Measured by APM?

ERIC Educational Resources Information Center

Ren, Xuezhu; Goldhammer, Frank; Moosbrugger, Helfried; Schweizer, Karl

2012-01-01

The aim of the present study was to clarify the nature of the ability-specific and position-specific components of Raven's Advanced Progressive Matrices (APM) by relating them to a number of types of attention. The ability-specific component represents the constant part of cognitive performance whereas the position-specific component reflects the…

Impact of metals in surface matrices from formal and informal electronic-waste recycling around Metro Manila, the Philippines, and intra-Asian comparison.

PubMed

Fujimori, Takashi; Takigami, Hidetaka; Agusa, Tetsuro; Eguchi, Akifumi; Bekki, Kanae; Yoshida, Aya; Terazono, Atsushi; Ballesteros, Florencio C

2012-06-30

We report concentrations, enrichment factors, and hazard indicators of 11 metals (Ag, As, Cd, Co, Cu, Fe, In, Mn, Ni, Pb, and Zn) in soil and dust surface matrices from formal and informal electronic waste (e-waste) recycling sites around Metro Manila, the Philippines, referring to soil guidelines and previous data from various e-waste recycling sites in Asia. Surface dust from e-waste recycling sites had higher levels of metal contamination than surface soil. Comparison of formal and informal e-waste recycling sites (hereafter, "formal" and "informal") revealed differences in specific contaminants. Formal dust contained a mixture of serious pollutant metals (Ni, Cu, Pb, and Zn) and Cd (polluted modestly), quite high enrichment metals (Ag and In), and crust-derived metals (As, Co, Fe, and Mn). For informal soil, concentration levels of specific metals (Cd, Co, Cu, Mn, Ni, Pb, and Zn) were similar among Asian recycling sites. Formal dust had significantly higher hazardous risk than the other matrices (p<0.005), excluding informal dust (p=0.059, almost significant difference). Thus, workers exposed to formal dust should protect themselves from hazardous toxic metals (Pb and Cu). There is also a high health risk for children ingesting surface matrices from informal e-waste recycling sites. Copyright © 2012 Elsevier B.V. All rights reserved.

Introduction of organic/hydro-organic matrices in inductively coupled plasma optical emission spectrometry and mass spectrometry: a tutorial review. Part II. Practical considerations.

PubMed

Leclercq, Amélie; Nonell, Anthony; Todolí Torró, José Luis; Bresson, Carole; Vio, Laurent; Vercouter, Thomas; Chartier, Frédéric

2015-07-23

Inductively coupled plasma optical emission spectrometry (ICP-OES) and mass spectrometry (ICP-MS) are increasingly used to carry out analyses in organic/hydro-organic matrices. The introduction of such matrices into ICP sources is particularly challenging and can be the cause of numerous drawbacks. This tutorial review, divided in two parts, explores the rich literature related to the introduction of organic/hydro-organic matrices in ICP sources. Part I provided theoretical considerations associated with the physico-chemical properties of such matrices, in an attempt to understand the induced phenomena. Part II of this tutorial review is dedicated to more practical considerations on instrumentation, instrumental and operating parameters, as well as analytical strategies for elemental quantification in such matrices. Two important issues are addressed in this part: the first concerns the instrumentation and optimization of instrumental and operating parameters, pointing out (i) the description, benefits and drawbacks of different kinds of nebulization and desolvation devices and the impact of more specific instrumental parameters such as the injector characteristics and the material used for the cone; and, (ii) the optimization of operating parameters, for both ICP-OES and ICP-MS. Even if it is at the margin of this tutorial review, Electrothermal Vaporization and Laser Ablation will also be shortly described. The second issue is devoted to the analytical strategies for elemental quantification in such matrices, with particular insight into the isotope dilution technique, particularly used in speciation analysis by ICP-coupled separation techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Fabrication of chemically cross-linked porous gelatin matrices.

PubMed

Bozzini, Sabrina; Petrini, Paola; Altomare, Lina; Tanzi, Maria Cristina

2009-01-01

The aim of this study was to chemically cross-link gelatin, by reacting its free amino groups with an aliphatic diisocyanate. To produce hydrogels with controllable properties, the number of reacting amino groups was carefully determined. Porosity was introduced into the gelatin-based hydrogels through the lyophilization process. Porous and non-porous matrices were characterized with respect to their chemical structure, morphology, water uptake and mechanical properties. The physical, chemical and mechanical properties of the porous matrices are related to the extent of their cross-linking, showing that they can be controlled by varying the reaction parameters. Water uptake values (24 hours) vary between 160% and 200% as the degree of cross-linking increases. The flexibility of the samples also decreases by changing the extent of cross-linking. Young's modulus shows values between 0.188 KPa, for the highest degree, and 0.142 KPa for the lowest degree. The matrices are potential candidates for use as tissue-engineering scaffolds by modulating their physical chemical properties according to the specific application.

Excipient foods: designing food matrices that improve the oral bioavailability of pharmaceuticals and nutraceuticals.

PubMed

McClements, David Julian; Xiao, Hang

2014-07-25

The oral bioavailability of many lipophilic bioactive agents (pharmaceuticals and nutraceuticals) is limited due to various physicochemical and physiological processes: poor release from food or drug matrices; low solubility in gastrointestinal fluids; metabolism or chemical transformation within the gastrointestinal tract; low epithelium cell permeability. The bioavailability of these agents can be improved by specifically designing food matrices that control their release, solubilization, transport, metabolism, and absorption within the gastrointestinal tract. This article discusses the impact of food composition and structure on oral bioavailability, and how this knowledge can be used to design excipient foods for improving the oral bioavailability of lipophilic bioactives. Excipient foods contain ingredients or structures that may have no bioactivity themselves, but that are able to promote the bioactivity of co-ingested bioactives. These bioactives may be lipophilic drugs in pharmaceutical preparations (such as capsules, pills, or syrups) or nutraceuticals present within food matrices (such as natural or processed foods and beverages).

Further thoughts on the utility of risk matrices.

PubMed

Ball, David J; Watt, John

2013-11-01

Risk matrices are commonly encountered devices for rating hazards in numerous areas of risk management. Part of their popularity is predicated on their apparent simplicity and transparency. Recent research, however, has identified serious mathematical defects and inconsistencies. This article further examines the reliability and utility of risk matrices for ranking hazards, specifically in the context of public leisure activities including travel. We find that (1) different risk assessors may assign vastly different ratings to the same hazard, (2) even following lengthy reflection and learning scatter remains high, and (3) the underlying drivers of disparate ratings relate to fundamentally different worldviews, beliefs, and a panoply of psychosocial factors that are seldom explicitly acknowledged. It appears that risk matrices when used in this context may be creating no more than an artificial and even untrustworthy picture of the relative importance of hazards, which may be of little or no benefit to those trying to manage risk effectively and rationally. © 2013 Society for Risk Analysis.

A comparative intelligibility study of single-microphone noise reduction algorithms.

PubMed

Hu, Yi; Loizou, Philipos C

2007-09-01

The evaluation of intelligibility of noise reduction algorithms is reported. IEEE sentences and consonants were corrupted by four types of noise including babble, car, street and train at two signal-to-noise ratio levels (0 and 5 dB), and then processed by eight speech enhancement methods encompassing four classes of algorithms: spectral subtractive, sub-space, statistical model based and Wiener-type algorithms. The enhanced speech was presented to normal-hearing listeners for identification. With the exception of a single noise condition, no algorithm produced significant improvements in speech intelligibility. Information transmission analysis of the consonant confusion matrices indicated that no algorithm improved significantly the place feature score, significantly, which is critically important for speech recognition. The algorithms which were found in previous studies to perform the best in terms of overall quality, were not the same algorithms that performed the best in terms of speech intelligibility. The subspace algorithm, for instance, was previously found to perform the worst in terms of overall quality, but performed well in the present study in terms of preserving speech intelligibility. Overall, the analysis of consonant confusion matrices suggests that in order for noise reduction algorithms to improve speech intelligibility, they need to improve the place and manner feature scores.

Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

PubMed

Zhao, Zhongming; Guo, An-Yuan; van den Oord, Edwin J C G; Aliev, Fazil; Jia, Peilin; Edenberg, Howard J; Riley, Brien P; Dick, Danielle M; Bettinger, Jill C; Davies, Andrew G; Grotewiel, Michael S; Schuckit, Marc A; Agrawal, Arpana; Kramer, John; Nurnberger, John I; Kendler, Kenneth S; Webb, Bradley T; Miles, Michael F

2012-01-01

A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism. These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.

Matrix-specific distribution and diastereomeric profiles of hexabromocyclododecane (HBCD) in a multimedia environment: Air, soil, sludge, sediment, and fish.

PubMed

Jo, Hyeyeong; Son, Min-Hui; Seo, Sung-Hee; Chang, Yoon-Seok

2017-07-01

Hexabromocyclododecane (HBCD) contamination and its diastereomeric profile were investigated in a multi-media environment along a river at the local scale in air, soil, sludge, sediment, and fish samples. The spatial distribution of HBCD in each matrix showed a different result. The highest concentrations of HBCD in air and soil were detected near a general industrial complex; in the sediment and sludge samples, they were detected in the down-stream region (i.e., urban area). Each matrix showed the specific distribution patterns of HBCD diastereomers, suggesting continuous inputs of contaminants, different physicochemical properties, or isomerizations. The particle phases in air, sludge, and fish matrices were dominated by α-HBCD, owing to HBCD's various isomerization processes and different degradation rate in the environment, and metabolic capabilities of the fish; in contrast, the sediment and soil matrices were dominated by γ-HBCD because of the major composition of the technical mixtures and the strong adsorption onto solid particles. Based on these results, the prevalent and matrix-specific distribution of HBCD diastereomers suggested that more careful consideration should be given to the characteristics of the matrices and their effects on the potential influence of HBCD at the diastereomeric level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reversed headspace analysis for characterization, identification, and analysis of solid and liquid matrices: Part I.

PubMed

Markelov, M; Bershevits, O

2006-03-01

This paper offers a methodology of an experimentally simple reversed headspace (RHS) analysis for measuring of matrix effects and their use for identification and characterization of condensed matrices such as pharmaceuticals, polymers, chromatographic packing, etc. applicable for both quality control monitoring and research and development investigation. In RHS methods, the matrix is spiked and equilibrated with a mixture of volatile chemicals containing various functional groups (molecular sensor array or MSA mixture). Headspace chromatograms of the same spikes of a sample and an empty vial are compared. Examination of basic headspace theory shows that matrix specific constants (M), rather than partition coefficients (K), can be calculated from the headspace chromatograms and M=(K-1)xbeta, where beta is a degree of matrix volume change during equilibration. Matrix specific constants can be plotted against any property of chemicals (polarity, dielectric constant, solubility parameter, vapor pressure, etc.) or just against a set of consecutive numbers, each representing a chemical in MSA. This plot is, in a sense, a molecular affinity spectrum (MAS) specific for a given matrix at a given temperature and is independent of an instrument. Changes in MAS that correspond to chemicals with a particular functional group give an insight to the type of differences between matrices and may quantitatively define them.

Cognitive Performance in Euthymic Patients with Bipolar Disorder vs Healthy Controls: A Neuropsychological Investigation.

PubMed

Palazzo, M Carlotta; Arici, Chiara; Cremaschi, Laura; Cristoffanini, Marta; Dobrea, Cristina; Dell'Osso, Bernardo; Altamura, A Carlo

2017-01-01

Cognitive impairment may affect patients with Bipolar Disorder (BD) beyond the acute episodes, qualifying as a potential endophenotype. However, which cognitive domains are specifically affected in euthymic patients with BD and the potential influence of confounding factors ( e.g. , age and concomitant pharmacological treatment) are still a matter of debate. The present study was, therefore, conducted to assess cognitive performance across specific domains in euthymic bipolar patients, not older than 50 years (to avoid potential age-related bias) versus healthy controls (HCs). A cognitive task battery, including the Wisconsin Card Test, Span Attention Test, Tower of London, Trail Making Test, Verbal Fluency Test, Matrices Scores and N-Back, was administered to 62 subjects (30 bipolar patients and 32 matched HCs) and differences between the groups analyzed. Bipolar patients performed significantly worse than HCs in the Span Forward task, in the expression of Verbal Fluency Test (Category) and in the N-Back task (all p<.05), with marginal differences between BD I and BD II patients. The present study pointed out significant differences in terms of cognitive performance between euthymic bipolar patients and HCs, supporting the notion that specific cognitive functions may remain impaired even after the resolution of the acute episodes in subjects suffering from BD. Future studies on larger samples are warranted to confirm the present results and further explore potential differences in cognitive impairment across specific bipolar subtypes.

Standards application and development plan for solar thermal technologies

NASA Astrophysics Data System (ADS)

Cobb, H. R. W.

1981-07-01

Functional and standards matrices, developed from input from ST users and from the industry that will be continually reviewed and updated as commercial aspects develop are presented. The matrices highlight codes, standards, test methods, functions and definitions that need to be developed. They will be submitted through ANSI for development by national consensus bodies. A contingency action is proposed for standards development if specific input is lacking at the committee level or if early development of a standard would hasten commercialization or gain needed jurisdictional acceptance.

Invariant Poisson-Nijenhuis structures on Lie groups and classification

NASA Astrophysics Data System (ADS)

Ravanpak, Zohreh; Rezaei-Aghdam, Adel; Haghighatdoost, Ghorbanali

We study right-invariant (respectively, left-invariant) Poisson-Nijenhuis structures (P-N) on a Lie group G and introduce their infinitesimal counterpart, the so-called r-n structures on the corresponding Lie algebra 𝔤. We show that r-n structures can be used to find compatible solutions of the classical Yang-Baxter equation (CYBE). Conversely, two compatible r-matrices from which one is invertible determine an r-n structure. We classify, up to a natural equivalence, all r-matrices and all r-n structures with invertible r on four-dimensional symplectic real Lie algebras. The result is applied to show that a number of dynamical systems which can be constructed by r-matrices on a phase space whose symmetry group is Lie group a G, can be specifically determined.

Prediction of general mental ability based on neural oscillation measures of sleep.

PubMed

Bódizs, Róbert; Kis, Tamás; Lázár, Alpár Sándor; Havrán, Linda; Rigó, Péter; Clemens, Zsófia; Halász, Péter

2005-09-01

The usual assessment of general mental ability (or intelligence) is based on performance attained in reasoning and problem-solving tasks. Differences in general mental ability have been associated with event-related neural activity patterns of the wakeful working brain or physical, chemical and electrical brain features measured during wakeful resting conditions. Recent evidences suggest that specific sleep electroencephalogram oscillations are related to wakeful cognitive performances. Our aim is to reveal the relationship between non-rapid eye movement sleep-specific oscillations (the slow oscillation, delta activity, slow and fast sleep spindle density, the grouping of slow and fast sleep spindles) and general mental ability assessed by the Raven Progressive Matrices Test (RPMT). The grouping of fast sleep spindles by the cortical slow oscillation in the left frontopolar derivation (Fp1) as well as the density of fast sleep spindles over the right frontal area (Fp2, F4), correlated positively with general mental ability. Data from those selected electrodes that showed the high correlations with general mental ability explained almost 70% of interindividual variance in RPMT scores. Results suggest that individual differences in general mental ability are reflected in fast sleep spindle-related oscillatory activity measured over the frontal cortex.

Penile Reconstruction with Skin Grafts and Dermal Matrices: Indications and Management

PubMed Central

Triana Junco, Paloma; Dore, Mariela; Nuñez Cerezo, Vanesa; Jimenez Gomez, Javier; Miguel Ferrero, Miriam; Díaz González, Mercedes; Lopez-Pereira, Pedro; Lopez-Gutierrez, Juan Carlos

2017-01-01

Introduction  The penis eventually needs specific cutaneous coverage in the context of reconstructive procedures following trauma or congenital anomalies. Local flaps are the first choice but are not always available after multiple previous procedures. In these cases, skin graft and dermal matrices should be considered. Materials and Methods  This study was a retrospective review of the past 4 years of four patients with severe loss of penile shaft skin who underwent skin reconstruction. Dermal matrices and skin grafts were utilized. Dermal matrices were placed for a median of 4.5 weeks (3.0–6.0 weeks). The skin graft was harvested from the inner thigh region for split-thickness skin graft (STSG) and the inguinal region for full-thickness skin graft (FTSG). Results  The four patients presented with complete loss of skin in the penile shaft. One patient had a vesical exstrophy, one had a buried penis with only one corpus cavernosum, one had a wide congenital lymphedema of the genitalia, and one had a lack of skin following circumcision at home. They underwent reconstruction with three patients undergoing split-thickness skin graft; two dermal matrices; and one full-thickness graft, respectively, thereby achieving a good cosmetic and functional result. There were no complications, and all the patients successfully accepted the graft. Conclusion  Dermal matrices and skin grafts may serve as effective tools in the management of severe penile skin defects unable to be covered with local flaps. PMID:28868232

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations

PubMed Central

Esteve-Altava, Borja; Rasskin-Gutman, Diego

2014-01-01

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non-facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton. PMID:24975579

Compressive elasticity of three-dimensional nanofiber matrix directs mesenchymal stem cell differentiation to vascular cells with endothelial or smooth muscle cell markers.

PubMed

Wingate, K; Bonani, W; Tan, Y; Bryant, S J; Tan, W

2012-04-01

The importance of mesenchymal stem cells (MSC) in vascular regeneration is becoming increasingly recognized. However, few in vitro studies have been performed to identify the effects of environmental elasticity on the differentiation of MSC into vascular cell types. Electrospinning and photopolymerization techniques were used to fabricate a three-dimensional (3-D) polyethylene glycol dimethacrylate nanofiber hydrogel matrix with tunable elasticity for use as a cellular substrate. Compression testing demonstrated that the elastic modulus of the hydrated 3-D matrices ranged from 2 to 15 kPa, similar to the in vivo elasticity of the intima basement membrane and media layer. MSC seeded on rigid matrices (8-15 kPa) showed an increase in cell area compared with those seeded on soft matrices (2-5 kPa). Furthermore, the matrix elasticity guided the cells to express different vascular-specific phenotypes with high differentiation efficiency. Around 95% of MSC seeded on the 3-D matrices with an elasticity of 3 kPa showed Flk-1 endothelial markers within 24h, while only 20% of MSC seeded on the matrices with elasticity >8 kPa demonstrated Flk-1 marker. In contrast, ∼80% of MSC seeded on 3-D matrices with elasticity >8 kPa demonstrated smooth muscle α-actin marker within 24h, while fewer than 10% of MSC seeded on 3-D matrices with elasticity <5 kPa showed α-actin markers. The ability to control MSC differentiation into either endothelial or smooth muscle-like cells based purely on the local elasticity of the substrate could be a powerful tool for vascular tissue regeneration. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Dietary risk ranking for residual antibiotics in cultured aquatic products around Tai Lake, China.

PubMed

Song, Chao; Li, Le; Zhang, Cong; Qiu, Liping; Fan, Limin; Wu, Wei; Meng, Shunlong; Hu, Gengdong; Chen, Jiazhang; Liu, Ying; Mao, Aimin

2017-10-01

Antibiotics are widely used in aquaculture and therefore may be present as a dietary risk in cultured aquatic products. Using the Tai Lake Basin as a study area, we assessed the presence of 15 antibiotics in 5 widely cultured aquatic species using a newly developed dietary risk ranking approach. By assigning scores to each factor involved in the ranking matrices, the scores of dietary risks per antibiotic and per aquatic species were calculated. The results indicated that fluoroquinolone antibiotics posed the highest dietary risk in all aquatic species. Then, the total scores per aquatic species were summed by all 15 antibiotic scores of antibiotics, it was found that Crab (Eriocheir sinensis) had the highest dietary risks. Finally, the most concerned antibiotic category and aquatic species were selected. This study highlighted the importance of dietary risk ranking in the production and consumption of cultured aquatic products around Tai Lake. Copyright © 2017 Elsevier Inc. All rights reserved.

A strategy for simultaneous determination of fatty acid composition, fatty acid position, and position-specific isotope contents in triacylglycerol matrices by 13C-NMR.

PubMed

Merchak, Noelle; Silvestre, Virginie; Loquet, Denis; Rizk, Toufic; Akoka, Serge; Bejjani, Joseph

2017-01-01

Triacylglycerols, which are quasi-universal components of food matrices, consist of complex mixtures of molecules. Their site-specific 13 C content, their fatty acid profile, and their position on the glycerol moiety may significantly vary with the geographical, botanical, or animal origin of the sample. Such variables are valuable tracers for food authentication issues. The main objective of this work was to develop a new method based on a rapid and precise 13 C-NMR spectroscopy (using a polarization transfer technique) coupled with multivariate linear regression analyses in order to quantify the whole set of individual fatty acids within triacylglycerols. In this respect, olive oil samples were analyzed by means of both adiabatic 13 C-INEPT sequence and gas chromatography (GC). For each fatty acid within the studied matrix and for squalene as well, a multivariate prediction model was constructed using the deconvoluted peak areas of 13 C-INEPT spectra as predictors, and the data obtained by GC as response variables. This 13 C-NMR-based strategy, tested on olive oil, could serve as an alternative to the gas chromatographic quantification of individual fatty acids in other matrices, while providing additional compositional and isotopic information. Graphical abstract A strategy based on the multivariate linear regression of variables obtained by a rapid 13 C-NMR technique was developed for the quantification of individual fatty acids within triacylglycerol matrices. The conceived strategy was tested on olive oil.

Human 3D vascularized organotypic microfluidic assays to study breast cancer cell extravasation

PubMed Central

Jeon, Jessie S.; Bersini, Simone; Gilardi, Mara; Dubini, Gabriele; Charest, Joseph L.; Moretti, Matteo; Kamm, Roger D.

2015-01-01

A key aspect of cancer metastases is the tendency for specific cancer cells to home to defined subsets of secondary organs. Despite these known tendencies, the underlying mechanisms remain poorly understood. Here we develop a microfluidic 3D in vitro model to analyze organ-specific human breast cancer cell extravasation into bone- and muscle-mimicking microenvironments through a microvascular network concentrically wrapped with mural cells. Extravasation rates and microvasculature permeabilities were significantly different in the bone-mimicking microenvironment compared with unconditioned or myoblast containing matrices. Blocking breast cancer cell A3 adenosine receptors resulted in higher extravasation rates of cancer cells into the myoblast-containing matrices compared with untreated cells, suggesting a role for adenosine in reducing extravasation. These results demonstrate the efficacy of our model as a drug screening platform and a promising tool to investigate specific molecular pathways involved in cancer biology, with potential applications to personalized medicine. PMID:25524628

TOPICAL REVIEW: Artificial extracellular matrix for embryonic stem cell cultures: a new frontier of nanobiomaterials

NASA Astrophysics Data System (ADS)

Amranul Haque, Md; Nagaoka, Masato; Hexig, Bayar; Akaike, Toshihiro

2010-02-01

Nanobiomaterials can play a central role in regenerative medicine and tissue engineering by facilitating cellular behavior and function, such as those where extracellular matrices (ECMs) direct embryonic stem (ES) cell morphogenesis, proliferation, differentiation and apoptosis. However, controlling ES cell proliferation and differentiation using matrices from natural sources is still challenging due to complex and heterogeneous culture conditions. Moreover, the systemic investigation of the regulation of self-renewal and differentiation to lineage specific cells depends on the use of defined and stress-free culture conditions. Both goals can be achieved by the development of biomaterial design targeting ECM or growth factors for ES cell culture. This targeted application will benefit from expansion of ES cells for transplantation, as well as the production of a specific differentiated cell type either by controlling the differentiation in a very specific pathway or by elimination of undesirable cell types.

Human 3D vascularized organotypic microfluidic assays to study breast cancer cell extravasation.

PubMed

Jeon, Jessie S; Bersini, Simone; Gilardi, Mara; Dubini, Gabriele; Charest, Joseph L; Moretti, Matteo; Kamm, Roger D

2015-01-06

A key aspect of cancer metastases is the tendency for specific cancer cells to home to defined subsets of secondary organs. Despite these known tendencies, the underlying mechanisms remain poorly understood. Here we develop a microfluidic 3D in vitro model to analyze organ-specific human breast cancer cell extravasation into bone- and muscle-mimicking microenvironments through a microvascular network concentrically wrapped with mural cells. Extravasation rates and microvasculature permeabilities were significantly different in the bone-mimicking microenvironment compared with unconditioned or myoblast containing matrices. Blocking breast cancer cell A3 adenosine receptors resulted in higher extravasation rates of cancer cells into the myoblast-containing matrices compared with untreated cells, suggesting a role for adenosine in reducing extravasation. These results demonstrate the efficacy of our model as a drug screening platform and a promising tool to investigate specific molecular pathways involved in cancer biology, with potential applications to personalized medicine.

Self-shaping composites with programmable bioinspired microstructures.

PubMed

Erb, Randall M; Sander, Jonathan S; Grisch, Roman; Studart, André R

2013-01-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material's microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

Self-shaping composites with programmable bioinspired microstructures

NASA Astrophysics Data System (ADS)

Erb, Randall M.; Sander, Jonathan S.; Grisch, Roman; Studart, André R.

2013-04-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material’s microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

Layered Metal Nanoparticle Structures on Electrodes for Sensing, Switchable Controlled Uptake/Release, and Photo-electrochemical Applications.

PubMed

Tel-Vered, Ran; Kahn, Jason S; Willner, Itamar

2016-01-06

Layered metal nanoparticle (NP) assemblies provide highly porous and conductive composites of unique electrical and optical (plasmonic) properties. Two methods to construct layered metal NP matrices are described, and these include the layer-by-layer deposition of NPs, or the electropolymerization of monolayer-functionalized NPs, specifically thioaniline-modified metal NPs. The layered NP composites are used as sensing matrices through the use of electrochemistry or surface plasmon resonance (SPR) as transduction signals. The crosslinking of the metal NP composites with molecular receptors, or the imprinting of molecular recognition sites into the electropolymerized NP matrices lead to selective and chiroselective sensing interfaces. Furthermore, the electrosynthesis of redox-active, imprinted, bis-aniline bridged Au NP composites yields electrochemically triggered "sponges" for the switchable uptake and release of electron-acceptor substrates, and results in conductive surfaces of electrochemically controlled wettability. Also, photosensitizer-relay-crosslinked Au NP composites, or electrochemically polymerized layered semiconductor quantum dot/metal NP matrices on electrodes, are demonstrated as functional nanostructures for photoelectrochemical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On-Chip Neural Data Compression Based On Compressed Sensing With Sparse Sensing Matrices.

PubMed

Zhao, Wenfeng; Sun, Biao; Wu, Tong; Yang, Zhi

2018-02-01

On-chip neural data compression is an enabling technique for wireless neural interfaces that suffer from insufficient bandwidth and power budgets to transmit the raw data. The data compression algorithm and its implementation should be power and area efficient and functionally reliable over different datasets. Compressed sensing is an emerging technique that has been applied to compress various neurophysiological data. However, the state-of-the-art compressed sensing (CS) encoders leverage random but dense binary measurement matrices, which incur substantial implementation costs on both power and area that could offset the benefits from the reduced wireless data rate. In this paper, we propose two CS encoder designs based on sparse measurement matrices that could lead to efficient hardware implementation. Specifically, two different approaches for the construction of sparse measurement matrices, i.e., the deterministic quasi-cyclic array code (QCAC) matrix and -sparse random binary matrix [-SRBM] are exploited. We demonstrate that the proposed CS encoders lead to comparable recovery performance. And efficient VLSI architecture designs are proposed for QCAC-CS and -SRBM encoders with reduced area and total power consumption.

The tangled bank of amino acids

PubMed Central

Pollock, David D.

2016-01-01

Abstract The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. PMID:27028523

Fluid intelligence, traits of personality and personality disorders in a cohort of adult KS patients with the classic 47, XXY karyotype.

PubMed

Liberato, D; Granato, S; Grimaldi, D; Rossi, F M; Tahani, N; Gianfrilli, D; Anzuini, A; Lenzi, A; Cavaggioni, G; Radicioni, A F

2017-11-01

Klinefelter's syndrome (KS) is associated with specific neurobehavioral features and personality traits. The aim of our study was to investigate fluid intelligence, personality traits and personality disorders (PD) and possible correlations with testosterone in a cohort of adult KS patients. We analyzed 58 adult KS patients with the classic 47, XXY karyotype. The Structured Clinical Interview for axis II disorders was used to assess DSM IV personality disorders. Personality traits were assessed using MMPI-2. Fluid intelligence was tested by using Raven's Standard Progressive Matrices (SPM) Test. Testosterone blood concentration was measured by CMIA. PD prevalence was 31%. Four altered MMPI scales (Social Responsibility, Dominance, Ego Strength and Repression) were found in more than 40% of patients. Overcontrolled hostility and MacAndrew Alcoholism Scale-Revised scales were altered in the PD- group only. Biz-Odd Thinking and Post-Traumatic Stress Disorder scale were associated with the presence of personality disorder. The raw SPM score was 44 ± 10.8 without any significant correlation with testosterone. No significant difference in mean age, SPM raw score and MMPI score was observed between eugonadal, hypogonadal and treated patients. Most KS patients had average fluid intelligence. PD prevalence was higher than in the general population. Testosterone was not correlated with fluid intelligence, personality traits or PD, but a reduction in marital distress was observed in treated patients. This could suggest that testosterone therapy can improve physical symptoms and this effect could also improve relationship abilities and wellness awareness.

The value of Bayes' theorem for interpreting abnormal test scores in cognitively healthy and clinical samples.

PubMed

Gavett, Brandon E

2015-03-01

The base rates of abnormal test scores in cognitively normal samples have been a focus of recent research. The goal of the current study is to illustrate how Bayes' theorem uses these base rates--along with the same base rates in cognitively impaired samples and prevalence rates of cognitive impairment--to yield probability values that are more useful for making judgments about the absence or presence of cognitive impairment. Correlation matrices, means, and standard deviations were obtained from the Wechsler Memory Scale--4th Edition (WMS-IV) Technical and Interpretive Manual and used in Monte Carlo simulations to estimate the base rates of abnormal test scores in the standardization and special groups (mixed clinical) samples. Bayes' theorem was applied to these estimates to identify probabilities of normal cognition based on the number of abnormal test scores observed. Abnormal scores were common in the standardization sample (65.4% scoring below a scaled score of 7 on at least one subtest) and more common in the mixed clinical sample (85.6% scoring below a scaled score of 7 on at least one subtest). Probabilities varied according to the number of abnormal test scores, base rates of normal cognition, and cutoff scores. The results suggest that interpretation of base rates obtained from cognitively healthy samples must also account for data from cognitively impaired samples. Bayes' theorem can help neuropsychologists answer questions about the probability that an individual examinee is cognitively healthy based on the number of abnormal test scores observed.

Investigation on formaldehyde release from preservatives in cosmetics.

PubMed

Lv, C; Hou, J; Xie, W; Cheng, H

2015-10-01

To understand formaldehyde residue in cosmetics, an investigation on formaldehyde release from eight preservatives (methenamine - MA, paraformaldehyde - PF, poly(p-toluenesulfonamide-co-formaldehyde) -PTSAF, quaternium-15 - QU, imidazolidinyl urea - IU, diazolidinyl urea - DU, dimethyloldimethyl hydantoin - DMDM and bronopol - BP) under various conditions was performed. The concentration of released formaldehyde was determined by high-performance liquid chromatography with photodiode array detection after derivatization with 2,4-dinitrophenylhydrazine. The amounts of formaldehyde release were in the order of PF > DU > DMDM ≈ QU ≈ IU > MA > BP > PTSAF. The releasing amounts of formaldehyde were the highest in the presence of aqueous matrices for the releasers except QU and IU, and the releasing effect was also relative to pH. More formaldehyde was released with longer storage time and higher temperature. Furthermore, all preservatives in cosmetic matrices released fewer amounts of formaldehyde than in pure aqueous or organic matrices, and the formaldehyde-releasing amounts were also cosmetic specific. Formaldehyde release was dependent on the matrix, pH, time and mainly temperature, and the releasing effect was also cosmetic specific. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Multiplex quantification of protein toxins in human biofluids and food matrices using immunoextraction and high-resolution targeted mass spectrometry.

PubMed

Dupré, Mathieu; Gilquin, Benoit; Fenaille, François; Feraudet-Tarisse, Cécile; Dano, Julie; Ferro, Myriam; Simon, Stéphanie; Junot, Christophe; Brun, Virginie; Becher, François

2015-08-18

The development of rapid methods for unambiguous identification and precise quantification of protein toxins in various matrices is essential for public health surveillance. Nowadays, analytical strategies classically rely on sensitive immunological assays, but mass spectrometry constitutes an attractive complementary approach thanks to direct measurement and protein characterization ability. We developed here an innovative multiplex immuno-LC-MS/MS method for the simultaneous and specific quantification of the three potential biological warfare agents, ricin, staphylococcal enterotoxin B, and epsilon toxin, in complex human biofluids and food matrices. At least 7 peptides were targeted for each toxin (43 peptides in total) with a quadrupole-Orbitrap high-resolution instrument for exquisite detection specificity. Quantification was performed using stable isotope-labeled toxin standards spiked early in the sample. Lower limits of quantification were determined at or close to 1 ng·mL(-1). The whole process was successfully applied to the quantitative analysis of toxins in complex samples such as milk, human urine, and plasma. Finally, we report new data on toxin stability with no evidence of toxin degradation in milk in a 48 h time frame, allowing relevant quantitative toxin analysis for samples collected in this time range.

Magnostics: Image-Based Search of Interesting Matrix Views for Guided Network Exploration.

PubMed

Behrisch, Michael; Bach, Benjamin; Hund, Michael; Delz, Michael; Von Ruden, Laura; Fekete, Jean-Daniel; Schreck, Tobias

2017-01-01

In this work we address the problem of retrieving potentially interesting matrix views to support the exploration of networks. We introduce Matrix Diagnostics (or Magnostics), following in spirit related approaches for rating and ranking other visualization techniques, such as Scagnostics for scatter plots. Our approach ranks matrix views according to the appearance of specific visual patterns, such as blocks and lines, indicating the existence of topological motifs in the data, such as clusters, bi-graphs, or central nodes. Magnostics can be used to analyze, query, or search for visually similar matrices in large collections, or to assess the quality of matrix reordering algorithms. While many feature descriptors for image analyzes exist, there is no evidence how they perform for detecting patterns in matrices. In order to make an informed choice of feature descriptors for matrix diagnostics, we evaluate 30 feature descriptors-27 existing ones and three new descriptors that we designed specifically for MAGNOSTICS-with respect to four criteria: pattern response, pattern variability, pattern sensibility, and pattern discrimination. We conclude with an informed set of six descriptors as most appropriate for Magnostics and demonstrate their application in two scenarios; exploring a large collection of matrices and analyzing temporal networks.

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations.

PubMed

Esteve-Altava, Borja; Rasskin-Gutman, Diego

2014-09-01

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non-facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton. © 2014 Anatomical Society.

Polygenic risk score, genome-wide association, and gene set analyses of cognitive domain deficits in schizophrenia.

PubMed

Nakahara, Soichiro; Medland, Sarah; Turner, Jessica A; Calhoun, Vince D; Lim, Kelvin O; Mueller, Bryon A; Bustillo, Juan R; O'Leary, Daniel S; Vaidya, Jatin G; McEwen, Sarah; Voyvodic, James; Belger, Aysenil; Mathalon, Daniel H; Ford, Judith M; Guffanti, Guia; Macciardi, Fabio; Potkin, Steven G; van Erp, Theo G M

2018-06-12

This study assessed genetic contributions to six cognitive domains, identified by the MATRICS Cognitive Consensus Battery as relevant for schizophrenia, cognition-enhancing, clinical trials. Psychiatric Genomics Consortium Schizophrenia polygenic risk scores showed significant negative correlations with each cognitive domain. Genome-wide association analyses identified loci associated with attention/vigilance (rs830786 within HNF4G), verbal memory (rs67017972 near NDUFS4), and reasoning/problem solving (rs76872642 within HDAC9). Gene set analysis identified unique and shared genes across cognitive domains. These findings suggest involvement of common and unique mechanisms across cognitive domains and may contribute to the discovery of new therapeutic targets to treat cognitive deficits in schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

Functional role and prognostic significance of CD157 in ovarian carcinoma.

PubMed

Ortolan, Erika; Arisio, Riccardo; Morone, Simona; Bovino, Paola; Lo-Buono, Nicola; Nacci, Giulia; Parrotta, Rossella; Katsaros, Dionyssios; Rapa, Ida; Migliaretti, Giuseppe; Ferrero, Enza; Volante, Marco; Funaro, Ada

2010-08-04

CD157, an ADP-ribosyl cyclase-related cell surface molecule, regulates leukocyte diapedesis during inflammation. Because CD157 is expressed in mesothelial cells and diapedesis resembles tumor cell migration, we investigated the role of CD157 in ovarian carcinoma. We assayed surgically obtained ovarian cancer and mesothelial cells and both native and engineered ovarian cancer cell lines for CD157 expression using flow cytometry and reverse transcription-polymerase chain reaction (RT-PCR), and for adhesion to extracellular matrices, migration, and invasion using cell-based assays. We investigated invasion of human peritoneal mesothelial cells by serous ovarian cancer cells with a three-dimensional coculture model. Experiments were performed with or without CD157-blocking antibodies. CD157 expression in tissue sections from ovarian cancer patients (n = 88) was examined by immunohistochemistry, quantified by histological score (H score), and categorized as at or above or below the median value of 60, and compared with clinical parameters. Statistical tests were two-sided. CD157 was expressed by ovarian cancer cells and mesothelium, and it potentiated the adhesion, migration, and invasion of serous ovarian cancer cells through different extracellular matrices. CD157-transfected ovarian cancer cells migrated twice as much as CD157-negative control cells (P = .001). Blockage of CD157 inhibited mesothelial invasion by serous ovarian cancer cells in a three-dimensional model. CD157 was expressed in 82 (93%) of the 88 epithelial ovarian cancer tissue specimens. In serous ovarian cancer, patients with CD157 H scores of 60 or greater had statistically significantly shorter disease-free survival and overall survival than patients with lower CD157 H scores (CD157 H score > or =60 vs <60: median disease-free survival = 18 months, 95% confidence interval [CI] = 5.92 to 30.07 vs unreached, P = .005; CD157 H score > or =60 vs <60: median overall survival = 45 months, 95% CI = 21.21 to 68.79 vs unreached, P = .024). Multivariable Cox regression showed that CD157 is an independent prognostic factor for recurrence (hazard ratio of disease recurrence = 3.01, 95% CI = 1.35 to 6.70, P = .007) and survival (hazard ratio of survival = 3.44, 95% CI = 1.27 to 9.31, P = .015). CD157 plays a pivotal role in the control of ovarian cancer cell migration and peritoneal invasion, and it may be clinically useful as a prognostic tool and therapeutic target.

Probing Majorana neutrino textures at DUNE

NASA Astrophysics Data System (ADS)

Bora, Kalpana; Borah, Debasish; Dutta, Debajyoti

2017-10-01

We study the possibility of probing different texture zero neutrino mass matrices at the long baseline neutrino experiment DUNE, particularly focusing on its sensitivity to the octant of atmospheric mixing angle θ23 and leptonic Dirac C P phase δcp. Assuming a diagonal charged lepton basis and Majorana nature of light neutrinos, we first classify the possible light neutrino mass matrices with one and two texture zeros and then numerically evaluate the parameter space which satisfies the texture zero conditions. Apart from using the latest global fit 3 σ values of neutrino oscillation parameters, we also use the latest bound on the sum of absolute neutrino masses (∑i |mi|) from the Planck mission data and the updated bound on effective neutrino mass Me e from neutrinoless double beta decay (0 ν β β ) experiments to find the allowed Majorana texture zero mass matrices. For the allowed texture zero mass matrices from all these constraints, we then feed the corresponding light neutrino parameter values satisfying the texture zero conditions into the numerical analysis in order to study the capability of DUNE to allow or exclude them once it starts taking data. We find that DUNE will be able to exclude some of these texture zero mass matrices which restrict (θ23-δcp) to a very specific range of values, depending on the values of the parameters that nature has chosen.

Associations of diet quality with cognition in children - the Physical Activity and Nutrition in Children Study.

PubMed

Haapala, Eero A; Eloranta, Aino-Maija; Venäläinen, Taisa; Schwab, Ursula; Lindi, Virpi; Lakka, Timo A

2015-10-14

Evidence on the associations of dietary patterns with cognition in children is limited. Therefore, we investigated the associations of the Baltic Sea Diet Score (BSDS) and the Dietary Approaches to Stop Hypertension (DASH) score with cognition in children. The present cross-sectional study sample included 428 children aged 6-8 years (216 boys and 212 girls). The BSDS and the DASH score were calculated using data from 4 d food records, higher scores indicating better diet quality. Cognition was assessed by the Raven's Coloured Progressive Matrices (CPM) score, a higher score indicating better cognition. Among all children, the BSDS (standardised regression coefficient β = 0·122, P =0·012) and the DASH score (β = 0·121, P =0·015) were directly associated with the Raven's CPM score. Among boys, a lower BSDS (β = 0·244, P< 0·001) and a lower DASH score (β = 0·202, P= 0·003) were related to a lower Raven's CPM score. Boys in the lowest quartile of the BSDS (22·5 v. 25·3, P= 0·029) and the DASH score (22·4 v. 25·7, P= 0·008) had a lower Raven's CPM score than those in the highest quartile of the corresponding score. Among girls, the BSDS or the DASH score were not associated with cognition. In conclusion, a poorer diet quality was associated with worse cognition in children, and the relationship was stronger in boys than in girls.

The impact of eszopiclone on sleep and cognition in patients with schizophrenia and insomnia: a double-blind, randomized, placebo-controlled trial.

PubMed

Tek, Cenk; Palmese, Laura B; Krystal, Andrew D; Srihari, Vinod H; DeGeorge, Pamela C; Reutenauer, Erin L; Guloksuz, Sinan

2014-12-01

Insomnia is frequent in schizophrenia and may contribute to cognitive impairment as well as overuse of weight inducing sedative antipsychotics. We investigated the effects of eszopiclone on sleep and cognition for patients with schizophrenia-related insomnia in a double-blind placebo controlled study, followed by a two-week, single-blind placebo phase. Thirty-nine clinically stable outpatients with schizophrenia or schizoaffective disorder and insomnia were randomized to either 3mg eszopiclone (n=20) or placebo (n=19). Primary outcome measure was change in Insomnia Severity Index (ISI) over 8 weeks. Secondary outcome measure was change in MATRICS Consensus Cognitive Battery (MATRICS). Sleep diaries, psychiatric symptoms, and quality of life were also monitored. ISI significantly improved more in eszopiclone (mean=-10.7, 95% CI=-13.2; -8.2) than in placebo (mean=-6.9, 95% CI=-9.5; -4.3) with a between-group difference of -3.8 (95% CI=-7.5; -0.2). MATRICS score change did not differ between groups. On further analysis there was a significant improvement in the working memory test, letter-number span component of MATRICS (mean=9.8±9.2, z=-2.00, p=0.045) only for subjects with schizophrenia on eszopiclone. There were improvements in sleep diary items in both groups with no between-group differences. Psychiatric symptoms remained stable. Discontinuation rates were similar. Sleep remained improved during single-blind placebo phase after eszopiclone was stopped, but the working memory improvement in patients with schizophrenia was not durable. Eszopiclone stands as a safe and effective alternative for the treatment of insomnia in patients with schizophrenia. Its effects on cognition require further study. Copyright © 2014 Elsevier B.V. All rights reserved.

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.

PubMed

Lundegaard, Claus; Lamberth, Kasper; Harndahl, Mikkel; Buus, Søren; Lund, Ole; Nielsen, Morten

2008-07-01

NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are based on artificial neural networks trained on data from 55 MHC alleles (43 Human and 12 non-human), and position-specific scoring matrices (PSSMs) for additional 67 HLA alleles. As only the MHC class I prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles. artificial neural network predictions are given as actual IC(50) values whereas PSSM predictions are given as a log-odds likelihood scores. The output is optionally available as download for easy post-processing. The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75-80% confirmed MHC binders. Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. The server is free of use and available at: http://www.cbs.dtu.dk/services/NetMHC.

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

PubMed Central

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

2017-01-01

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

Utilization of Methacrylates and Polymer Matrices for the Synthesis of Ion Specific Resins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czerwinski, Kenneth

2013-10-29

Disposal, storage, and/or transmutation of actinides such as americium (Am) will require the development of specific separation schemes. Existing efforts focus on solvent extraction systems for achieving suitable separation of actinide from lanthanides. However, previous work has shown the feasibility of ion-imprinting polymer-based resins for use in ion-exchange-type separations with metal ion recognition. Phenolic-based resins have been shown to function well for Am-Eu separations, but these resins exhibited slow kinetics and difficulties in the imprinting process. This project addresses the need for new and innovative methods for the selective separation of actinides through novel ion-imprinted resins. The project team willmore » explore incorporation of metals into extended frameworks, including the possibility of 3D polymerized matrices that can serve as a solid-state template for specific resin preparation. For example, an anhydrous trivalent f-element chain can be formed directly from a metal carbonate, and methacrylic acid from water. From these simple coordination complexes, molecules of discrete size or shape can be formed via the utilization of coordinating ligands or by use of an anionic multi-ligand system incorporating methacrylate. Additionally, alkyl methyl methacrylates have been used successfully to create template nanospaces, which underscores their potential utility as 3D polymerized matrices. This evidence provides a unique route for the preparation of a specific metal ion template for the basis of ion-exchange separations. Such separations may prove to be excellent discriminators of metal ions, even between f-elements. Resins were prepared and evaluated for sorption behavior, column properties, and proton exchange capacity.« less

Crosslinkable hydrogels derived from cartilage, meniscus, and tendon tissue.

PubMed

Visser, Jetze; Levett, Peter A; te Moller, Nikae C R; Besems, Jeremy; Boere, Kristel W M; van Rijen, Mattie H P; de Grauw, Janny C; Dhert, Wouter J A; van Weeren, P René; Malda, Jos

2015-04-01

Decellularized tissues have proven to be versatile matrices for the engineering of tissues and organs. These matrices usually consist of collagens, matrix-specific proteins, and a set of largely undefined growth factors and signaling molecules. Although several decellularized tissues have found their way to clinical applications, their use in the engineering of cartilage tissue has only been explored to a limited extent. We set out to generate hydrogels from several tissue-derived matrices, as hydrogels are the current preferred cell carriers for cartilage repair. Equine cartilage, meniscus, and tendon tissue was harvested, decellularized, enzymatically digested, and functionalized with methacrylamide groups. After photo-cross-linking, these tissue digests were mechanically characterized. Next, gelatin methacrylamide (GelMA) hydrogel was functionalized with these methacrylated tissue digests. Equine chondrocytes and mesenchymal stromal cells (MSCs) (both from three donors) were encapsulated and cultured in vitro up to 6 weeks. Gene expression (COL1A1, COL2A1, ACAN, MMP-3, MMP-13, and MMP-14), cartilage-specific matrix formation, and hydrogel stiffness were analyzed after culture. The cartilage, meniscus, and tendon digests were successfully photo-cross-linked into hydrogels. The addition of the tissue-derived matrices to GelMA affected chondrogenic differentiation of MSCs, although no consequent improvement was demonstrated. For chondrocytes, the tissue-derived matrix gels performed worse compared to GelMA alone. This work demonstrates for the first time that native tissues can be processed into crosslinkable hydrogels for the engineering of tissues. Moreover, the differentiation of encapsulated cells can be influenced in these stable, decellularized matrix hydrogels.

Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.

PubMed

Swenson, Luke C; Moores, Andrew; Low, Andrew J; Thielen, Alexander; Dong, Winnie; Woods, Conan; Jensen, Mark A; Wynhoven, Brian; Chan, Dennison; Glascock, Christopher; Harrigan, P Richard

2010-08-01

Tropism testing should rule out CXCR4-using HIV before treatment with CCR5 antagonists. Currently, the recombinant phenotypic Trofile assay (Monogram) is most widely utilized; however, genotypic tests may represent alternative methods. Independent triplicate amplifications of the HIV gp120 V3 region were made from either plasma HIV RNA or proviral DNA. These underwent standard, population-based sequencing with an ABI3730 (RNA n = 63; DNA n = 40), or "deep" sequencing with a Roche/454 Genome Sequencer-FLX (RNA n = 12; DNA n = 12). Position-specific scoring matrices (PSSMX4/R5) (-6.96 cutoff) and geno2pheno[coreceptor] (5% false-positive rate) inferred tropism from V3 sequence. These methods were then independently validated with a separate, blinded dataset (n = 278) of screening samples from the maraviroc MOTIVATE trials. Standard sequencing of HIV RNA with PSSM yielded 69% sensitivity and 91% specificity, relative to Trofile. The validation dataset gave 75% sensitivity and 83% specificity. Proviral DNA plus PSSM gave 77% sensitivity and 71% specificity. "Deep" sequencing of HIV RNA detected >2% inferred-CXCR4-using virus in 8/8 samples called non-R5 by Trofile, and <2% in 4/4 samples called R5. Triplicate analyses of V3 standard sequence data detect greater proportions of CXCR4-using samples than previously achieved. Sequencing proviral DNA and "deep" V3 sequencing may also be useful tools for assessing tropism.

Hybrid aerogel-derived Sn-Ni alloy immobilized within porous carbon/graphene dual matrices for high-performance lithium storage.

PubMed

Zhang, Hao; Zhang, Mengru; Zhang, Meiling; Zhang, Lin; Zhang, Anping; Zhou, Yiming; Wu, Ping; Tang, Yawen

2017-09-01

Nanoporous networks of tin-based alloys immobilized within carbon matrices possess unique structural and compositional superiorities toward lithium-storage, and are expected to manifest improved strain-accommodation and charge-transport capabilities and thus desirable anodic performance for advanced lithium-ion batteries (LIBs). Herein, a facile and scalable hybrid aerogel-derived thermal-autoreduction route has been developed for the construction of nanoporous network of SnNi alloy immobilized within carbon/graphene dual matrices (SnNi@C/G network). When applied as an anode material for LIBs, the SnNi@C/G network manifests desirable lithium-storage performances in terms of specific capacities, cycle life, and rate capability. The facile aerogel-derived route and desirable Li-storage performance of the SnNi@C/G network facilitate its practical application as a high-capacity, long-life, and high-rate anode material for advanced LIBs. Copyright © 2017 Elsevier Inc. All rights reserved.

Storage strategies of eddy-current FE-BI model for GPU implementation

NASA Astrophysics Data System (ADS)

Bardel, Charles; Lei, Naiguang; Udpa, Lalita

2013-01-01

In the past few years graphical processing units (GPUs) have shown tremendous improvements in computational throughput over standard CPU architecture. However, this comes at the cost of restructuring the algorithms to meet the strengths and drawbacks of this GPU architecture. A major drawback is the state of limited memory, and hence storage of FE stiffness matrices on the GPU is important. In contrast to storage on CPU the GPU storage format has significant influence on the overall performance. This paper presents an investigation of a storage strategy in the implementation of a two-dimensional finite element-boundary integral (FE-BI) model for Eddy current NDE applications, on GPU architecture. Specifically, the high dimensional matrices are manipulated by examining the matrix structure and optimally splitting into structurally independent component matrices for efficient storage and retrieval of each component. Results obtained using the proposed approach are compared to those of conventional CPU implementation for validating the method.

A composite material with CeO2-ZrO2 nanocrystallines embedded in SiO2 matrices and its enhanced thermal stability and oxygen storage capacity

NASA Astrophysics Data System (ADS)

Yang, Runnong; Liu, Yumei; Yu, Lin; Zhao, Xiangyun; Yang, Xiaobo; Sun, Ming; Luo, Junyin; Fan, Qun; Xiao, Jianming; Zhao, Yuzhong

2018-06-01

A simple hydrothermal procedure is introduced, which leads to the successful synthesis of a new composite material with fine CeO2-ZrO2 nanocrystallites embedded in amorphous and porous SiO2 matrices. The composite material possesses an extraordinary high thermal stability. After being calcined at 1000 °C, it retains CeO2-ZrO2 nanocrystallites of the size around 5 nm, a BET-specific surface area of 165 m2/g, and an oxygen storage capacity of 468 μmol/g. No phase segregation for CeO2-ZrO2 nanocrystallites is detected and the SiO2 matrices remain not crystallized. The composite material shows a great potential as a support of three-way catalyst, as evidenced in catalytic tests with supported Pt.

A user's guide to the SUDAN computer program for determining the vibration modes of structural systems. Ph.D. Thesis - Case Western Reserve Univ., Jun. 1963

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.; Durling, B. J.

1978-01-01

The use of the SUDAN computer program for analyzing structural systems for their natural modes and frequencies of vibration is described. SUDAN is intended for structures which can be represented as an equivalent system of beam, spring, and rigid-body substructures. User-written constraint equations are used to analytically join the mass and stiffness matrices of the substructures to form the mass and stiffness matrices of the complete structure from which all the frequencies and modes of the system are determined. The SUDAN program can treat the case in which both the mass and stiffness matrices of the coupled system may be singular simultaneously. A general description of the FORTRAN IV program is given, the computer hardware and software specifications are indicated, and the input required by the program is described.

Statistical similarity measures for link prediction in heterogeneous complex networks

NASA Astrophysics Data System (ADS)

Shakibian, Hadi; Charkari, Nasrollah Moghadam

2018-07-01

The majority of the link prediction measures in heterogeneous complex networks rely on the nodes connectivities while less attention has been paid to the importance of the nodes and paths. In this paper, we propose some new meta-path based statistical similarity measures to properly perform link prediction task. The main idea in the proposed measures is to drive some co-occurrence events in a number of co-occurrence matrices that are occurred between the visited nodes obeying a meta-path. The extracted co-occurrence matrices are analyzed in terms of the energy, inertia, local homogeneity, correlation, and information measure of correlation to determine various information theoretic measures. We evaluate the proposed measures, denoted as link energy, link inertia, link local homogeneity, link correlation, and link information measure of correlation, using a standard DBLP network data set. The results of the AUC score and Precision rate indicate the validity and accuracy of the proposed measures in comparison to the popular meta-path based similarity measures.

Rapid Radiochemical Methods for Asphalt Paving Material ...

EPA Pesticide Factsheets

Technical Brief Validated rapid radiochemical methods for alpha and beta emitters in solid matrices that are commonly encountered in urban environments were previously unavailable for public use by responding laboratories. A lack of tested rapid methods would delay the quick determination of contamination levels and the assessment of acceptable site-specific exposure levels. Of special concern are matrices with rough and porous surfaces, which allow the movement of radioactive material deep into the building material making it difficult to detect. This research focuses on methods that address preparation, radiochemical separation, and analysis of asphalt paving materials and asphalt roofing shingles. These matrices, common to outdoor environments, challenge the capability and capacity of very experienced radiochemistry laboratories. Generally, routine sample preparation and dissolution techniques produce liquid samples (representative of the original sample material) that can be processed using available radiochemical methods. The asphalt materials are especially difficult because they do not readily lend themselves to these routine sample preparation and dissolution techniques. The HSRP and ORIA coordinate radiological reference laboratory priorities and activities in conjunction with HSRP’s Partner Process. As part of the collaboration, the HSRP worked with ORIA to publish rapid radioanalytical methods for selected radionuclides in building material matrice

Nonlinear QR code based optical image encryption using spiral phase transform, equal modulus decomposition and singular value decomposition

NASA Astrophysics Data System (ADS)

Kumar, Ravi; Bhaduri, Basanta; Nishchal, Naveen K.

2018-01-01

In this study, we propose a quick response (QR) code based nonlinear optical image encryption technique using spiral phase transform (SPT), equal modulus decomposition (EMD) and singular value decomposition (SVD). First, the primary image is converted into a QR code and then multiplied with a spiral phase mask (SPM). Next, the product is spiral phase transformed with particular spiral phase function, and further, the EMD is performed on the output of SPT, which results into two complex images, Z 1 and Z 2. Among these, Z 1 is further Fresnel propagated with distance d, and Z 2 is reserved as a decryption key. Afterwards, SVD is performed on Fresnel propagated output to get three decomposed matrices i.e. one diagonal matrix and two unitary matrices. The two unitary matrices are modulated with two different SPMs and then, the inverse SVD is performed using the diagonal matrix and modulated unitary matrices to get the final encrypted image. Numerical simulation results confirm the validity and effectiveness of the proposed technique. The proposed technique is robust against noise attack, specific attack, and brutal force attack. Simulation results are presented in support of the proposed idea.

Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation.

PubMed

Aguilar, I; Misztal, I; Legarra, A; Tsuruta, S

2011-12-01

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries. © 2011 Blackwell Verlag GmbH.

The tangled bank of amino acids.

PubMed

Goldstein, Richard A; Pollock, David D

2016-07-01

The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. © 2016 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

High-throughput screening of dye-ligands for chromatography.

PubMed

Kumar, Sunil; Punekar, Narayan S

2014-01-01

Dye-ligand-based chromatography has become popular after Cibacron Blue, the first reactive textile dye, found application for protein purification. Many other textile dyes have since been successfully used to purify a number of proteins and enzymes. While the exact nature of their interaction with target proteins is often unclear, dye-ligands are thought to mimic the structural features of their corresponding substrates, cofactors, etc. The dye-ligand affinity matrices are therefore considered pseudo-affinity matrices. In addition, dye-ligands may simply bind with proteins due to electrostatic, hydrophobic, and hydrogen-bonding interactions. Because of their low cost, ready availability, and structural stability, dye-ligand affinity matrices have gained much popularity. Choice of a large number of dye structures offers a range of matrices to be prepared and tested. When presented in the high-throughput screening mode, these dye-ligand matrices provide a formidable tool for protein purification. One could pick from the list of dye-ligands already available or build a systematic library of such structures for use. A high-throughput screen may be set up to choose best dye-ligand matrix as well as ideal conditions for binding and elution, for a given protein. The mode of operation could be either manual or automated. The technology is available to test the performance of dye-ligand matrices in small volumes in an automated liquid-handling workstation. Screening a systematic library of dye-ligand structures can help establish a structure-activity relationship. While the origins of dye-ligand chromatography lay in exploiting pseudo-affinity, it is now possible to design very specific biomimetic dye structures. High-throughput screening will be of value in this endeavor as well.

Temporal pattern of soil matric suction in the unsaturated soil slope under different forest cover

NASA Astrophysics Data System (ADS)

Hayati, Elyas; Abdi, Ehsan; Mohseni Saravi, Mohsen; Nieber, John; Majnounian, Baris; Chirico, Giovanni

2017-04-01

In the vadose zone, usually, soils experience high matric suction during dry periods which results in a significant additional soil strength component (i.e., apparent cohesion) and thus plays a crucial role in the stability of unsaturated soil slopes. But, in the wet periods, when rain-water infiltrates into the soil, the matric suction of the soil dissipates partially or completely. It is a well-understood concept that vegetation can modify the hillslope hydrology and subsequent stability conditions by increasing soil matric suction through both interception of rainfall and depletion of soil water content via transpiration. Anthropogenic pressures, particularly clear-cutting and deforestation, affect many hydro-geomorphological processes including catchment and hillslope hydrology and stability. However, quantifying the changes in soil hydrologic conditions and the resulted stability of slopes due to these degrading activities remained an unresolved problem. To address this gap, a continuous measurement of soil water dynamics has been conducted at two adjacent hillslopes (one forested hillslope and one degraded hillslope) using PR2/6 profile probe for a 9-month period of time to demonstrate the forest cover-specific influence on the hillslope hydrology and stability during different seasons. The results have been then presented in terms of estimated soil matric suction to facilitate analyzing the resulted stability states due to the changes in soil water balance with time in the two studied hillslopes. The data were tested to check whether there are any differences between the forested and degraded hillslopes in terms of soil matric suction and augmented soil cohesion during different seasons. Finally, the response of soil hydrologic condition and the resulted slope stability for the 9-month period were analyzed and discussed for the different hillslopes.

Multi-group measurement invariance of the multiple sclerosis walking scale-12?

PubMed

Motl, Robert W; Mullen, Sean; McAuley, Edward

2012-03-01

One primary assumption underlying the interpretation of composite multiple sclerosis walking scale-12 (MSWS-12) scores across levels of disability status is multi-group measurement invariance. This assumption was tested in the present study between samples that differed in self-reported disability status. Participants (n = 867) completed a battery of questionnaires that included the MSWS-12 and patient-determined disease step (PDDS) scale. The multi-group invariance was tested between samples that had PDDS scores of ≤2 (i.e. no mobility limitation; n = 470) and PDDS scores ≥3 (onset of mobility limitation; n = 397) using Mplus 6·0. The omnibus test of equal covariance matrices indicated that the MSWS-12 was not invariant between the two samples that differed in disability status. The source of non-invariance occurred with the initial equivalence test of the factor structure itself. We provide evidence that questions the unambiguous interpretation of scores from the MSWS-12 as a measure of walking impairment between samples of persons with multiple sclerosis who differ in disability status.

Automated Enrichment of Sulfanilamide in Milk Matrices by Utilization of Aptamer-Linked Magnetic Particles.

PubMed

Fischer, Christin; Kallinich, Constanze; Klockmann, Sven; Schrader, Jil; Fischer, Markus

2016-12-07

The present work demonstrates the first automated enrichment approach for antibiotics in milk using specific DNA aptamers. First, aptamers toward the antibiotic sulfanilamide were selected and characterized regarding their dissociation constants and specificity toward relevant antibiotics via fluorescence assay and LC-MS/MS detection. The performed enrichment was automated using the KingFisherDuo and compared to a manual approach. Verifying the functionality, trapping was realized in different milk matrices: (i) 0.3% fat milk, (ii) 1.5% fat milk, (iii) 3.5% fat milk, and (iv) 0.3% fat cocoa milk drink. Enrichment factors up to 8-fold could be achieved. Furthermore, it could be shown that novel implementation of a magnetic separator increases the reproducibility and reduces the hands-on time from approximately half a day to 30 min.

Comparison of real-time PCR methods for the detection of Naegleria fowleri in surface water and sediment.

PubMed

Streby, Ashleigh; Mull, Bonnie J; Levy, Karen; Hill, Vincent R

2015-05-01

Naegleria fowleri is a thermophilic free-living ameba found in freshwater environments worldwide. It is the cause of a rare but potentially fatal disease in humans known as primary amebic meningoencephalitis. Established N. fowleri detection methods rely on conventional culture techniques and morphological examination followed by molecular testing. Multiple alternative real-time PCR assays have been published for rapid detection of Naegleria spp. and N. fowleri. Foursuch assays were evaluated for the detection of N. fowleri from surface water and sediment. The assays were compared for thermodynamic stability, analytical sensitivity and specificity, detection limits, humic acid inhibition effects, and performance with seeded environmental matrices. Twenty-one ameba isolates were included in the DNA panel used for analytical sensitivity and specificity analyses. N. fowleri genotypes I and III were used for method performance testing. Two of the real-time PCR assays were determined to yield similar performance data for specificity and sensitivity for detecting N. fowleri in environmental matrices.

Comparison of real-time PCR methods for the detection of Naegleria fowleri in surface water and sediment

PubMed Central

Streby, Ashleigh; Mull, Bonnie J.; Levy, Karen

2015-01-01

Naegleria fowleri is a thermophilic free-living ameba found in freshwater environments worldwide. It is the cause of a rare but potentially fatal disease in humans known as primary amebic meningoencephalitis. Established N. fowleri detection methods rely on conventional culture techniques and morphological examination followed by molecular testing. Multiple alternative real-time PCR assays have been published for rapid detection of Naegleria spp. and N. fowleri. Four such assays were evaluated for the detection of N. fowleri from surface water and sediment. The assays were compared for thermodynamic stability, analytical sensitivity and specificity, detection limits, humic acid inhibition effects, and performance with seeded environmental matrices. Twenty-one ameba isolates were included in the DNA panel used for analytical sensitivity and specificity analyses. N. fowleri genotypes I and III were used for method performance testing. Two of the real-time PCR assays were determined to yield similar performance data for specificity and sensitivity for detecting N. fowleri in environmental matrices. PMID:25855343

Isotope dilution liquid chromatography - mass spectrometry methods for fat- and water-soluble vitamins in nutritional formulations.

PubMed

Phinney, Karen W; Rimmer, Catherine A; Thomas, Jeanice Brown; Sander, Lane C; Sharpless, Katherine E; Wise, Stephen A

2011-01-01

Vitamins are essential to human health, and dietary supplements containing vitamins are widely used by individuals hoping to ensure they have adequate intake of these important nutrients. Measurement of vitamins in nutritional formulations is necessary to monitor regulatory compliance and in studies examining the nutrient intake of specific populations. Liquid chromatographic methods, primarily with UV absorbance detection, are well established for both fat- and water-soluble measurements, but they do have limitations for certain analytes and may suffer from a lack of specificity in complex matrices. Liquid chromatography-mass spectrometry (LC-MS) provides both sensitivity and specificity for the determination of vitamins in these matrices, and simultaneous analysis of multiple vitamins in a single analysis is often possible. In this work, LC-MS methods were developed for both fat- and water-soluble vitamins and applied to the measurement of these analytes in two NIST Standard Reference Materials. When possible, stable isotope labeled internal standards were employed for quantification.

Do We Really Become Smarter When Our Fluid-Intelligence Test Scores Improve?

PubMed Central

Hayes, Taylor R.; Petrov, Alexander A.; Sederberg, Per B.

2014-01-01

Recent reports of training-induced gains on fluid intelligence tests have fueled an explosion of interest in cognitive training—now a billion-dollar industry. The interpretation of these results is questionable because score gains can be dominated by factors that play marginal roles in the scores themselves, and because intelligence gain is not the only possible explanation for the observed control-adjusted far transfer across tasks. Here we present novel evidence that the test score gains used to measure the efficacy of cognitive training may reflect strategy refinement instead of intelligence gains. A novel scanpath analysis of eye movement data from 35 participants solving Raven’s Advanced Progressive Matrices on two separate sessions indicated that one-third of the variance of score gains could be attributed to test-taking strategy alone, as revealed by characteristic changes in eye-fixation patterns. When the strategic contaminant was partialled out, the residual score gains were no longer significant. These results are compatible with established theories of skill acquisition suggesting that procedural knowledge tacitly acquired during training can later be utilized at posttest. Our novel method and result both underline a reason to be wary of purported intelligence gains, but also provide a way forward for testing for them in the future. PMID:25395695

Do We Really Become Smarter When Our Fluid-Intelligence Test Scores Improve?

PubMed

Hayes, Taylor R; Petrov, Alexander A; Sederberg, Per B

2015-01-01

Recent reports of training-induced gains on fluid intelligence tests have fueled an explosion of interest in cognitive training-now a billion-dollar industry. The interpretation of these results is questionable because score gains can be dominated by factors that play marginal roles in the scores themselves, and because intelligence gain is not the only possible explanation for the observed control-adjusted far transfer across tasks. Here we present novel evidence that the test score gains used to measure the efficacy of cognitive training may reflect strategy refinement instead of intelligence gains. A novel scanpath analysis of eye movement data from 35 participants solving Raven's Advanced Progressive Matrices on two separate sessions indicated that one-third of the variance of score gains could be attributed to test-taking strategy alone, as revealed by characteristic changes in eye-fixation patterns. When the strategic contaminant was partialled out, the residual score gains were no longer significant. These results are compatible with established theories of skill acquisition suggesting that procedural knowledge tacitly acquired during training can later be utilized at posttest. Our novel method and result both underline a reason to be wary of purported intelligence gains, but also provide a way forward for testing for them in the future.

Modulation of hematopoietic progenitor cell fate in vitro by varying collagen oligomer matrix stiffness in the presence or absence of osteoblasts.

PubMed

Chitteti, Brahmananda Reddy; Kacena, Melissa A; Voytik-Harbin, Sherry L; Srour, Edward F

2015-10-01

To recreate the in vivo hematopoietic cell microenvironment or niche and to study the impact of extracellular matrix (ECM) biophysical properties on hematopoietic progenitor cell (HPC) proliferation and function, mouse bone-marrow derived HPC (Lin-Sca1+cKit+/(LSK) were cultured within three-dimensional (3D) type I collagen oligomer matrices. To generate a more physiologic milieu, 3D cultures were established in both the presence and absence of calvariae-derived osteoblasts (OB). Collagen oligomers were polymerized at varying concentration to give rise to matrices of different fibril densities and therefore matrix stiffness (shear storage modulus, 50-800 Pa). Decreased proliferation and increased clonogenicity of LSK cells was associated with increase of matrix stiffness regardless of whether OB were present or absent from the 3D culture system. Also, regardless of whether OB were or were not added to the 3D co-culture system, LSK within 800 Pa collagen oligomer matrices maintained the highest percentage of Lin-Sca1+ cells as well as higher percentage of cells in quiescent state (G0/G1) compared to 50 Pa or 200Pa matrices. Collectively, these data illustrate that biophysical features of collagen oligomer matrices, specifically fibril density-induced modulation of matrix stiffness, provide important guidance cues in terms of LSK expansion and differentiation and therefore maintenance of progenitor cell function. Copyright © 2015. Published by Elsevier B.V.

A preliminary quality of life questionnaire-bronchiectasis: a patient-reported outcome measure for bronchiectasis.

PubMed

Quittner, Alexandra L; Marciel, Kristen K; Salathe, Matthias A; O'Donnell, Anne E; Gotfried, Mark H; Ilowite, Jonathan S; Metersky, Mark L; Flume, Patrick A; Lewis, Sandra A; McKevitt, Matthew; Montgomery, A Bruce; O'Riordan, Thomas G; Barker, Alan F

2014-08-01

The Quality of Life Questionnaire-Bronchiectasis (QOL-B) is the first disease-specific, patient-reported outcome measure for patients with bronchiectasis. Content validity, cognitive testing, responsivity to open-label treatment, and psychometric analyses are presented. Reviews of literature, existing measures, and physician input were used to generate the initial QOL-B. Modifications following preliminary cognitive testing (N = 35 patients with bronchiectasis) generated version (V) 1.0. An open-ended patient interview study (N = 28) provided additional information and was content analyzed to derive saturation matrices, which summarized all disease-related topics mentioned by each participant. This resulted in QOL-B V2.0. Psychometric analyses were carried out using results from an open-label phase 2 trial, in which 89 patients were enrolled and treated with aztreonam for inhalation solution. Responsivity to open-label treatment was observed. Additional analyses generated QOL-B V3.0, with 37 items on eight scales: respiratory symptoms; physical, role, emotional, and social functioning; vitality; health perceptions; and treatment burden. For each scale, scores are standardized on a 0-to-100-point scale; higher scores indicate better health-related quality of life. No total score is calculated. A final cognitive testing study (N = 40) resulted in a minor change to one social functioning scale item (QOL-B V3.1). Content validity, cognitive testing, responsivity to open-label treatment, and initial psychometric analyses supported QOL-B items and structure. This interim QOL-B is a promising tool for evaluating the efficacy of new therapies for patients with bronchiectasis and for measuring symptoms, functioning, and quality of life in these patients on a routine basis. A final psychometric validation study is needed and is forthcoming. ClinicalTrials.gov; No.: NCT00805025; URL: www.clinicaltrials.gov.

Neurocognitive screening of lead-exposed andean adolescents and young adults.

PubMed

Counter, S Allen; Buchanan, Leo H; Ortega, Fernando

2009-01-01

This study was designed to assess the utility of two psychometric tests with putative minimal cultural bias for use in field screening of lead (Pb)-exposed Ecuadorian Andean workers. Specifically, the study evaluated the effectiveness in Pb-exposed adolescents and young adults of a nonverbal reasoning test standardized for younger children, and compared the findings with performance on a test of auditory memory. The Raven Coloured Progressive Matrices (RCPM) was used as a test of nonverbal intelligence, and the Digit Span subtest of the Wechsler IV intelligence scale was used to assess auditory memory/attention. The participants were 35 chronically Pb-exposed Pb-glazing workers, aged 12-21 yr. Blood lead (PbB) levels for the study group ranged from 3 to 86 microg/dl, with 65.7% of the group at and above 10 microg/dl. Zinc protoporphyrin heme ratios (ZPP/heme) ranged from 38 to 380 micromol/mol, with 57.1% of the participants showing abnormal ZPP/heme (>69 micromol/mol). ZPP/heme was significantly correlated with PbB levels, suggesting chronic Pb exposure. Performance on the RCPM was less than average on the U.S., British, and Puerto Rican norms, but average on the Peruvian norms. Significant inverse associations between PbB/ZPP concentrations and RCPM standard scores using the U.S., Puerto Rican, and Peruvian norms were observed, indicating decreasing RCPM test performance with increasing PbB and ZPP levels. RCPM scores were significantly correlated with performance on the Digit Span test for auditory memory. Mean Digit Span scale score was less than average, suggesting auditory memory/attention deficits. In conclusion, both the RCPM and Digit Span tests were found to be effective instruments for field screening of visual-spatial reasoning and auditory memory abilities, respectively, in Pb-exposed Andean adolescents and young adults.

XENOBIOTIC METHODS DEVELOPMENT FOR HUMAN EXPOSURE ASSESSMENT RESEARCH

EPA Science Inventory

Biomarkers from blood, breath, urine, and other physiological matrices can provide useful information regarding exposures to environmental pollutants. Once developed and applied appropriately, specific and sensitive methods can often provide definitive data identifying the vario...

Enhancing purification efficiency of affinity functionalized composite agarose micro beads using Fe3O4 nanoparticles.

PubMed

Amiri, S; Mehrnia, M R; Roudsari, F Pourasgharian

2017-01-15

In this work, a series of magnetic and nonmagnetic agarose matrices were fabricated for protein purification. Certain amounts of Fe 3 O 4 nanoparticles were encapsulated in agarose beads to form composite magnetic matrices with enhanced purification efficiency. Structure and morphology of prepared matrices were studied by optical and scanning electron microscopes, FT-IR, and BET-BJH analysis. The prepared matrices had regular spherical shape, followed by a uniform size distribution. By nanoparticles addition, the number of mesopores decreased while population of pores with radius ≤10nm increased; thus, higher specific area achieved. According to VSM results, magnetization degree was one of the characteristics affected by agarose content of the beads. A dye ligand, Cibacron Blue F3GA (CB), was covalently bound to beads to adsorb Bovine serum albumin. CB concentration was determined by elemental analysis. It was shown that magnetic beads hold higher CB concentrations than nonmagnetic ones due to higher specific area. As a result, magnetic 8%-agarose beads had the highest affinity adsorption capacity in static experiments. Moreover, breakthrough curves were monitored to calculate dynamic binding capacity. And, it was shown that magnetic 4%-agarose had the highest adsorbing amount (6.00mg/mL). It was implied that pore diffusion in magnetic 4%-agarose may be the reason for higher dynamic capacity. Plus, column efficiency was evaluated. It was revealed that all magnetic beads had lower HETP (0.11, 0.12 and 0.11cm for magnetic 4, 6, and 8%-agarose beads) than nonmagnetic ones (P-value<0.05). Copyright © 2016 Elsevier B.V. All rights reserved.

Zinc status and cognitive function of pregnant women in Southern Ethiopia

PubMed Central

Stoecker, BJ; Abebe, Y; Hubbs-Tait, L; Kennedy, TS; Gibson, RS; Arbide, I; Teshome, A; Westcott, J; Krebs, NF; Hambidge, KM

2015-01-01

The relation between zinc status and cognitive function was examined in a cross-sectional study in the Sidama area of Southern Ethiopia. Pregnant women >24 weeks of gestation from three adjacent rural villages volunteered to participate. Mean (s.d.) plasma zinc of 99 women was 6.97 (1.07) μmol/l (below the cutoff of 7.6 μmol/l indicative of zinc deficiency at this stage of gestation). The Raven’s Coloured Progressive Matrices (CPM) test was administered individually. Scores for the Raven’s scale A, which is the simplest scale, ranged from 4 to 10 of a possible 12. Women with plasma zinc <7.6 μmol/l had significantly lower Raven’s CPM scale A scores than women with plasma zinc concentrations >7.6 μmol/l. Plasma zinc and maternal age and education predicted 17% of the variation in Raven’s CPM scale A scores. We conclude that zinc deficiency is a major factor affecting cognition in these pregnant women. PMID:19190668

What's wrong with hazard-ranking systems? An expository note.

PubMed

Cox, Louis Anthony Tony

2009-07-01

Two commonly recommended principles for allocating risk management resources to remediate uncertain hazards are: (1) select a subset to maximize risk-reduction benefits (e.g., maximize the von Neumann-Morgenstern expected utility of the selected risk-reducing activities), and (2) assign priorities to risk-reducing opportunities and then select activities from the top of the priority list down until no more can be afforded. When different activities create uncertain but correlated risk reductions, as is often the case in practice, then these principles are inconsistent: priority scoring and ranking fails to maximize risk-reduction benefits. Real-world risk priority scoring systems used in homeland security and terrorism risk assessment, environmental risk management, information system vulnerability rating, business risk matrices, and many other important applications do not exploit correlations among risk-reducing opportunities or optimally diversify risk-reducing investments. As a result, they generally make suboptimal risk management recommendations. Applying portfolio optimization methods instead of risk prioritization ranking, rating, or scoring methods can achieve greater risk-reduction value for resources spent.

Intellectual Growth in Children as a Function of Domain Specific and Domain General Working Memory Subgroups

ERIC Educational Resources Information Center

Swanson, H. Lee

2011-01-01

This study examined whether children's growth on measures of fluid (Raven Colored Progressive Matrices) and crystallized (reading and math achievement) intelligence was attributable to domain-specific or domain-general functions of working memory (WM). A sample of 290 elementary school children was tested on measures of intelligence across three…

Prediction of β-turns in proteins from multiple alignment using neural network

PubMed Central

Kaur, Harpreet; Raghava, Gajendra Pal Singh

2003-01-01

A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033

Predicting β-Turns in Protein Using Kernel Logistic Regression

PubMed Central

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, FangXiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case. PMID:23509793

Predicting β-turns in protein using kernel logistic regression.

PubMed

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, Fangxiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case.

Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic TCR and MHC peptide ligands.

PubMed

Zhao, Y; Gran, B; Pinilla, C; Markovic-Plese, S; Hemmer, B; Tzou, A; Whitney, L W; Biddison, W E; Martin, R; Simon, R

2001-08-15

The interaction of TCRs with MHC peptide ligands can be highly flexible, so that many different peptides are recognized by the same TCR in the context of a single restriction element. We provide a quantitative description of such interactions, which allows the identification of T cell epitopes and molecular mimics. The response of T cell clones to positional scanning synthetic combinatorial libraries is analyzed with a mathematical approach that is based on a model of independent contribution of individual amino acids to peptide Ag recognition. This biometric analysis compares the information derived from these libraries composed of trillions of decapeptides with all the millions of decapeptides contained in a protein database to rank and predict the most stimulatory peptides for a given T cell clone. We demonstrate the predictive power of the novel strategy and show that, together with gene expression profiling by cDNA microarrays, it leads to the identification of novel candidate autoantigens in the inflammatory autoimmune disease, multiple sclerosis.

Acoustooptic linear algebra processors - Architectures, algorithms, and applications

NASA Technical Reports Server (NTRS)

Casasent, D.

1984-01-01

Architectures, algorithms, and applications for systolic processors are described with attention to the realization of parallel algorithms on various optical systolic array processors. Systolic processors for matrices with special structure and matrices of general structure, and the realization of matrix-vector, matrix-matrix, and triple-matrix products and such architectures are described. Parallel algorithms for direct and indirect solutions to systems of linear algebraic equations and their implementation on optical systolic processors are detailed with attention to the pipelining and flow of data and operations. Parallel algorithms and their optical realization for LU and QR matrix decomposition are specifically detailed. These represent the fundamental operations necessary in the implementation of least squares, eigenvalue, and SVD solutions. Specific applications (e.g., the solution of partial differential equations, adaptive noise cancellation, and optimal control) are described to typify the use of matrix processors in modern advanced signal processing.

Decryption of pure-position permutation algorithms.

PubMed

Zhao, Xiao-Yu; Chen, Gang; Zhang, Dan; Wang, Xiao-Hong; Dong, Guang-Chang

2004-07-01

Pure position permutation image encryption algorithms, commonly used as image encryption investigated in this work are unfortunately frail under known-text attack. In view of the weakness of pure position permutation algorithm, we put forward an effective decryption algorithm for all pure-position permutation algorithms. First, a summary of the pure position permutation image encryption algorithms is given by introducing the concept of ergodic matrices. Then, by using probability theory and algebraic principles, the decryption probability of pure-position permutation algorithms is verified theoretically; and then, by defining the operation system of fuzzy ergodic matrices, we improve a specific decryption algorithm. Finally, some simulation results are shown.

Design of robust iterative learning control schemes for systems with polytopic uncertainties and sector-bounded nonlinearities

NASA Astrophysics Data System (ADS)

Boski, Marcin; Paszke, Wojciech

2017-01-01

This paper deals with designing of iterative learning control schemes for uncertain systems with static nonlinearities. More specifically, the nonlinear part is supposed to be sector bounded and system matrices are assumed to range in the polytope of matrices. For systems with such nonlinearities and uncertainties the repetitive process setting is exploited to develop a linear matrix inequality based conditions for computing the feedback and feedforward (learning) controllers. These controllers guarantee acceptable dynamics along the trials and ensure convergence of the trial-to-trial error dynamics, respectively. Numerical examples illustrate the theoretical results and confirm effectiveness of the designed control scheme.

Hg-Xe exciplex formation in mixed Xe/Ar matrices: molecular dynamics and luminescence study.

PubMed

Lozada-García, Rolando; Rojas-Lorenzo, Germán; Crépin, Claudine; Ryan, Maryanne; McCaffrey, John G

2015-03-19

Luminescence of Hg((3)P1) atoms trapped in mixed Ar/Xe matrices containing a small amount of Xe is reported. Broad emission bands, strongly red-shifted from absorption are recorded which are assigned to strong complexes formed between the excited mercury Hg* and xenon atoms. Molecular dynamics calculations are performed on simulated Xe/Ar samples doped with Hg to follow the behavior of Hg* in the mixed rare gas matrices leading to exciplex formation. The role of Xe atoms in the first solvation shell (SS1) around Hg was investigated in detail, revealing the formation of two kinds of triatomic exciplexes; namely, Xe-Hg*-Xe and Ar-Hg*-Xe. The first species exists only when two xenon atoms are present in SS1 with specific geometries allowing the formation of a linear or quasi-linear exciplex. In the other geometries, or in the presence of only one Xe in SS1, a linear Ar-Hg*-Xe exciplex is formed. The two kinds of exciplexes have different emission bands, the most red-shifted being that involving two Xe atoms, whose emission is very close to that observed in pure Xe matrices. Simulations give a direct access to the analysis of the experimental absorption, emission, and excitation spectra, together with the dynamics of exciplexes formation.

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

Identifying correlation structure is important to achieving estimation efficiency in analyzing longitudinal data, and is also crucial for drawing valid statistical inference for large size clustered data. In this paper, we propose a nonparametric method to estimate the correlation structure, which is applicable for discrete longitudinal data. We utilize eigenvector-based basis matrices to approximate the inverse of the empirical correlation matrix and determine the number of basis matrices via model selection. A penalized objective function based on the difference between the empirical and model approximation of the correlation matrices is adopted to select an informative structure for the correlation matrix. The eigenvector representation of the correlation estimation is capable of reducing the risk of model misspecification, and also provides useful information on the specific within-cluster correlation pattern of the data. We show that the proposed method possesses the oracle property and selects the true correlation structure consistently. The proposed method is illustrated through simulations and two data examples on air pollution and sonar signal studies. PMID:26361433

Isolation, Separation, and Preconcentration of Biologically Active Compounds from Plant Matrices by Extraction Techniques.

PubMed

Raks, Victoria; Al-Suod, Hossam; Buszewski, Bogusław

2018-01-01

Development of efficient methods for isolation and separation of biologically active compounds remains an important challenge for researchers. Designing systems such as organomineral composite materials that allow extraction of a wide range of biologically active compounds, acting as broad-utility solid-phase extraction agents, remains an important and necessary task. Selective sorbents can be easily used for highly selective and reliable extraction of specific components present in complex matrices. Herein, state-of-the-art approaches for selective isolation, preconcentration, and separation of biologically active compounds from a range of matrices are discussed. Primary focus is given to novel extraction methods for some biologically active compounds including cyclic polyols, flavonoids, and oligosaccharides from plants. In addition, application of silica-, carbon-, and polymer-based solid-phase extraction adsorbents and membrane extraction for selective separation of these compounds is discussed. Potential separation process interactions are recommended; their understanding is of utmost importance for the creation of optimal conditions to extract biologically active compounds including those with estrogenic properties.

Evaluation of indirect impedance for measuring microbial growth in complex food matrices.

PubMed

Johnson, N; Chang, Z; Bravo Almeida, C; Michel, M; Iversen, C; Callanan, M

2014-09-01

The suitability of indirect impedance to accurately measure microbial growth in real food matrices was investigated. A variety of semi-solid and liquid food products were inoculated with Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Lactobacillus plantarum, Pseudomonas aeruginosa, Escherichia coli, Salmonella enteriditis, Candida tropicalis or Zygosaccharomyces rouxii and CO2 production was monitored using a conductimetric (Don Whitely R.A.B.I.T.) system. The majority (80%) of food and microbe combinations produced a detectable growth signal. The linearity of conductance responses in selected food products was investigated and a good correlation (R(2) ≥ 0.84) was observed between inoculum levels and times to detection. Specific growth rate estimations from the data were sufficiently accurate for predictive modeling in some cases. This initial evaluation of the suitability of indirect impedance to generate microbial growth data in complex food matrices indicates significant potential for the technology as an alternative to plating methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

Decellularized Tissue and Cell-Derived Extracellular Matrices as Scaffolds for Orthopaedic Tissue Engineering

PubMed Central

Cheng, Christina W.; Solorio, Loran D.; Alsberg, Eben

2014-01-01

The reconstruction of musculoskeletal defects is a constant challenge for orthopaedic surgeons. Musculoskeletal injuries such as fractures, chondral lesions, infections and tumor debulking can often lead to large tissue voids requiring reconstruction with tissue grafts. Autografts are currently the gold standard in orthopaedic tissue reconstruction; however, there is a limit to the amount of tissue that can be harvested before compromising the donor site. Tissue engineering strategies using allogeneic or xenogeneic decellularized bone, cartilage, skeletal muscle, tendon and ligament have emerged as promising potential alternative treatment. The extracellular matrix provides a natural scaffold for cell attachment, proliferation and differentiation. Decellularization of in vitro cell-derived matrices can also enable the generation of autologous constructs from tissue specific cells or progenitor cells. Although decellularized bone tissue is widely used clinically in orthopaedic applications, the exciting potential of decellularized cartilage, skeletal muscle, tendon and ligament cell-derived matrices has only recently begun to be explored for ultimate translation to the orthopaedic clinic. PMID:24417915

Evaluation of ceramic packed-rod regenerator matrices

NASA Technical Reports Server (NTRS)

Lawless, W. N.; Arenz, R. W.

1981-01-01

An extensive evaluation of a modified cryocooler with various regenerator matrices is reported. The matrices examined are 0.015 in. diam. Pb spheres and 0.008, 0.015, and 0.030 in. diam. rods of a 0.2% SnCl2 doped ceramic labelled LS-8A. Specific heat and thermal conductivity data on these rod materials are also reported. The chronic pulverization/dusting problem common to Pb spheres was investigated. During a 1000 hr life test with 0.0008 in. diam. rods there was no degradation of the refrigerator performance, and a subsequent examination of the rods themselves revealed no evidence of breakage or pulverization. The load temperature characteristics for the rod packed regenerators were inferior to that for the Pb spheres, the effect being to shift the Pb spheres load curve up in temperature. This temperature shift was 5.0, 7.4, and 11.6K for the 0.0008, 0.015, and 0.030 in. diam. rods, respectively.

An Overview of Conventional and Emerging Analytical Methods for the Determination of Mycotoxins

PubMed Central

Cigić, Irena Kralj; Prosen, Helena

2009-01-01

Mycotoxins are a group of compounds produced by various fungi and excreted into the matrices on which they grow, often food intended for human consumption or animal feed. The high toxicity and carcinogenicity of these compounds and their ability to cause various pathological conditions has led to widespread screening of foods and feeds potentially polluted with them. Maximum permissible levels in different matrices have also been established for some toxins. As these are quite low, analytical methods for determination of mycotoxins have to be both sensitive and specific. In addition, an appropriate sample preparation and pre-concentration method is needed to isolate analytes from rather complicated samples. In this article, an overview of methods for analysis and sample preparation published in the last ten years is given for the most often encountered mycotoxins in different samples, mainly in food. Special emphasis is on liquid chromatography with fluorescence and mass spectrometric detection, while in the field of sample preparation various solid-phase extraction approaches are discussed. However, an overview of other analytical and sample preparation methods less often used is also given. Finally, different matrices where mycotoxins have to be determined are discussed with the emphasis on their specific characteristics important for the analysis (human food and beverages, animal feed, biological samples, environmental samples). Various issues important for accurate qualitative and quantitative analyses are critically discussed: sampling and choice of representative sample, sample preparation and possible bias associated with it, specificity of the analytical method and critical evaluation of results. PMID:19333436

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

PubMed

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

2017-01-09

The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DIMETHYLITHIOARSINIC ANHYDRIDE: A STANDARD FOR ARSENIC SPECIATION

EPA Science Inventory

Recently, sulfar analogs of well know arsenicals have been identfied in biolgical, dietary and environmental matrices. These discoveries have generated a need for stable species-specific standards. This presentation will forcus on the isolation and characterization of a standar...

An Analysis of the Max-Min Texture Measure.

DTIC Science & Technology

1982-01-01

PANC 33 D2 Confusion Matrices for Scene A, IR 34 D3 Confusion Matrices for Scene B, PANC 35 D4 Confusion Matrices for Scene B, IR 36 D5 Confusion...Matrices for Scene C, PANC 37 D6 Confusion Matrices for Scene C, IR 38 D7 Confusion Matrices for Scene E, PANC 39 D8 Confusion Matrices for Scene E, IR 40...D9 Confusion Matrices for Scene H, PANC 41 DIO Confusion Matrices for Scene H, JR 42 3 .D 10CnuinMtie o cn ,IR4 AN ANALYSIS OF THE MAX-MIN TEXTURE

Issues Related to Obtaining Intelligence Quotient-Matched Controls in Autism Research

PubMed Central

Rao, Vanitha S.; Raman, Vijaya; Mysore, Ashok V.

2015-01-01

Background: Intelligence Quotient (IQ) is considered to be an index of global cognitive functioning and has traditionally been used as a fulcral measure in case-control studies in neuro-developmental disorders such as autism. Aim: The aim is to highlight the issues of “matching for IQ” with controls in autism research. Materials and Methods: Percentile scores on the Coloured Progressive Matrices of 20 children with autism in the age range of 5 to 12 years have been graphically compared with 21 age matched typically developing children. Results and Conclusions: The percentile scores of the so-called high functioning children with autism from special schools were well below that of typically developing children. There are many challenges when using IQ in case-control studies of autism. Alternative approaches need to be considered. PMID:25969598

The Level and Nature of Autistic Intelligence

PubMed Central

Dawson, Michelle; Soulières, Isabelle; Ann Gernsbacher, Morton; Mottron, Laurent

2015-01-01

Autistics are presumed to be characterized by cognitive impairment, and their cognitive strengths (e.g., in Block Design performance) are frequently interpreted as low-level by-products of high-level deficits, not as direct manifestations of intelligence. Recent attempts to identify the neuroanatomical and neurofunctional signature of autism have been positioned on this universal, but untested, assumption. We therefore assessed a broad sample of 38 autistic children on the preeminent test of fluid intelligence, Raven’s Progressive Matrices. Their scores were, on average, 30 percentile points, and in some cases more than 70 percentile points, higher than their scores on the Wechsler scales of intelligence. Typically developing control children showed no such discrepancy, and a similar contrast was observed when a sample of autistic adults was compared with a sample of nonautistic adults. We conclude that intelligence has been underestimated in autistics. PMID:17680932

Ascertainment bias from imputation methods evaluation in wheat.

PubMed

Brandariz, Sofía P; González Reymúndez, Agustín; Lado, Bettina; Malosetti, Marcos; Garcia, Antonio Augusto Franco; Quincke, Martín; von Zitzewitz, Jarislav; Castro, Marina; Matus, Iván; Del Pozo, Alejandro; Castro, Ariel J; Gutiérrez, Lucía

2016-10-04

Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel. In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available. Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel.

Affinity chromatography matrices for depletion and purification of casein glycomacropeptide from bovine whey.

PubMed

Baieli, María F; Urtasun, Nicolás; Martinez, María J; Hirsch, Daniela B; Pilosof, Ana M R; Miranda, María V; Cascone, Osvaldo; Wolman, Federico J

2017-01-01

Casein glycomacropeptide (CMP) is a 64- amino acid peptide found in cheese whey, which is released after κ-casein specific cleavage by chymosin. CMP lacks aromatic amino acids, a characteristic that makes it usable as a nutritional supplement for people with phenylketonuria. CMP consists of two nonglycosylated isoforms (aCMP A and aCMP B) and its different glycosylated forms (gCMP A and gCMP B). The most predominant carbohydrate of gCMP is N-acetylneuraminic acid (sialic acid). Here, we developed a CMP purification process based on the affinity of sialic acid for wheat germ agglutinin (WGA). After formation of chitosan beads and adsorption of WGA, the agglutinin was covalently attached with glutaraldehyde. Two matrices with different WGA density were assayed for CMP adsorption. Maximum adsorption capacities were calculated according to the Langmuir model from adsorption isotherms developed at pH 7.0, being 137.0 mg/g for the matrix with the best performance. In CMP reduction from whey, maximum removal percentage was 79% (specifically 33.7% of gCMP A and B, 75.8% of aCMP A, and 93.9% of aCMP B). The CMP was recovered as an aggregate with an overall yield of 64%. Therefore, the matrices developed are promising for CMP purification from cheese whey. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:171-180, 2017. © 2016 American Institute of Chemical Engineers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, R.C.; Garard, R.J.; Lokhandwala, K.K.

The crush behavior (specific energy absorption and crush load stability) of unidirectional fiber composite rods having tougher matrices than vinyl ester were investigated and compared with the crush behavior of similar specimens having a vinyl ester matrix. The matrices were a cyclic polyester and two rubber-toughened vinyl esters. The specific energy absorption with the cyclic polyester matrix, 180 MJ/m{sup 3}, was slightly lower than that with the vinyl ester matrix, 230 MJ/m{sup 3}. On the other hand, the crush stability was markedly better. The average deviation of the crush load about the mean was as small as 3.5% with themore » cyclic polyester matrix, in contrast to about 12% with the vinyl ester matrix. The higher ductility of the cyclic polyester and the good fiber-matrix bond strength together resulted in less fracturing of the matrix and more uniform kink-band formation across the composite cross section than occurred with the vinyl ester matrix. There was also a reduction in the tendency for fibers at the periphery of the rod to splay outward rather than being crushed. Of the two rubber-toughened vinyl ester matrices, a 30% reduction was found in the average deviation of the crush load about the mean with the matrix toughened with a core-shell material, although no improvement was found with the CTBN rubber-modified vinyl ester resin.« less

Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

NASA Astrophysics Data System (ADS)

Vira, J.; Sofiev, M.

2014-08-01

This paper describes assimilation of trace gas observations into the chemistry transport model SILAM using the 3D-Var method. Assimilation results for year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the Airbase observation database, which provides the observational dataset used in this study. Attention is paid to the background and observation error covariance matrices, which are obtained primarily by iterative application of a posteriori diagnostics. The diagnostics are computed separately for two months representing summer and winter conditions, and further disaggregated by time of day. This allows deriving background and observation error covariance definitions which include both seasonal and diurnal variation. The consistency of the obtained covariance matrices is verified using χ2 diagnostics. The analysis scores are computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values is improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

Functional brain networks associated with eating behaviors in obesity.

PubMed

Park, Bo-Yong; Seo, Jongbum; Park, Hyunjin

2016-03-31

Obesity causes critical health problems including diabetes and hypertension that affect billions of people worldwide. Obesity and eating behaviors are believed to be closely linked but their relationship through brain networks has not been fully explored. We identified functional brain networks associated with obesity and examined how the networks were related to eating behaviors. Resting state functional magnetic resonance imaging (MRI) scans were obtained for 82 participants. Data were from an equal number of people of healthy weight (HW) and non-healthy weight (non-HW). Connectivity matrices were computed with spatial maps derived using a group independent component analysis approach. Brain networks and associated connectivity parameters with significant group-wise differences were identified and correlated with scores on a three-factor eating questionnaire (TFEQ) describing restraint, disinhibition, and hunger eating behaviors. Frontoparietal and cerebellum networks showed group-wise differences between HW and non-HW groups. Frontoparietal network showed a high correlation with TFEQ disinhibition scores. Both frontoparietal and cerebellum networks showed a high correlation with body mass index (BMI) scores. Brain networks with significant group-wise differences between HW and non-HW groups were identified. Parts of the identified networks showed a high correlation with eating behavior scores.

Nutritional and socioeconomic status in cognitive development of Santal children of Purulia district, India.

PubMed

Chowdhury, Sutanu Dutta; Ghosh, Tusharkanti

2011-03-01

Cognitive development of children depends on nutritional and socioeconomic factors. The objectives of the present study were to assess the cognitive development and to investigate the relationship of nutritional and socioeconomic status (SES) to cognitive development in 5-12 year old Santal children of Purulia district of West Bengal, India. The nutritional status of each child was assessed by z-score of height-for-age, weight-for-height and weight-for-age parameters. SES was measured using the updated Kuppusswami scale. Cognitive development was measured by Raven's Coloured Progressive Matrices (RCPM). The growth curve of RCPM scores of Santal children remained around the 5(th) percentile values of British children. The RCPM scores of the adequately nourished children and upper-lower SES were significantly higher (p < 0.05) than the children with lower SES and nutritional status. About 42.96% and 27.69% of Santal children were found to be in the intellectually deficient and below average groups, respectively. RCPM scores of Santal children were significantly correlated with nutritional status and socioeconomic factors (p < 0.01). The surveyed children showed poor cognitive functions. The vulnerable nutritional and socioeconomic statuses of Santal children are the major causes for their poor cognitive development.

Periodic GMP Matrices

NASA Astrophysics Data System (ADS)

Eichinger, Benjamin

2016-07-01

We recall criteria on the spectrum of Jacobi matrices such that the corresponding isospectral torus consists of periodic operators. Motivated by those known results for Jacobi matrices, we define a new class of operators called GMP matrices. They form a certain Generalization of matrices related to the strong Moment Problem. This class allows us to give a parametrization of almost periodic finite gap Jacobi matrices by periodic GMP matrices. Moreover, due to their structural similarity we can carry over numerous results from the direct and inverse spectral theory of periodic Jacobi matrices to the class of periodic GMP matrices. In particular, we prove an analogue of the remarkable ''magic formula'' for this new class.

Review Over a 3-Year Period of European Union Proficiency Tests for Detection of Staphylococcal Enterotoxins in Food Matrices.

PubMed

Nia, Yacine; Mutel, Isabelle; Assere, Adrien; Lombard, Bertrand; Auvray, Frederic; Hennekinne, Jacques-Antoine

2016-04-13

Staphylococcal food poisoning outbreaks are a major cause of foodborne illnesses in Europe and their notifications have been mandatory since 2005. Even though the European regulation on microbiological criteria for food defines a criterion on staphylococcal enterotoxin (SE) only in cheese and dairy products, European Food Safety Authority (EFSA) data reported that various types of food matrices are involved in staphylococcal food poisoning outbreaks. The European Screening Method (ESM) of European Union Reference Laboratory for Coagulase Positive Staphylococci (EURL CPS) was validated in 2011 for SE detection in food matrices and is currently the official method used for screening purposes in Europe. In this context, EURLCPS is annually organizing Inter-Laboratory Proficiency Testing Trials (ILPT) to evaluate the competency of the European countries' National Reference Laboratories (NRLs) to analyse SE content in food matrices. A total of 31 NRLs representing 93% of European countries participated in these ILPTs. Eight food matrices were used for ILPT over the period 2013-2015, including cheese, freeze-dried cheese, tuna, mackerel, roasted chicken, ready-to-eat food, milk, and pastry. Food samples were spiked with four SE types (i.e., SEA, SEC, SED, and SEE) at various concentrations. Homogeneity and stability studies showed that ILPT samples were both homogeneous and stable. The analysis of results obtained by participants for a total of 155 blank and 620 contaminated samples allowed for evaluation of trueness (>98%) and specificity (100%) of ESM. Further to the validation study of ESM carried out in 2011, these three ILPTs allowed for the assessment of the proficiency of the NRL network and the performance of ESM on a large variety of food matrices and samples. The ILPT design presented here will be helpful for the organization of ILPT on SE detection by NRLs or other expert laboratories.

EXPOSURE ASSESSMENT IN THE NATIONAL CHILDREN'S STUDY-INTRODUCTION

EPA Science Inventory

The science of exposure assessment is relatively new and evolving rapidly with the advancement of sophisticated methods for specific measurements at the picogram per gram level or lower in a variety of environmental and biologic matrices. Without this measurement capability, envi...

A pragmatic approach for mortality prediction after surgery in infective endocarditis: optimizing and refining EuroSCORE.

PubMed

Fernández-Hidalgo, N; Ferreria-González, I; Marsal, J R; Ribera, A; Aznar, M L; de Alarcón, A; García-Cabrera, E; Gálvez-Acebal, J; Sánchez-Espín, G; Reguera-Iglesias, J M; De La Torre-Lima, J; Lomas, J M; Hidalgo-Tenorio, C; Vallejo, N; Miranda, B; Santos-Ortega, A; Castro, M A; Tornos, P; García-Dorado, D; Almirante, B

2018-03-03

To simplify and optimize the ability of EuroSCORE I and II to predict early mortality after surgery for infective endocarditis (IE). Multicentre retrospective study (n = 775). Simplified scores, eliminating irrelevant variables, and new specific scores, adding specific IE variables, were created. The performance of the original, recalibrated and specific EuroSCOREs was assessed by Brier score, C-statistic and calibration plot in bootstrap samples. The Net Reclassification Index was quantified. Recalibrated scores including age, previous cardiac surgery, critical preoperative state, New York Heart Association >I, and emergent surgery (EuroSCORE I and II); renal failure and pulmonary hypertension (EuroSCORE I); and urgent surgery (EuroSCORE II) performed better than the original EuroSCOREs (Brier original and recalibrated: EuroSCORE I: 0.1770 and 0.1667; EuroSCORE II: 0.2307 and 0.1680). Performance improved with the addition of fistula, staphylococci and mitral location (EuroSCORE I and II) (Brier specific: EuroSCORE I 0.1587, EuroSCORE II 0.1592). Discrimination improved in specific models (C-statistic original, recalibrated and specific: EuroSCORE I: 0.7340, 0.7471 and 0.7728; EuroSCORE II: 0.7442, 0.7423 and 0.7700). Calibration improved in both EuroSCORE I models (intercept 0.295, slope 0.829 (original); intercept -0.094, slope 0.888 (recalibrated); intercept -0.059, slope 0.925 (specific)) but only in specific EuroSCORE II model (intercept 2.554, slope 1.114 (original); intercept -0.260, slope 0.703 (recalibrated); intercept -0.053, slope 0.930 (specific)). Net Reclassification Index was 5.1% and 20.3% for the specific EuroSCORE I and II CONCLUSIONS: The use of simplified EuroSCORE I and EuroSCORE II models in IE with the addition of specific variables may lead to simpler and more accurate models. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research.

PubMed

Waller, Niels G

2016-01-01

For a fixed set of standardized regression coefficients and a fixed coefficient of determination (R-squared), an infinite number of predictor correlation matrices will satisfy the implied quadratic form. I call such matrices fungible correlation matrices. In this article, I describe an algorithm for generating positive definite (PD), positive semidefinite (PSD), or indefinite (ID) fungible correlation matrices that have a random or fixed smallest eigenvalue. The underlying equations of this algorithm are reviewed from both algebraic and geometric perspectives. Two simulation studies illustrate that fungible correlation matrices can be profitably used in Monte Carlo research. The first study uses PD fungible correlation matrices to compare penalized regression algorithms. The second study uses ID fungible correlation matrices to compare matrix-smoothing algorithms. R code for generating fungible correlation matrices is presented in the supplemental materials.

Porous Aluminum Oxide and Magnesium Oxide Films Using Organic Hydrogels as Structure Matrices

PubMed Central

Chen, Zimei

2018-01-01

We describe the synthesis of mesoporous Al2O3 and MgO layers on silicon wafer substrates by using poly(dimethylacrylamide) hydrogels as porogenic matrices. Hydrogel films are prepared by spreading the polymer through spin-coating, followed by photo-cross-linking and anchoring to the substrate surface. The metal oxides are obtained by swelling the hydrogels in the respective metal nitrate solutions and subsequent thermal conversion. Combustion of the hydrogel results in mesoporous metal oxide layers with thicknesses in the μm range and high specific surface areas up to 558 m2∙g−1. Materials are characterized by SEM, FIB ablation, EDX, and Kr physisorption porosimetry. PMID:29565802

Thiol-ene mediated neoglycosylation of collagen patches: a preliminary study.

PubMed

Russo, Laura; Battocchio, Chiara; Secchi, Valeria; Magnano, Elena; Nappini, Silvia; Taraballi, Francesca; Gabrielli, Luca; Comelli, Francesca; Papagni, Antonio; Costa, Barbara; Polzonetti, Giovanni; Nicotra, Francesco; Natalello, Antonino; Doglia, Silvia M; Cipolla, Laura

2014-02-11

Despite the relevance of carbohydrates as cues in eliciting specific biological responses, the covalent surface modification of collagen-based matrices with small carbohydrate epitopes has been scarcely investigated. We report thereby the development of an efficient procedure for the chemoselective neoglycosylation of collagen matrices (patches) via a thiol-ene approach, between alkene-derived monosaccharides and the thiol-functionalized material surface. Synchrotron radiation-induced X-ray photoelectron spectroscopy (SR-XPS), Fourier transform-infrared (FT-IR), and enzyme-linked lectin assay (ELLA) confirmed the effectiveness of the collagen neoglycosylation. Preliminary biological evaluation in osteoarthritic models is reported. The proposed methodology can be extended to any thiolated surface for the development of smart biomaterials for innovative approaches in regenerative medicine.

Brief announcement: Hypergraph parititioning for parallel sparse matrix-matrix multiplication

DOE PAGES

Ballard, Grey; Druinsky, Alex; Knight, Nicholas; ...

2015-01-01

The performance of parallel algorithms for sparse matrix-matrix multiplication is typically determined by the amount of interprocessor communication performed, which in turn depends on the nonzero structure of the input matrices. In this paper, we characterize the communication cost of a sparse matrix-matrix multiplication algorithm in terms of the size of a cut of an associated hypergraph that encodes the computation for a given input nonzero structure. Obtaining an optimal algorithm corresponds to solving a hypergraph partitioning problem. Furthermore, our hypergraph model generalizes several existing models for sparse matrix-vector multiplication, and we can leverage hypergraph partitioners developed for that computationmore » to improve application-specific algorithms for multiplying sparse matrices.« less

Simulating Multivariate Nonnormal Data Using an Iterative Algorithm

ERIC Educational Resources Information Center

Ruscio, John; Kaczetow, Walter

2008-01-01

Simulating multivariate nonnormal data with specified correlation matrices is difficult. One especially popular method is Vale and Maurelli's (1983) extension of Fleishman's (1978) polynomial transformation technique to multivariate applications. This requires the specification of distributional moments and the calculation of an intermediate…

Impairments in proverb interpretation following focal frontal lobe lesions☆

PubMed Central

Murphy, Patrick; Shallice, Tim; Robinson, Gail; MacPherson, Sarah E.; Turner, Martha; Woollett, Katherine; Bozzali, Marco; Cipolotti, Lisa

2013-01-01

The proverb interpretation task (PIT) is often used in clinical settings to evaluate frontal “executive” dysfunction. However, only a relatively small number of studies have investigated the relationship between frontal lobe lesions and performance on the PIT. We compared 52 patients with unselected focal frontal lobe lesions with 52 closely matched healthy controls on a proverb interpretation task. Participants also completed a battery of neuropsychological tests, including a fluid intelligence task (Raven’s Advanced Progressive Matrices). Lesions were firstly analysed according to a standard left/right sub-division. Secondly, a finer-grained analysis compared the performance of patients with medial, left lateral and right lateral lesions with healthy controls. Thirdly, a contrast of specific frontal subgroups compared the performance of patients with medial lesions with patients with lateral frontal lesions. The results showed that patients with left frontal lesions were significantly impaired on the PIT, while in patients with right frontal lesions the impairments approached significance. Medial frontal patients were the only frontal subgroup impaired on the PIT, relative to healthy controls and lateral frontal patients. Interestingly, an error analysis indicated that a significantly higher number of concrete responses were found in the left lateral subgroup compared to healthy controls. We found no correlation between scores on the PIT and on the fluid intelligence task. Overall our results suggest that specific regions of the frontal lobes contribute to the performance on the PIT. PMID:23850600

Cytotoxic T Lymphocyte Trafficking and Survival in an Augmented Fibrin Matrix Carrier

PubMed Central

Zou, Zhaoxia; Denny, Erin; Brown, Christine E.; Jensen, Michael C.; Li, Gang; Fujii, Tatsuhiro; Neman, Josh; Jandial, Rahul; Chen, Mike

2012-01-01

Cell-based therapies have intriguing potential for the treatment of a variety of neurological disorders. One such example is genetically engineered cytotoxic T lymphocytes (CTLs) that are being investigated in brain tumor clinical trials. The development of methods for CTL delivery is critical to their use in the laboratory and clinical setting. In our study, we determined whether CTLs can migrate through fibrin matrices and if their migration, survival, and function could be modulated by adding chemokines to the matrix. Our results indicated that CTLs can freely migrate through fibrin matrices. As expected, the addition of the monocyte chemotactic protein-1 (MCP-1), also known as chemokine C-C motif ligand 2 (CCL2), to the surrounding media increased egress of the CTLs out of the fibrin clot. Interleukin (IL) -2 and/or IL-15 embedded in the matrix enhanced T cell survival and further promoted T cell migration. The interleukin-13 receptor alpha 2 specific (IL-13R alpha2) T cells that traveled out of the fibrin clot retained the capacity to kill U251 glioma cells. In summary, CTLs can survive and migrate robustly in fibrin matrices. These processes can be influenced by modification of matrix constituents. We conclude that fibrin matrices may be suitable T cell carriers and can be used to facilitate understanding of T cell interaction with the surrounding microenvironment. PMID:22496835

Cytotoxic T lymphocyte trafficking and survival in an augmented fibrin matrix carrier.

PubMed

Zou, Zhaoxia; Denny, Erin; Brown, Christine E; Jensen, Michael C; Li, Gang; Fujii, Tatsuhiro; Neman, Josh; Jandial, Rahul; Chen, Mike

2012-01-01

Cell-based therapies have intriguing potential for the treatment of a variety of neurological disorders. One such example is genetically engineered cytotoxic T lymphocytes (CTLs) that are being investigated in brain tumor clinical trials. The development of methods for CTL delivery is critical to their use in the laboratory and clinical setting. In our study, we determined whether CTLs can migrate through fibrin matrices and if their migration, survival, and function could be modulated by adding chemokines to the matrix. Our results indicated that CTLs can freely migrate through fibrin matrices. As expected, the addition of the monocyte chemotactic protein-1 (MCP-1), also known as chemokine C-C motif ligand 2 (CCL2), to the surrounding media increased egress of the CTLs out of the fibrin clot. Interleukin (IL) -2 and/or IL-15 embedded in the matrix enhanced T cell survival and further promoted T cell migration. The interleukin-13 receptor alpha 2 specific (IL-13R alpha2) T cells that traveled out of the fibrin clot retained the capacity to kill U251 glioma cells. In summary, CTLs can survive and migrate robustly in fibrin matrices. These processes can be influenced by modification of matrix constituents. We conclude that fibrin matrices may be suitable T cell carriers and can be used to facilitate understanding of T cell interaction with the surrounding microenvironment.

Fully constrained Majorana neutrino mass matrices using \\varvec{Σ(72× 3)}

NASA Astrophysics Data System (ADS)

Krishnan, R.; Harrison, P. F.; Scott, W. G.

2018-01-01

In 2002, two neutrino mixing ansatze having trimaximally mixed middle (ν _2) columns, namely tri-chi-maximal mixing ( {T}χ {M}) and tri-phi-maximal mixing ( {T}φ {M}), were proposed. In 2012, it was shown that {T}χ {M} with χ =± π /16 as well as {T}φ {M} with φ = ± π /16 leads to the solution, sin ^2 θ _{13} = 2/3 sin ^2 π /16, consistent with the latest measurements of the reactor mixing angle, θ _{13}. To obtain {T}χ {M}_{(χ =± π /16)} and {T}φ {M}_{(φ =± π /16)}, the type I see-saw framework with fully constrained Majorana neutrino mass matrices was utilised. These mass matrices also resulted in the neutrino mass ratios, m_1:m_2:m_3=( 2+√{2}) /1+√{2(2+√{2)}}:1:( 2+√{2}) /-1+√{2(2+√{2)}}. In this paper we construct a flavour model based on the discrete group Σ (72× 3) and obtain the aforementioned results. A Majorana neutrino mass matrix (a symmetric 3× 3 matrix with six complex degrees of freedom) is conveniently mapped into a flavon field transforming as the complex six-dimensional representation of Σ (72× 3). Specific vacuum alignments of the flavons are used to arrive at the desired mass matrices.

Response of selected binomial coefficients to varying degrees of matrix sparseness and to matrices with known data interrelationships

USGS Publications Warehouse

Archer, A.W.; Maples, C.G.

1989-01-01

Numerous departures from ideal relationships are revealed by Monte Carlo simulations of widely accepted binomial coefficients. For example, simulations incorporating varying levels of matrix sparseness (presence of zeros indicating lack of data) and computation of expected values reveal that not only are all common coefficients influenced by zero data, but also that some coefficients do not discriminate between sparse or dense matrices (few zero data). Such coefficients computationally merge mutually shared and mutually absent information and do not exploit all the information incorporated within the standard 2 ?? 2 contingency table; therefore, the commonly used formulae for such coefficients are more complicated than the actual range of values produced. Other coefficients do differentiate between mutual presences and absences; however, a number of these coefficients do not demonstrate a linear relationship to matrix sparseness. Finally, simulations using nonrandom matrices with known degrees of row-by-row similarities signify that several coefficients either do not display a reasonable range of values or are nonlinear with respect to known relationships within the data. Analyses with nonrandom matrices yield clues as to the utility of certain coefficients for specific applications. For example, coefficients such as Jaccard, Dice, and Baroni-Urbani and Buser are useful if correction of sparseness is desired, whereas the Russell-Rao coefficient is useful when sparseness correction is not desired. ?? 1989 International Association for Mathematical Geology.

Texture zero neutrino models and their connection with resonant leptogenesis

NASA Astrophysics Data System (ADS)

Achelashvili, Avtandil; Tavartkiladze, Zurab

2018-04-01

Within the low scale resonant leptogenesis scenario, the cosmological CP asymmetry may arise by radiative corrections through the charged lepton Yukawa couplings. While in some cases, as one expects, decisive role is played by the λτ coupling, we show that in specific neutrino textures only by inclusion of the λμ the cosmological CP violation is generated at 1-loop level. With the purpose to relate the cosmological CP violation to the leptonic CP phase δ, we consider an extension of MSSM with two right handed neutrinos (RHN), which are degenerate in mass at high scales. Together with this, we first consider two texture zero 3 × 2 Dirac Yukawa matrices of neutrinos. These via see-saw generated neutrino mass matrices augmented by single ΔL = 2 dimension five (d = 5) operator give predictive neutrino sectors with calculable CP asymmetries. The latter is generated through λμ,τ coupling(s) at 1-loop level. Detailed analysis of the leptogenesis is performed. We also revise some one texture zero Dirac Yukawa matrices, considered earlier, and show that addition of a single ΔL = 2, d = 5 entry in the neutrino mass matrices, together with newly computed 1-loop corrections to the CP asymmetries, give nice accommodation of the neutrino sector and desirable amount of the baryon asymmetry via the resonant leptogenesis even for rather low RHN masses (∼few TeV-107 GeV).

Comprehensive proteomic characterization of stem cell-derived extracellular matrices.

PubMed

Ragelle, Héloïse; Naba, Alexandra; Larson, Benjamin L; Zhou, Fangheng; Prijić, Miralem; Whittaker, Charles A; Del Rosario, Amanda; Langer, Robert; Hynes, Richard O; Anderson, Daniel G

2017-06-01

In the stem-cell niche, the extracellular matrix (ECM) serves as a structural support that additionally provides stem cells with signals that contribute to the regulation of stem-cell function, via reciprocal interactions between cells and components of the ECM. Recently, cell-derived ECMs have emerged as in vitro cell culture substrates to better recapitulate the native stem-cell microenvironment outside the body. Significant changes in cell number, morphology and function have been observed when mesenchymal stem cells (MSC) were cultured on ECM substrates as compared to standard tissue-culture polystyrene (TCPS). As select ECM components are known to regulate specific stem-cell functions, a robust characterization of cell-derived ECM proteomic composition is critical to better comprehend the role of the ECM in directing cellular processes. Here, we characterized and compared the protein composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts from different donors, employing quantitative proteomic methods. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential survival and gene-expression profiles among the cell types and as compared to TCPS, indicating that the cell-derived ECMs influence each cell type in a different manner. This general approach to understanding the protein composition of different tissue-specific and cell-derived ECM will inform the rational design of defined systems and biomaterials that recapitulate critical ECM signals for stem-cell culture and tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inactivation of Adenovirus Type 5, Rotavirus WA and Male Specific Coliphage (MS2) in Biosolids by Lime Stabilization

PubMed Central

Hansen, Jacqueline J.; Warden, Paul S.; Margolin, Aaron B.

2007-01-01

The use of lime to reduce or eliminate pathogen content is a cost-effective treatment currently employed in many Class B biosolids production plants in the United States. A bench scale model of lime stabilization was designed to evaluate the survival of adenovirus type 5, rotavirus Wa, and the male specific bacteriophage, MS2, in various matrices. Each virus was initially evaluated independently in a reverse osmosis treated water matrix limed with an aqueous solution of calcium hydroxide for 24-hr at 22 ± 5°C. In all R/O water trials, adenovirus type 5, rotavirus Wa and MS2 were below detectable levels (<100.5 TCID50/mL and <1 PFU/mL respectively) following 0.1-hr of liming. Adenovirus type 5, rotavirus Wa, and MS2, were inoculated into composted, raw and previously limed matrices, representative of sludge and biosolids, to achieve a final concentration of approximately 104 PFU or TCID50/mL. Each matrix was limed for 24-hr at 22 ± 5°C and 4 ± 2°C. In all trials virus was below detectable levels following a 24-hr incubation. The time required for viral inactivation varied depending on the temperature and sample matrix. This research demonstrates reduction of adenovirus type 5, rotavirus Wa, and male-specific bacteriophage, in water, sludge and biosolids matrices following addition of an 8% calcium hydroxide slurry to achieve a pH of 12 for 2-hr reduced to 11.5 for 22-hr by addition of 0.1 N HCl. In these trials, MS2 was a conservative indicator of the efficacy of lime stabilization of adenovirus Type 5 and rotavirus Wa and therefore is proposed as a useful indicator organism. PMID:17431317

A core-shell column approach to a comprehensive high-performance liquid chromatography phenolic analysis of Vitis vinifera L. and interspecific hybrid grape juices, wines, and other matrices following either solid phase extraction or direct injection.

PubMed

Manns, David C; Mansfield, Anna Katharine

2012-08-17

Four high-throughput reverse-phase chromatographic protocols utilizing two different core-shell column chemistries have been developed to analyze the phenolic profiles of complex matrices, specifically targeting juices and wines produced from interspecific hybrid grape cultivars. Following pre-fractionation via solid-phase extraction or direct injection, individual protocols were designed to resolve, identify and quantify specific chemical classes of compounds including non-anthocyanin monomeric phenolics, condensed tannins following acid hydrolysis, and anthocyanins. Detection levels ranging from 1.2 ppb to 27.5 ppb, analyte %RSDs ranging from 0.04 to 0.38, and linear ranges of quantitation approaching five orders of magnitude were achieved using conventional HPLC instrumentation. Using C(18) column chemistry, the non-anthocyanin monomeric protocol effectively separated a set of 16 relevant phenolic compounds comprised flavan-3-ols, hydroxycinnamic acids, and flavonols in under 14 min. The same column was used to develop a 15-min protocol for hydrolyzed condensed tannin analysis. Two anthocyanin protocols are presented, one utilizing the same C(18) column, best suited for anthocyanidin and monoglucoside analysis, the other utilizing a pentafluorophenyl chemistry optimized to effectively separate complex mixtures of coexisting mono- and diglucoside anthocyanins. These protocols and column chemistries have been used initially to explore a wide variety of complex phenolic matrices, including red and white juices and wines produced from Vitis vinifera and interspecific hybrid grape cultivars, juices, teas, and plant extracts. Each protocol displayed robust matrix responses as written, yet are flexible enough to be easily modified to suit specifically tailored analytical requirements. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of nanoparticles with an optical sensor based on carbon nanotubes

NASA Astrophysics Data System (ADS)

Stäb, J.; Furin, D.; Fechner, P.; Proll, G.; Soriano-Dotor, L. M.; Ruiz-Palomero, C.; Valcárcel, M.; Gauglitz, G.

2017-05-01

Nanomaterials play an important role in science and in every day products. This is due to their varied and specific properties, whereby especially engineered nanoparticles (ENPs) have shown various beneficial properties for a wide range of application in consumables (e.g. cosmetics, drinks, food and food packaging). Silver nanoparticles for instance are hidden in meat packaging materials or in deodorants. Reasons for this can be found in the antibacterial effect of silver, which leads to high applicability in consumer products. However, ENPs are under permanent discussion due to their unforeseen hazards and an unknown disposition in living organisms and the environment. So far, there is a lack of methods, which allows for the fast and effective characterization and quantification of such nanoparticles in complex matrices (e.g. creams, fruit juice), since matrix components can impede a specific detection of the analyte. It was the objective of project INSTANT to address this topic and compose a method to detect nanoparticles as a first step. Therefore, the development of a sensor system with an upstream sample preparation for the characterization and quantification of specific nanoparticles in complex matrices using a label free optical sensor array in combination with novel recognition elements was developed. The promising optical technology iRIfS (imaging reflectometric interference sensor) was used for this purpose. As a recognition element, functionalized carbon nanotubes can be effectively used. Owing to their excellent electronical, mechanical and chemical properties, CNTs have already been used for extracting ENPs from complex matrices as sorbent material by filtration. After successful immobilization of CNTs on microscope glass slides e.g. the detection of stabilized silver nanoparticles extracted by a sample preparation unit using the iRIfS technology was performed.

Fluid intelligence and psychosocial outcome: from logical problem solving to social adaptation.

PubMed

Huepe, David; Roca, María; Salas, Natalia; Canales-Johnson, Andrés; Rivera-Rei, Álvaro A; Zamorano, Leandro; Concepción, Aimée; Manes, Facundo; Ibañez, Agustín

2011-01-01

While fluid intelligence has proved to be central to executive functioning, logical reasoning and other frontal functions, the role of this ability in psychosocial adaptation has not been well characterized. A random-probabilistic sample of 2370 secondary school students completed measures of fluid intelligence (Raven's Progressive Matrices, RPM) and several measures of psychological adaptation: bullying (Delaware Bullying Questionnaire), domestic abuse of adolescents (Conflict Tactic Scale), drug intake (ONUDD), self-esteem (Rosenberg's Self Esteem Scale) and the Perceived Mental Health Scale (Spanish adaptation). Lower fluid intelligence scores were associated with physical violence, both in the role of victim and victimizer. Drug intake, especially cannabis, cocaine and inhalants and lower self-esteem were also associated with lower fluid intelligence. Finally, scores on the perceived mental health assessment were better when fluid intelligence scores were higher. Our results show evidence of a strong association between psychosocial adaptation and fluid intelligence, suggesting that the latter is not only central to executive functioning but also forms part of a more general capacity for adaptation to social contexts.

Fluid Intelligence and Psychosocial Outcome: From Logical Problem Solving to Social Adaptation

PubMed Central

Huepe, David; Roca, María; Salas, Natalia; Canales-Johnson, Andrés; Rivera-Rei, Álvaro A.; Zamorano, Leandro; Concepción, Aimée; Manes, Facundo; Ibañez, Agustín

2011-01-01

Background While fluid intelligence has proved to be central to executive functioning, logical reasoning and other frontal functions, the role of this ability in psychosocial adaptation has not been well characterized. Methodology/Principal Findings A random-probabilistic sample of 2370 secondary school students completed measures of fluid intelligence (Raven's Progressive Matrices, RPM) and several measures of psychological adaptation: bullying (Delaware Bullying Questionnaire), domestic abuse of adolescents (Conflict Tactic Scale), drug intake (ONUDD), self-esteem (Rosenberg's Self Esteem Scale) and the Perceived Mental Health Scale (Spanish adaptation). Lower fluid intelligence scores were associated with physical violence, both in the role of victim and victimizer. Drug intake, especially cannabis, cocaine and inhalants and lower self-esteem were also associated with lower fluid intelligence. Finally, scores on the perceived mental health assessment were better when fluid intelligence scores were higher. Conclusions/Significance Our results show evidence of a strong association between psychosocial adaptation and fluid intelligence, suggesting that the latter is not only central to executive functioning but also forms part of a more general capacity for adaptation to social contexts. PMID:21957464

Complex numbers in chemometrics: examples from multivariate impedance measurements on lipid monolayers.

PubMed

Geladi, Paul; Nelson, Andrew; Lindholm-Sethson, Britta

2007-07-09

Electrical impedance gives multivariate complex number data as results. Two examples of multivariate electrical impedance data measured on lipid monolayers in different solutions give rise to matrices (16x50 and 38x50) of complex numbers. Multivariate data analysis by principal component analysis (PCA) or singular value decomposition (SVD) can be used for complex data and the necessary equations are given. The scores and loadings obtained are vectors of complex numbers. It is shown that the complex number PCA and SVD are better at concentrating information in a few components than the naïve juxtaposition method and that Argand diagrams can replace score and loading plots. Different concentrations of Magainin and Gramicidin A give different responses and also the role of the electrolyte medium can be studied. An interaction of Gramicidin A in the solution with the monolayer over time can be observed.

Three Tier Unified Process Model for Requirement Negotiations and Stakeholder Collaborations

NASA Astrophysics Data System (ADS)

Niazi, Muhammad Ashraf Khan; Abbas, Muhammad; Shahzad, Muhammad

2012-11-01

This research paper is focused towards carrying out a pragmatic qualitative analysis of various models and approaches of requirements negotiations (a sub process of requirements management plan which is an output of scope managementís collect requirements process) and studies stakeholder collaborations methodologies (i.e. from within communication management knowledge area). Experiential analysis encompass two tiers; first tier refers to the weighted scoring model while second tier focuses on development of SWOT matrices on the basis of findings of weighted scoring model for selecting an appropriate requirements negotiation model. Finally the results are simulated with the help of statistical pie charts. On the basis of simulated results of prevalent models and approaches of negotiations, a unified approach for requirements negotiations and stakeholder collaborations is proposed where the collaboration methodologies are embeded into selected requirements negotiation model as internal parameters of the proposed process alongside some external required parameters like MBTI, opportunity analysis etc.

The growth of IQ among Estonian schoolchildren from ages 7 to 19.

PubMed

Pullmann, Helle; Allik, Jüri; Lynn, Richard

2004-11-01

The Standard Progressive Matrices test was standardized in Estonia on a representative sample of 4874 schoolchildren aged from 7 to 19 years. When the IQ of Estonian children was expressed in relation to British and Icelandic norms, both demonstrated a similar sigmoid relationship. The youngest Estonian group scored higher than the British and Icelandic norms: after first grade, the score fell below 100 and remained lower until age 12, and after that age it increased above the mean level of these two comparison countries. The difference between the junior school children and the secondary school children may be due to schooling, sampling error or different trajectories of intellectual maturation in different populations. Systematic differences in the growth pattern suggest that the development of intellectual capacities proceeds at different rates and the maturation process can take longer in some populations than in others.

Early life exposure to malaria and cognition in adulthood: evidence from Mexico.

PubMed

Venkataramani, Atheendar S

2012-09-01

This study examines the impact of early life malaria exposure on cognition in sample of Mexican adults, using the nationwide introduction of malaria eradication efforts to identify causal impacts. The core findings are that birth year exposure to malaria eradication was associated with increases in Raven Progressive Matrices test scores and consumption expenditures, but not schooling. Additionally, cohorts born after eradication both entered and exited school earlier than their pre-eradication counterparts. These effects were only seen for men and explanations for this are assessed. Collectively, these findings suggest that improvements in infant health help explain secular increases in cognitive test scores, that better cognition may link early life health to adulthood earnings, and that human capital investments through childhood and young adulthood respond sensitively to market returns to early life endowment shocks. Copyright © 2012 Elsevier B.V. All rights reserved.

HEAVY DUTY DIESEL VEHICLE LOAD ESTIMATION: DEVELOPMENT OF VEHICLE ACTIVITY OPTIMIZATION ALGORITHM

EPA Science Inventory

The Heavy-Duty Vehicle Modal Emission Model (HDDV-MEM) developed by the Georgia Institute of Technology(Georgia Tech) has a capability to model link-specific second-by-second emissions using speed/accleration matrices. To estimate emissions, engine power demand calculated usin...

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering

PubMed Central

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time. PMID:26270539

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

PubMed

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time.

Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products.

PubMed

Fraiture, Marie-Alice; Herman, Philippe; Taverniers, Isabel; De Loose, Marc; Van Nieuwerburgh, Filip; Deforce, Dieter; Roosens, Nancy H

2015-04-15

To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

The brief negative symptom scale: psychometric properties.

PubMed

Kirkpatrick, Brian; Strauss, Gregory P; Nguyen, Linh; Fischer, Bernard A; Daniel, David G; Cienfuegos, Angel; Marder, Stephen R

2011-03-01

The participants in the NIMH-MATRICS Consensus Development Conference on Negative Symptoms recommended that an instrument be developed that measured blunted affect, alogia, asociality, anhedonia, and avolition. The Brief Negative Symptom Scale (BNSS) is a 13-item instrument designed for clinical trials and other studies that measures these 5 domains. The interrater, test-retest, and internal consistency of the instrument were strong, with respective intraclass correlation coefficients of 0.93 for the BNSS total score and values of 0.89-0.95 for individual subscales. Comparisons with positive symptoms and other negative symptom instruments supported the discriminant and concurrent validity of the instrument.

Establishing homologies in protein sequences

NASA Technical Reports Server (NTRS)

Dayhoff, M. O.; Barker, W. C.; Hunt, L. T.

1983-01-01

Computer-based statistical techniques used to determine homologies between proteins occurring in different species are reviewed. The technique is based on comparison of two protein sequences, either by relating all segments of a given length in one sequence to all segments of the second or by finding the best alignment of the two sequences. Approaches discussed include selection using printed tabulations, identification of very similar sequences, and computer searches of a database. The use of the SEARCH, RELATE, and ALIGN programs (Dayhoff, 1979) is explained; sample data are presented in graphs, diagrams, and tables and the construction of scoring matrices is considered.

Meat authentication: a new HPLC-MS/MS based method for the fast and sensitive detection of horse and pork in highly processed food.

PubMed

von Bargen, Christoph; Brockmeyer, Jens; Humpf, Hans-Ulrich

2014-10-01

Fraudulent blending of food products with meat from undeclared species is a problem on a global scale, as exemplified by the European horse meat scandal in 2013. Routinely used methods such as ELISA and PCR can suffer from limited sensitivity or specificity when processed food samples are analyzed. In this study, we have developed an optimized method for the detection of horse and pork in different processed food matrices using MRM and MRM(3) detection of species-specific tryptic marker peptides. Identified marker peptides were sufficiently stable to resist thermal processing of different meat products and thus allow the sensitive and specific detection of pork or horse in processed food down to 0.24% in a beef matrix system. In addition, we were able to establish a rapid 2-min extraction protocol for the efficient protein extraction from processed food using high molar urea and thiourea buffers. Together, we present here the specific and sensitive detection of horse and pork meat in different processed food matrices using MRM-based detection of marker peptides. Notably, prefractionation of proteins using 2D-PAGE or off-gel fractionation is not necessary. The presented method is therefore easily applicable in analytical routine laboratories without dedicated proteomics background.

Parallel transmission RF pulse design with strict temperature constraints.

PubMed

Deniz, Cem M; Carluccio, Giuseppe; Collins, Christopher

2017-05-01

RF safety in parallel transmission (pTx) is generally ensured by imposing specific absorption rate (SAR) limits during pTx RF pulse design. There is increasing interest in using temperature to ensure safety in MRI. In this work, we present a local temperature correlation matrix formalism and apply it to impose strict constraints on maximum absolute temperature in pTx RF pulse design for head and hip regions. Electromagnetic field simulations were performed on the head and hip of virtual body models. Temperature correlation matrices were calculated for four different exposure durations ranging between 6 and 24 min using simulated fields and body-specific constants. Parallel transmission RF pulses were designed using either SAR or temperature constraints, and compared with each other and unconstrained RF pulse design in terms of excitation fidelity and safety. The use of temperature correlation matrices resulted in better excitation fidelity compared with the use of SAR in parallel transmission RF pulse design (for the 6 min exposure period, 8.8% versus 21.0% for the head and 28.0% versus 32.2% for the hip region). As RF exposure duration increases (from 6 min to 24 min), the benefit of using temperature correlation matrices on RF pulse design diminishes. However, the safety of the subject is always guaranteed (the maximum temperature was equal to 39°C). This trend was observed in both head and hip regions, where the perfusion rates are very different. Copyright © 2017 John Wiley & Sons, Ltd.

Intelligence and psychopathy: a correlational study on insane female offenders.

PubMed

Spironelli, C; Segrè, D; Stegagno, L; Angrilli, A

2014-01-01

The occurrence of a significant relationship between psychopathic traits and intelligence is still open to debate. Most of the relevant information has been obtained from crystallized IQ tests or on psychopathic male offenders. In this study we hypothesized a negative correlation between psychopathic traits and fluid intelligence on a sample of criminal female in-patients. We carried out a correlational study on a selected sample of 56 criminal female offenders. Variables that were measured include the Hare Psychopathy Checklist Revised (PCL-R) total score (and, separately, the scores from its four subscales: Interpersonal, Affective, Lifestyle and Antisocial) and fluid IQ measured by Raven's Progressive Matrices (RPM). Pearson's correlation between RPM IQ and total PCL-R score was negative (r(54) = -0.55, p < 0.001); women with greater psychopathy traits (total PCL-R score) had lower IQ scores. Negative correlations were also found between IQ and the four PCL-R subscales, Interpersonal, Affective, Lifestyle and Antisocial (r(54) = -0.35, p < 0.01, r(54) = -0.52, p < 0.001, r(54) = -0.53, p < 0.001, and r(54) = -0.49, p < 0.001 respectively). The results indicate a general negative relationship between PCL-R and IQ, equally distributed across the four subcomponents of the psychopathic trait, and support the view that unsuccessful psychopathic women have poor planning and are unable to foresee and represent future consequences of their actions.

CMV matrices in random matrix theory and integrable systems: a survey

NASA Astrophysics Data System (ADS)

Nenciu, Irina

2006-07-01

We present a survey of recent results concerning a remarkable class of unitary matrices, the CMV matrices. We are particularly interested in the role they play in the theory of random matrices and integrable systems. Throughout the paper we also emphasize the analogies and connections to Jacobi matrices.

Basal Cell Carcinoma With Matrical Differentiation: Clinicopathologic, Immunohistochemical, and Molecular Biological Study of 22 Cases.

PubMed

Kyrpychova, Liubov; Carr, Richard A; Martinek, Petr; Vanecek, Tomas; Perret, Raul; Chottová-Dvořáková, Magdalena; Zamecnik, Michal; Hadravsky, Ladislav; Michal, Michal; Kazakov, Dmitry V

2017-06-01

Basal cell carcinoma (BCC) with matrical differentiation is a fairly rare neoplasm, with about 30 cases documented mainly as isolated case reports. We studied a series of this neoplasm, including cases with an atypical matrical component, a hitherto unreported feature. Lesions coded as BCC with matrical differentiation were reviewed; 22 cases were included. Immunohistochemical studies were performed using antibodies against BerEp4, β-catenin, and epithelial membrane antigen (EMA). Molecular genetic studies using Ion AmpliSeq Cancer Hotspot Panel v2 by massively parallel sequencing on Ion Torrent PGM were performed in 2 cases with an atypical matrical component (1 was previously subjected to microdissection to sample the matrical and BCC areas separately). There were 13 male and 9 female patients, ranging in age from 41 to 89 years. Microscopically, all lesions manifested at least 2 components, a BCC area (follicular germinative differentiation) and areas with matrical differentiation. A BCC component dominated in 14 cases, whereas a matrical component dominated in 4 cases. Matrical differentiation was recognized as matrical/supramatrical cells (n=21), shadow cells (n=21), bright red trichohyaline granules (n=18), and blue-gray corneocytes (n=18). In 2 cases, matrical areas manifested cytologic atypia, and a third case exhibited an infiltrative growth pattern, with the tumor metastasizing to a lymph node. BerEP4 labeled the follicular germinative cells, whereas it was markedly reduced or negative in matrical areas. The reverse pattern was seen with β-catenin. EMA was negative in BCC areas but stained a proportion of matrical/supramatrical cells. Genetic studies revealed mutations of the following genes: CTNNB1, KIT, CDKN2A, TP53, SMAD4, ERBB4, and PTCH1, with some differences between the matrical and BCC components. It is concluded that matrical differentiation in BCC in most cases occurs as multiple foci. Rare neoplasms manifest atypia in the matrical areas. Immunohistochemical analysis for BerEP4, EMA, and β-catenin can be helpful in limited biopsy specimens. From a molecular biological prospective, BCC and matrical components appear to share some of the gene mutations but have differences in others, but this observation must be validated in a large series.

Generalised Assignment Matrix Methodology in Linear Programming

ERIC Educational Resources Information Center

Jerome, Lawrence

2012-01-01

Discrete Mathematics instructors and students have long been struggling with various labelling and scanning algorithms for solving many important problems. This paper shows how to solve a wide variety of Discrete Mathematics and OR problems using assignment matrices and linear programming, specifically using Excel Solvers although the same…

Space station data system analysis/architecture study. Task 4: System definition report. Appendix

NASA Technical Reports Server (NTRS)

1985-01-01

Appendices to the systems definition study for the space station Data System are compiled. Supplemental information on external interface specification, simulation and modeling, and function design characteristics is presented along with data flow diagrams, a data dictionary, and function allocation matrices.

Reproducibility of F18-FDG PET radiomic features for different cervical tumor segmentation methods, gray-level discretization, and reconstruction algorithms.

PubMed

Altazi, Baderaldeen A; Zhang, Geoffrey G; Fernandez, Daniel C; Montejo, Michael E; Hunt, Dylan; Werner, Joan; Biagioli, Matthew C; Moros, Eduardo G

2017-11-01

Site-specific investigations of the role of radiomics in cancer diagnosis and therapy are emerging. We evaluated the reproducibility of radiomic features extracted from 18 Flourine-fluorodeoxyglucose ( 18 F-FDG) PET images for three parameters: manual versus computer-aided segmentation methods, gray-level discretization, and PET image reconstruction algorithms. Our cohort consisted of pretreatment PET/CT scans from 88 cervical cancer patients. Two board-certified radiation oncologists manually segmented the metabolic tumor volume (MTV 1 and MTV 2 ) for each patient. For comparison, we used a graphical-based method to generate semiautomated segmented volumes (GBSV). To address any perturbations in radiomic feature values, we down-sampled the tumor volumes into three gray-levels: 32, 64, and 128 from the original gray-level of 256. Finally, we analyzed the effect on radiomic features on PET images of eight patients due to four PET 3D-reconstruction algorithms: maximum likelihood-ordered subset expectation maximization (OSEM) iterative reconstruction (IR) method, fourier rebinning-ML-OSEM (FOREIR), FORE-filtered back projection (FOREFBP), and 3D-Reprojection (3DRP) analytical method. We extracted 79 features from all segmentation method, gray-levels of down-sampled volumes, and PET reconstruction algorithms. The features were extracted using gray-level co-occurrence matrices (GLCM), gray-level size zone matrices (GLSZM), gray-level run-length matrices (GLRLM), neighborhood gray-tone difference matrices (NGTDM), shape-based features (SF), and intensity histogram features (IHF). We computed the Dice coefficient between each MTV and GBSV to measure segmentation accuracy. Coefficient values close to one indicate high agreement, and values close to zero indicate low agreement. We evaluated the effect on radiomic features by calculating the mean percentage differences (d¯) between feature values measured from each pair of parameter elements (i.e. segmentation methods: MTV 1 -MTV 2 , MTV 1 -GBSV, MTV 2 -GBSV; gray-levels: 64-32, 64-128, and 64-256; reconstruction algorithms: OSEM-FORE-OSEM, OSEM-FOREFBP, and OSEM-3DRP). We used |d¯| as a measure of radiomic feature reproducibility level, where any feature scored |d¯| ±SD ≤ |25|% ± 35% was considered reproducible. We used Bland-Altman analysis to evaluate the mean, standard deviation (SD), and upper/lower reproducibility limits (U/LRL) for radiomic features in response to variation in each testing parameter. Furthermore, we proposed U/LRL as a method to classify the level of reproducibility: High- ±1% ≤ U/LRL ≤ ±30%; Intermediate- ±30% < U/LRL ≤ ±45%; Low- ±45 < U/LRL ≤ ±50%. We considered any feature below the low level as nonreproducible (NR). Finally, we calculated the interclass correlation coefficient (ICC) to evaluate the reliability of radiomic feature measurements for each parameter. The segmented volumes of 65 patients (81.3%) scored Dice coefficient >0.75 for all three volumes. The result outcomes revealed a tendency of higher radiomic feature reproducibility among segmentation pair MTV 1 -GBSV than MTV 2 -GBSV, gray-level pairs of 64-32 and 64-128 than 64-256, and reconstruction algorithm pairs of OSEM-FOREIR and OSEM-FOREFBP than OSEM-3DRP. Although the choice of cervical tumor segmentation method, gray-level value, and reconstruction algorithm may affect radiomic features, some features were characterized by high reproducibility through all testing parameters. The number of radiomic features that showed insensitivity to variations in segmentation methods, gray-level discretization, and reconstruction algorithms was 10 (13%), 4 (5%), and 1 (1%), respectively. These results suggest that a careful analysis of the effects of these parameters is essential prior to any radiomics clinical application. © 2017 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Identification of Candidate Transcription Factor Binding Sites in the Cattle Genome

PubMed Central

Bickhart, Derek M.; Liu, George E.

2013-01-01

A resource that provides candidate transcription factor binding sites (TFBSs) does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach—using sequence conservation across cattle, human and dog—and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection (MGC) annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCK1, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the Illumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http://bfgl.anri.barc.usda.gov/BovineTFBS/ or http://199.133.54.77/BovineTFBS. PMID:23433959

Integration of biological responses from a suite of bioassays for the Venice Lagoon (Italy) through sediment toxicity index - part A: development and comparison of two methodological approaches.

PubMed

Losso, Chiara; Novelli, Alessandra Arizzi; De Salvador, Davide; Ghetti, Pier Francesco; Ghirardini, Annamaria Volpi

2010-12-01

Marine and coastal quality assessment, based on test batteries involving a wide array of endpoints, organisms and test matrices, needs for setting up toxicity indices that integrate multiple toxicological measures for decision-making processes and that classify the continuous toxicity response into discrete categories according to the European Water Framework Directive. Two toxicity indices were developed for the lagoon environment such as the Venice Lagoon. Stepwise procedure included: the construction of a database that identified test-matrix pairs (indicators); the selection of a minimum number of ecotoxicological indicators, called toxicological core metrics (CMs-tox) on the basis of specific criteria; the development of toxicity scores for each CM-tox; the integration of the CMs-tox into two indices, the Toxicity Effect Index (TEI), based on the transformation of Toxic Unit (TU) data that were integrated as logarithmic sum, and the Weighted Average Toxicity Index (WATI), starting from toxicity classes integrated as weighted mean. Results from the indices are compared; advantages and drawbacks of both approaches are discussed. Copyright © 2010. Published by Elsevier Ltd.

Performance of customized DCT quantization tables on scientific data

NASA Technical Reports Server (NTRS)

Ratnakar, Viresh; Livny, Miron

1994-01-01

We show that it is desirable to use data-specific or customized quantization tables for scaling the spatial frequency coefficients obtained using the Discrete Cosine Transform (DCT). DCT is widely used for image and video compression (MP89, PM93) but applications typically use default quantization matrices. Using actual scientific data gathered from divers sources such as spacecrafts and electron-microscopes, we show that the default compression/quality tradeoffs can be significantly improved upon by using customized tables. We also show that significant improvements are possible for the standard test images Lena and Baboon. This work is part of an effort to develop a practical scheme for optimizing quantization matrices for any given image or video stream, under any given quality or compression constraints.

Ballistic Transport for Limit-Periodic Jacobi Matrices with Applications to Quantum Many-Body Problems

NASA Astrophysics Data System (ADS)

Fillman, Jake

2017-03-01

We study Jacobi matrices that are uniformly approximated by periodic operators. We show that if the rate of approximation is sufficiently rapid, then the associated quantum dynamics are ballistic in a rather strong sense; namely, the (normalized) Heisenberg evolution of the position operator converges strongly to a self-adjoint operator that is injective on the space of absolutely summable sequences. In particular, this means that all transport exponents corresponding to well-localized initial states are equal to one. Our result may be applied to a class of quantum many-body problems. Specifically, we establish a lower bound on the Lieb-Robinson velocity for an isotropic XY spin chain on the integers with limit-periodic couplings.

Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini.

PubMed

Wang, Yu; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

2017-11-01

Various bacterial pathogens can deliver their secreted substrates also called as effectors through type IV secretion systems (T4SSs) into host cells and cause diseases. Since T4SS secreted effectors (T4SEs) play important roles in pathogen-host interactions, identifying them is crucial to our understanding of the pathogenic mechanisms of T4SSs. A few computational methods using machine learning algorithms for T4SEs prediction have been developed by using features of C-terminal residues. However, recent studies have shown that targeting information can also be encoded in the N-terminal region of at least some T4SEs. In this study, we present an effective method for T4SEs prediction by novelly integrating both N-terminal and C-terminal sequence information. First, we collected a comprehensive dataset across multiple bacterial species of known T4SEs and non-T4SEs from literatures. Then, three types of distinctive features, namely amino acid composition, composition, transition and distribution and position-specific scoring matrices were calculated for 50 N-terminal and 100 C-terminal residues. After that, we employed information gain represent to rank the importance score of the 150 different position residues for T4SE secretion signaling. At last, 125 distinctive position residues were singled out for the prediction model to classify T4SEs and non-T4SEs. The support vector machine model yields a high receiver operating curve of 0.916 in the fivefold cross-validation and an accuracy of 85.29% for the independent test set.

Diversity among Cynodon accessions and taxa based on DNA amplification fingerprinting.

PubMed

Assefa, S; Taliaferro, C M; Anderson, M P; de los Reyes, B G; Edwards, R M

1999-06-01

The genus Cynodon (Gramineae), comprised of 9 species, is geographically widely distributed and genetically diverse. Information on the amounts of molecular genetic variation among and within Cynodon taxa is needed to enhance understanding of phylogenetic relations and facilitate germplasm management and breeding improvement efforts. Genetic relatedness among 62 Cynodon accessions, representing eight species, was assessed using DNA amplification fingerprinting (DAF). Ten 8-mer oligonucleotides were used to amplify specific Cynodon genomic sequences. The DNA amplification products of individual accessions were scored for presence (1) or absence (0) of bands. Similarity matrices were developed and the accessions were grouped by cluster (UPGMA) and principal coordinate analysis. Analyses were conducted within ploidy level (2x = 18 and 4x = 36) and over ploidy levels. Each primer revealed polymorphic loci among accessions within species. Of 539 loci (bands) scored, 496 (92%) were polymorphic. Cynodon arcuatus was clearly separated from other species by numerous monomorphic bands. The strongest species similarities were between C. aethiopicus and C. arcuatus, C. transvaalensis and C. plectostachyus, and C. incompletus and C. nlemfuensis. Intraspecific variation was least for C. aethiopicus, C. arcuatus, and C. transvaalensis, and greatest for C. dactylon. Accessions of like taxonomic classification were generally clustered, except the cosmopolitan C. dactylon var. dactylon and C. dactylon var. afganicus. Within taxa, accessions differing in chromosome number clustered in all instances indicating the 2x and 4x forms to be closely related. Little, if any, relationship was found between relatedness as indicated by the DAF profiles and previous estimates of hybridization potential between the different taxa.

Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini

NASA Astrophysics Data System (ADS)

Wang, Yu; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

2017-11-01

Various bacterial pathogens can deliver their secreted substrates also called as effectors through type IV secretion systems (T4SSs) into host cells and cause diseases. Since T4SS secreted effectors (T4SEs) play important roles in pathogen-host interactions, identifying them is crucial to our understanding of the pathogenic mechanisms of T4SSs. A few computational methods using machine learning algorithms for T4SEs prediction have been developed by using features of C-terminal residues. However, recent studies have shown that targeting information can also be encoded in the N-terminal region of at least some T4SEs. In this study, we present an effective method for T4SEs prediction by novelly integrating both N-terminal and C-terminal sequence information. First, we collected a comprehensive dataset across multiple bacterial species of known T4SEs and non-T4SEs from literatures. Then, three types of distinctive features, namely amino acid composition, composition, transition and distribution and position-specific scoring matrices were calculated for 50 N-terminal and 100 C-terminal residues. After that, we employed information gain represent to rank the importance score of the 150 different position residues for T4SE secretion signaling. At last, 125 distinctive position residues were singled out for the prediction model to classify T4SEs and non-T4SEs. The support vector machine model yields a high receiver operating curve of 0.916 in the fivefold cross-validation and an accuracy of 85.29% for the independent test set.

A Brief Historical Introduction to Matrices and Their Applications

ERIC Educational Resources Information Center

Debnath, L.

2014-01-01

This paper deals with the ancient origin of matrices, and the system of linear equations. Included are algebraic properties of matrices, determinants, linear transformations, and Cramer's Rule for solving the system of algebraic equations. Special attention is given to some special matrices, including matrices in graph theory and electrical…

Laminin active peptide/agarose matrices as multifunctional biomaterials for tissue engineering.

PubMed

Yamada, Yuji; Hozumi, Kentaro; Aso, Akihiro; Hotta, Atsushi; Toma, Kazunori; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

2012-06-01

Cell adhesive peptides derived from extracellular matrix components are potential candidates to afford bio-adhesiveness to cell culture scaffolds for tissue engineering. Previously, we covalently conjugated bioactive laminin peptides to polysaccharides, such as chitosan and alginate, and demonstrated their advantages as biomaterials. Here, we prepared functional polysaccharide matrices by mixing laminin active peptides and agarose gel. Several laminin peptide/agarose matrices showed cell attachment activity. In particular, peptide AG73 (RKRLQVQLSIRT)/agarose matrices promoted strong cell attachment and the cell behavior depended on the stiffness of agarose matrices. Fibroblasts formed spheroid structures on the soft AG73/agarose matrices while the cells formed a monolayer with elongated morphologies on the stiff matrices. On the stiff AG73/agarose matrices, neuronal cells extended neuritic processes and endothelial cells formed capillary-like networks. In addition, salivary gland cells formed acini-like structures on the soft matrices. These results suggest that the peptide/agarose matrices are useful for both two- and three-dimensional cell culture systems as a multifunctional biomaterial for tissue engineering. Copyright © 2012 Elsevier Ltd. All rights reserved.

Prevalence and clinical characteristics of attention deficit hyperactivity disorder among primary school students in Bangkok.

PubMed

Benjasuwantep, Banchaun; Ruangdaraganon, Nichara; Visudhiphan, Pongsakdi

2002-11-01

Attention deficit hyperactivity disorder (ADHD) is an important disorder because it is the most prevalent chronic health condition affecting school aged children. Children with ADHD are at risk for academic and behavior problems. There are several studies in many countries worldwide. In Thailand, there have been a few published papers about ADHD. Most of them were studies in a clinically referred population. Four hundred and thirty-three first to sixth grade students from Wat Samiennaree School were included in this study. All children were administered Raven's progressive matrices test for estimation of intellectual functioning and were observed for their behavior in the classrooms by one researcher. Their demographic data was collected by questionnaires. The revised Conners rating scales were scored for each student. Students whose parents did not score the Conners parent rating scale were excluded. The parents of students, whose scores were positive for ADHD, were interviewed according to DSM IV criteria. 353 (81.5%) students from 433 were enrolled in this study. 23 students were diagnosed with ADHD making a prevalence of 6.5 per cent. There were 11 boys and 12 girls. The ratio of male to female was 1:1.09. The ADHD students had lower scores in mathematics than the group without this diagnosis with statistical significance (p = 0.006).

Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function.

PubMed

Yang, Zheng Rong; Thomson, Rebecca; Hodgman, T Charles; Dry, Jonathan; Doyle, Austin K; Narayanan, Ajit; Wu, XiKun

2003-11-01

This paper presents an algorithm which is able to extract discriminant rules from oligopeptides for protease proteolytic cleavage activity prediction. The algorithm is developed using genetic programming. Three important components in the algorithm are a min-max scoring function, the reverse Polish notation (RPN) and the use of minimum description length. The min-max scoring function is developed using amino acid similarity matrices for measuring the similarity between an oligopeptide and a rule, which is a complex algebraic equation of amino acids rather than a simple pattern sequence. The Fisher ratio is then calculated on the scoring values using the class label associated with the oligopeptides. The discriminant ability of each rule can therefore be evaluated. The use of RPN makes the evolutionary operations simpler and therefore reduces the computational cost. To prevent overfitting, the concept of minimum description length is used to penalize over-complicated rules. A fitness function is therefore composed of the Fisher ratio and the use of minimum description length for an efficient evolutionary process. In the application to four protease datasets (Trypsin, Factor Xa, Hepatitis C Virus and HIV protease cleavage site prediction), our algorithm is superior to C5, a conventional method for deriving decision trees.

The effects of individual differences, prior experience and cognitive load on the transfer of dynamic decision-making performance.

PubMed

Nicholson, Brad; O'Hare, David

2014-01-01

Situational awareness is recognised as an important factor in the performance of individuals and teams in dynamic decision-making (DDM) environments (Salmon et al. 2014 ). The present study was designed to investigate whether the scores on the WOMBAT™ Situational Awareness and Stress Tolerance Test (Roscoe and North 1980 ) would predict the transfer of DDM performance from training under different levels of cognitive load to a novel situation. Participants practised a simulated firefighting task under either low or high conditions of cognitive load and then performed a (transfer) test in an alternative firefighting environment under an intermediate level of cognitive load. WOMBAT™ test scores were a better predictor of DDM performance than scores on the Raven Matrices. Participants with high WOMBAT™ scores performed better regardless of their training condition. Participants with recent gaming experience who practised under low cognitive load showed better practice phase performance but worse transfer performance than those who practised under high cognitive load. The relationship between task experience, situational awareness ability, cognitive load and the transfer of dynamic decision-making (DDM) performance was investigated. Results showed that the WOMBAT™ test predicted transfer of DDM performance regardless of task cognitive load. The effects of cognitive load on performance varied according to previous task-relevant experience.

Right unilateral electroconvulsive therapy does not cause more cognitive impairment than pharmacologic treatment in treatment-resistant bipolar depression: A 6-month randomized controlled trial follow-up study.

PubMed

Bjoerke-Bertheussen, Jeanette; Schoeyen, Helle; Andreassen, Ole A; Malt, Ulrik F; Oedegaard, Ketil J; Morken, Gunnar; Sundet, Kjetil; Vaaler, Arne E; Auestad, Bjoern; Kessler, Ute

2017-12-21

Electroconvulsive therapy is an effective treatment for bipolar depression, but there are concerns about whether it causes long-term neurocognitive impairment. In this multicenter randomized controlled trial, in-patients with treatment-resistant bipolar depression were randomized to either algorithm-based pharmacologic treatment or right unilateral electroconvulsive therapy. After the 6-week treatment period, all of the patients received maintenance pharmacotherapy as recommended by their clinician guided by a relevant treatment algorithm. Patients were assessed at baseline and at 6 months. Neurocognitive functions were assessed using the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) Consensus Cognitive Battery, and autobiographical memory consistency was assessed using the Autobiographical Memory Interview-Short Form. Seventy-three patients entered the trial, of whom 51 and 26 completed neurocognitive assessments at baseline and 6 months, respectively. The MATRICS Consensus Cognitive Battery composite score improved by 4.1 points in both groups (P = .042) from baseline to 6 months (from 40.8 to 44.9 and from 41.9 to 46.0 in the algorithm-based pharmacologic treatment and electroconvulsive therapy groups, respectively). The Autobiographical Memory Interview-Short Form consistency scores were reduced in both groups (72.3% vs 64.3% in the algorithm-based pharmacologic treatment and electroconvulsive therapy groups, respectively; P = .085). This study did not find that right unilateral electroconvulsive therapy caused long-term impairment in neurocognitive functions compared to algorithm-based pharmacologic treatment in bipolar depression as measured using standard neuropsychological tests, but due to the low number of patients in the study the results should be interpreted with caution. ClinicalTrials.gov: NCT00664976. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A Spanish Twilight Zone: Mood, Syntax, and Past Temporal Reference.

ERIC Educational Resources Information Center

Studeros, Leonard H.

1981-01-01

Explores the interrelationships among mood usage, syntactic contrast and past temporal reference in Spanish. Describes specific effects of varying temporal reference on mood and syntactic signaling, and employs an inventory of five subjunctive determining matrices to show that such effects are best explained by means of a…

Corpus Linguistics, Network Analysis and Co-Occurrence Matrices

ERIC Educational Resources Information Center

Stuart, Keith; Botella, Ana

2009-01-01

This article describes research undertaken in order to design a methodology for the reticular representation of knowledge of a specific discourse community. To achieve this goal, a representative corpus of the scientific production of the members of this discourse community (Universidad Politecnica de Valencia, UPV) was created. This article…

Novel Strategy to Create Hypoallergenic Peanut Protein-Polyphenol Edible Matrices for Oral Immunotherapy

USDA-ARS?s Scientific Manuscript database

Peanut allergy is an IgE-mediated hypersensitivity. Upon peanut consumption by an allergic individual, epitopes on peanut proteins bind and cross-link peanut-specific IgE on mast cell and basophil surfaces triggering the cells to release inflammatory mediators responsible for allergic reactions. P...

Simultaneous Inference Procedures for Means.

ERIC Educational Resources Information Center

Krishnaiah, P. R.

Some aspects of simultaneous tests for means are reviewed. Specifically, the comparison of univariate or multivariate normal populations based on the values of the means or mean vectors when the variances or covariance matrices are equal is discussed. Tukey's and Dunnett's tests for multiple comparisons of means, Scheffe's method of examining…

ARSENIC SPECIATION IN PROBLEMATIC SEAFOOD MATRICES: THE IMPORTANCE OF A SPECIES SPECIFIC MASS BALANCE

EPA Science Inventory

Arsenic has two major exposure routes: dietary and drinking water ingestion. Dietary exposures can easily exceed those typically associated with drinking water but the risk associated with these exposures is strongly influenced by the toxicity of the arsenicals present in the s...

Speciation analysis of arsenic in biological matrices by automated hydride generation-cryotrapping-atomic absorption spectrometry with multiple microflame quartz tube atomizer (multiatomizer).

EPA Science Inventory

This paper describes an automated system for the oxidation state specific speciation of inorganic and methylated arsenicals by selective hydride generation - cryotrapping- gas chromatography - atomic absorption spectrometry with the multiatomizer. The corresponding arsines are ge...

Isolation by ion-exchange methods. In Sarker S.D. (ed) Natural Products Isolation, 3rd edition

USDA-ARS?s Scientific Manuscript database

The primary goal of many natural products chemists is to extract, isolate, and characterize specific analytes from complex plant, animal, microbial, and food matrices. To achieve this goal, they rely considerably on highly sophisticated and highly hyphenated modern instrumentation. Yet, the vast maj...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2013 CFR

2013-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2014 CFR

2014-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2011 CFR

2011-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2012 CFR

2012-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Expert review of protocols. 766.28...

Miscellaneous methods for measuring matric or water potential

USGS Publications Warehouse

Scanlon, Bridget R.; Andraski, Brian J.; Bilskie, Jim; Dane, Jacob H.; Topp, G. Clarke

2002-01-01

A variety of techniques to measure matric potential or water potential in the laboratory and in the field are described in this section. The techniques described herein require equilibration of some medium whose matric or water potential can be determined from previous calibration or can be measured directly. Under equilibrium conditions the matric or water potential of the medium is equal to that of the soil. The techniques can be divided into: (i) those that measure matric potential and (ii) those that measure water potential (sum of matric and osmotic potentials). Matric potential is determined when the sensor matrix is in direct contact with the soil, so salts are free to diffuse in or out of the sensor matrix, and the equilibrium measurement therefore reflects matric forces acting on the water. Water potential is determined when the sensor is separated from the soil by a vapor gap, so salts are not free to move in or out of the sensor, and the equilibrium measurement reflects the sum of the matric and osmotic forces acting on the water.Seven different techniques are described in this section. Those that measure matric potential include (i) heat dissipation sensors, (ii) electrical resistance sensors, (iii) frequency domain and time domain sensors, and (iv) electro-optical switches. A method that can be used to measure matric potential or water potential is the (v) filter paper method. Techniques that measure water potential include (vi) the Dew Point Potentiameter (Decagon Devices, Inc., Pullman, WA1) (water activity meter) and (vii) vapor equilibration.The first four techniques are electronically based methods for measuring matric potential. Heat dissipation sensors and electrical resistance sensors infer matric potential from previously determined calibration relations between sensor heat dissipation or electrical resistance and matric potential. Frequency-domain and timedomain matric potential sensors measure water content, which is related to matric potential of the sensor through calibration. Electro-optical switches measure changes in light transmission through thin, nylon filters as they absorb or desorb water in response to changes in matric potential. Heat dissipation sensors and electrical resistance sensors are used primarily in the field to provide information on matric potential. Frequency domain matric potential sensors are new and have not been widely used. Time domain matric potential sensors and electro-optical switches are new and have not been commercialized. For the fifth technique, filter paper is used as the standard matrix. The filter paper technique measures matric potential when the filter paper is in direct contact with soil or water potential when separated from soil by a vapor gap. The Dew Point Potentiameter calculates water potential from the measured dew point and sample temperature. The vapor equilibration technique involves equilibration of soil samples with salt solutions of known osmotic potential. The filter paper, Dew Point Potentiameter, and vapor equilibration techniques are generally used in the laboratory to measure water potential of disturbed field samples or to measure water potential for water retention functions.

A European network for food-borne parasites (Euro-FBP): meeting report on 'Analytical methods for food-borne parasites in human and veterinary diagnostics and in food matrices'.

PubMed

Klotz, Christian; Šoba, Barbara; Skvarč, Miha; Gabriël, Sarah; Robertson, Lucy J

2017-11-09

Food-borne parasites (FBPs) are a neglected topic in food safety, partly due to a lack of awareness of their importance for public health, especially as symptoms tend not to develop immediately after exposure. In addition, methodological difficulties with both diagnosis in infected patients and detection in food matrices result in under-detection and therefore the potential for underestimation of their burden on our societies. This, in consequence, leads to lower prioritization for basic research, e.g. for development new and more advanced detection methods for different food matrices and diagnostic samples, and thus a vicious circle of neglect and lack of progress is propagated. The COST Action FA1408, A European Network for Foodborne Parasites (Euro-FBP) aims to combat the impact of FBP on public health by facilitating the multidisciplinary cooperation and partnership between groups of researchers and between researchers and stakeholders. The COST Action TD1302, the European Network for cysticercosis/taeniosis, CYSTINET, has a specific focus on Taenia solium and T. saginata, two neglected FBPs, and aims to advance knowledge and understanding of these zoonotic disease complexes via collaborations in a multidisciplinary scientific network. This report summarizes the results of a meeting within the Euro-FBP consortium entitled 'Analytical methods for food-borne parasites in human and veterinary diagnostics and in food matrices' and of the joined Euro-FBP and CYSTINET meeting.

Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

NASA Astrophysics Data System (ADS)

Vira, J.; Sofiev, M.

2015-02-01

This paper describes the assimilation of trace gas observations into the chemistry transport model SILAM (System for Integrated modeLling of Atmospheric coMposition) using the 3D-Var method. Assimilation results for the year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the AirBase observation database, which provides the observational data set used in this study. Attention was paid to the background and observation error covariance matrices, which were obtained primarily by the iterative application of a posteriori diagnostics. The diagnostics were computed separately for 2 months representing summer and winter conditions, and further disaggregated by time of day. This enabled the derivation of background and observation error covariance definitions, which included both seasonal and diurnal variation. The consistency of the obtained covariance matrices was verified using χ2 diagnostics. The analysis scores were computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values was improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

Assessing environmental quality status by integrating chemical and biological effect data: The Cartagena coastal zone as a case.

PubMed

Martínez-Gómez, Concepción; Fernández, Beatriz; Robinson, Craig D; Campillo, J Antonio; León, Víctor M; Benedicto, José; Hylland, Ketil; Vethaak, A Dick

2017-03-01

Cartagena coastal zone (W Mediterranean) was chosen for a practical case study to investigate the suitability of an integrated indicator framework for marine monitoring and assessment of chemicals and their effects, which was developed by ICES and OSPAR. Red mullet (Mullus barbatus) and the Mediterranean mussel (Mytilus galloprovincialis) were selected as target species. Concentrations of contaminants in sediment and biota, and contaminant-related biomarkers were analysed. To assess environmental quality in the Cartagena coastal zone with respect to chemical pollution, data were assessed using available assessment criteria, and then integrated for different environmental matrices. A qualitative scoring method was used to rank the overall assessments into selected categories and to evaluate the confidence level of the final integrated assessment. The ICES/OSPAR integrated assessment framework, originally designed for the North Atlantic, was found to be applicable for Mediterranean species and environmental matrices. Further development of assessment criteria of chemical and biological parameters in sediments and target species from the Mediterranean will, however, be required before this framework can be fully applied for determining Good Environmental Status (GES) of the Marine Strategy Framework Directive in these regions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Relationship between consonant recognition in noise and hearing threshold.

PubMed

Yoon, Yang-soo; Allen, Jont B; Gooler, David M

2012-04-01

Although poorer understanding of speech in noise by listeners who are hearing-impaired (HI) is known not to be directly related to audiometric hearing threshold, HT (f), grouping HI listeners with HT (f) is widely practiced. In this article, the relationship between consonant recognition and HT (f) is considered over a range of signal-to-noise ratios (SNRs). Confusion matrices (CMs) from 25 HI ears were generated in response to 16 consonant-vowel syllables presented at 6 different SNRs. Individual differences scaling (INDSCAL) was applied to both feature-based matrices and CMs in order to evaluate the relationship between HT (f) and consonant recognition among HI listeners. The results showed no predictive relationship between the percent error scores (Pe) and HT (f) across SNRs. The multiple regression models showed that the HT (f) accounted for 39% of the total variance of the slopes of the Pe. Feature-based INDSCAL analysis showed consistent grouping of listeners across SNRs, but not in terms of HT (f). Systematic relationship between measures was also not defined by CM-based INDSCAL analysis across SNRs. HT (f) did not account for the majority of the variance (39%) in consonant recognition in noise when the complete body of the CM was considered.

Good cognitive performances in a child with Prader-Willi syndrome.

PubMed

Nugnes, Rosa; Zito, Eugenio; Mozzillo, Enza; Camarca, Maria Erminia; Riccio, Maria Pia; Terrone, Gaetano; Melis, Daniela; Bravaccio, Carmela; Franzese, Adriana

2013-11-15

We report the case of a child affected by Prader-Willi syndrome (PWS) with good cognitive performances and without relevant behavioral abnormalities.The diagnosis of PWS, suspected on the basis of clinical features and past history, was confirmed by DNA methylation analysis. Additional genetic testing revealed a maternal uniparental disomy. Intellectual profile was analyzed by WISC-III and Raven's Progressive Matrices CPM, while the behavior was evaluated by K-SADS-PL and Child Behavior Checklist/4-18 to the parents.WISC-III test showed a Total Intelligence Quotient (T-IQ = 79) at the border level for age. The Verbal Intelligence Quotient (V-IQ) showed a lower score than the Performance Intelligence Quotient (P-IQ) (78 and 85, respectively). Raven's Matrices CPM showed an intelligence level at 75-90° percentile for age. Concerning behavioral evaluation, a difficulty in impulse control was observed, with persistent but controllable search for food, without a clear psychopathological meaning. Also according to K-SADS-PL no areas of psychopathological dimensions were detected. In conclusion, in presence of consisting clinical features of PWS and high diagnostic suspicion, the diagnosis of PWS should be considered even in presence of a borderline IQ and in absence of psychopathological abnormalities.

European Proficiency testing of national reference laboratories for the confirmation of sulfonamide residues in muscle and milk.

PubMed

Juhel-Gaugain, Murielle; Fourmond, Marie-Pierre; Delepine, Bernard; Laurentie, Michel; Brigitte, Roudaut; Sanders, Pascal

2005-03-01

Two interlaboratory studies were organized in 2002-2003 in order to check the proficiency of laboratories in confirming the presence of sulfonamide residues in muscle and milk. These studies involved 25 EU National Reference Laboratories (NRLs) from 21 different European Countries in charge of statutory monitoring of antimicrobial residues in food of animal origin at a national level. The study was conducted according to international and national guidelines by the Community Reference Laboratory (CRL) in charge of antimicrobial substances. Four different test matrices of sheep muscle and four different test matrices of bovine milk containing different sulfonamide substances were prepared and sent to the participants. Each participant was asked to use his own routine confirmatory method and to analyse each sample in triplicate within a period of about six weeks during which the stability of the materials was checked by the organizer. The sulfonamide content of each material was determined by calculating the robust means of all the results and the deviation of the results from the assigned values was assessed by calculating Z-scores. Overall, results were satisfactory, particularly considering that it was the first proficiency test dealing with sulfonamides organised by the Community Reference Laboratory.

Citation analytics: Data exploration and comparative analyses of CiteScores of Open Access and Subscription-Based publications indexed in Scopus (2014-2016).

PubMed

Atayero, Aderemi A; Popoola, Segun I; Egeonu, Jesse; Oludayo, Olumuyiwa

2018-08-01

Citation is one of the important metrics that are used in measuring the relevance and the impact of research publications. The potentials of citation analytics may be exploited to understand the gains of publishing scholarly peer-reviewed research outputs in either Open Access (OA) sources or Subscription-Based (SB) sources in the bid to increase citation impact. However, relevant data required for such comparative analysis must be freely accessible for evidence-based findings and conclusions. In this data article, citation scores ( CiteScores ) of 2542 OA sources and 15,040 SB sources indexed in Scopus from 2014 to 2016 were presented and analyzed based on a set of five inclusion criteria. A robust dataset, which contains the CiteScores of OA and SB publication sources included, is attached as supplementary material to this data article to facilitate further reuse. Descriptive statistics and frequency distributions of OA CiteScores and SB CiteScores are presented in tables. Boxplot representations and scatter plots are provided to show the statistical distributions of OA CiteScores and SB CiteScores across the three sub-categories (Book Series, Journal, and Trade Journal). Correlation coefficient and p-value matrices are made available within the data article. In addition, Probability Density Functions (PDFs) and Cumulative Distribution Functions (CDFs) of OA CiteScores and SB CiteScores are computed and the results are presented using tables and graphs. Furthermore, Analysis of Variance (ANOVA) and multiple comparison post-hoc tests are conducted to understand the statistical difference (and its significance, if any) in the citation impact of OA publication sources and SB publication source based on CiteScore . In the long run, the data provided in this article will help policy makers and researchers in Higher Education Institutions (HEIs) to identify the appropriate publication source type and category for dissemination of scholarly research findings with maximum citation impact.

Genetic code, hamming distance and stochastic matrices.

PubMed

He, Matthew X; Petoukhov, Sergei V; Ricci, Paolo E

2004-09-01

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are doubly stochastic and symmetric. We determine the frequency distributions of the Hamming distances, building blocks of the matrices, decomposition and iterations of matrices. We present an explicit decomposition formula for the genetic code-based matrix in terms of permutation matrices, which provides a hypercube representation of the genetic code. It is also observed that there is a Hamiltonian cycle in a genetic code-based hypercube.

Tumor cell invasion of collagen matrices requires coordinate lipid agonist-induced G-protein and membrane-type matrix metalloproteinase-1-dependent signaling.

PubMed

Fisher, Kevin E; Pop, Andreia; Koh, Wonshill; Anthis, Nicholas J; Saunders, W Brian; Davis, George E

2006-12-08

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) are bioactive lipid signaling molecules implicated in tumor dissemination. Membrane-type matrix metalloproteinase 1 (MT1-MMP) is a membrane-tethered collagenase thought to be involved in tumor invasion via extracellular matrix degradation. In this study, we investigated the molecular requirements for LPA- and S1P-regulated tumor cell migration in two dimensions (2D) and invasion of three-dimensional (3D) collagen matrices and, in particular, evaluated the role of MT1-MMP in this process. LPA stimulated while S1P inhibited migration of most tumor lines in Boyden chamber assays. Conversely, HT1080 fibrosarcoma cells migrated in response to both lipids. HT1080 cells also markedly invaded 3D collagen matrices (approximatly 700 microm over 48 hours) in response to either lipid. siRNA targeting of LPA1 and Rac1, or S1P1, Rac1, and Cdc42 specifically inhibited LPA- or S1P-induced HT1080 invasion, respectively. Analysis of LPA-induced HT1080 motility on 2D substrates vs. 3D matrices revealed that synthetic MMP inhibitors markedly reduced the distance (approximately 125 microm vs. approximately 45 microm) and velocity of invasion (approximately 0.09 microm/min vs. approximately 0.03 microm/min) only when cells navigated 3D matrices signifying a role for MMPs exclusively in invasion. Additionally, tissue inhibitors of metalloproteinases (TIMPs)-2, -3, and -4, but not TIMP-1, blocked lipid agonist-induced invasion indicating a role for membrane-type (MT)-MMPs. Furthermore, MT1-MMP expression in several tumor lines directly correlated with LPA-induced invasion. HEK293s, which neither express MT1-MMP nor invade in the presence of LPA, were transfected with MT1-MMP cDNA, and subsequently invaded in response to LPA. When HT1080 cells were seeded on top of or within collagen matrices, siRNA targeting of MT1-MMP, but not other MMPs, inhibited lipid agonist-induced invasion establishing a requisite role for MT1-MMP in this process. LPA is a fundamental regulator of MT1-MMP-dependent tumor cell invasion of 3D collagen matrices. In contrast, S1P appears to act as an inhibitory stimulus in most cases, while stimulating only select tumor lines. MT1-MMP is required only when tumor cells navigate 3D barriers and not when cells migrate on 2D substrata. We demonstrate that tumor cells require coordinate regulation of LPA/S1P receptors and Rho GTPases to migrate, and additionally, require MT1-MMP in order to invade collagen matrices during neoplastic progression.

Cell-adhesive RGD peptide-displaying M13 bacteriophage/PLGA nanofiber matrices for growth of fibroblasts.

PubMed

Shin, Yong Cheol; Lee, Jong Ho; Jin, Linhua; Kim, Min Jeong; Oh, Jin-Woo; Kim, Tai Wan; Han, Dong-Wook

2014-01-01

M13 bacteriophages can be readily fabricated as nanofibers due to non-toxic bacterial virus with a nanofiber-like shape. In the present study, we prepared hybrid nanofiber matrices composed of poly(lactic-co-glycolic acid, PLGA) and M13 bacteriophages which were genetically modified to display the RGD peptide on their surface (RGD-M13 phage). The surface morphology and chemical composition of hybrid nanofiber matrices were characterized by scanning electron microscopy (SEM) and Raman spectroscopy, respectively. Immunofluorescence staining was conducted to investigate the existence of M13 bacteriophages in RGD-M13 phage/PLGA hybrid nanofibers. In addition, the attachment and proliferation of three different types of fibroblasts on RGD-M13 phage/PLGA nanofiber matrices were evaluated to explore how fibroblasts interact with these matrices. SEM images showed that RGD-M13 phage/PLGA hybrid matrices had the non-woven porous structure, quite similar to that of natural extracellular matrices, having an average fiber diameter of about 190 nm. Immunofluorescence images and Raman spectra revealed that RGD-M13 phages were homogeneously distributed in entire matrices. Moreover, the attachment and proliferation of fibroblasts cultured on RGD-M13 phage/PLGA matrices were significantly enhanced due to enriched RGD moieties on hybrid matrices. These results suggest that RGD-M13 phage/PLGA matrices can be efficiently used as biomimetic scaffolds for tissue engineering applications.

Response of human macrophages to wound matrices in vitro.

PubMed

Witherel, Claire E; Graney, Pamela L; Freytes, Donald O; Weingarten, Michael S; Spiller, Kara L

2016-05-01

Chronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro-inflammatory M1, anti-inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross-linked with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross-linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte-derived macrophages to four commercially available wound matrices were compared-Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte-derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down-regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up-regulation of TNFa (M1) and CD163 (M2c) and down-regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up-regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by the sum of M2 genes. This preliminary study suggested that biomaterials influenced the wound microenvironment to affect macrophage phenotype. © 2016 by the Wound Healing Society.

Accounting for ethnic-cultural and linguistic diversity in neuropsychological assessment of patients with drug-resistant epilepsy: A retrospective study.

PubMed

Peviani, Valeria; Scarpa, Pina; Toraldo, Alessio; Bottini, Gabriella

2016-11-01

Neuropsychological assessment is critical in both diagnosis and prognosis of patients with epilepsy. Beyond electrophysiological and anatomical alterations, other factors including different ethnic-cultural and linguistic backgrounds might affect neuropsychological performance. Only a few studies considered migration and acculturation effects and they typically concerned nonclinical samples. The current study aimed at investigating the influence of ethnic background and time spent in Italy on a full neuropsychological battery administered to both Italian and foreign-born patients and at providing a brief interview for obtaining relevant information on each patient's transcultural and language-related history. Clinical reports from 43 foreign-born patients with drug-resistant epilepsy were collected from the archives of Milan Niguarda Hospital. Epileptogenic zone, age, education, profession, illness duration, seizure frequency, handedness, and gender were considered in selecting 43 Italian controls. Ethnicity (Italian/foreign-born) and years spent in Italy were analyzed as main predictors on 21 neuropsychological scales by means of General(ized) Linear Models. An additional analysis studied two composite scores of overall verbal and nonverbal abilities. Ethnicity significantly affected the following: the verbal overall score, Verbal Fluency, Naming, Token-test, Digit Span, Attentional Matrices, Trail-Making-Test, Line-Orientation-Test, and Raven matrices; no effects were found on the nonverbal overall score, Word Pairs Learning, Episodic Memory, reading accuracy, visual span, Bells test, Rey Figure, and face memory and recognition. No significant effects of years spent in Italy emerged. While years spent in Italy does not predict neuropsychological performance, linguistic background had a strong impact on it. With respect to Italian-speaking patients, those who were foreign-born showed large task-related variability, with an especially low performance on language-related tests. Hence, language tests should not be considered as valid measures of neuropsychological impairment in this population, not even in foreign-born patients with good Italian fluency. Clinicians should consider such asymmetries in order to improve the accuracy of neuropsychological assessment of foreign-born patients. Copyright © 2016 Elsevier Inc. All rights reserved.

Statistical modeling of temperature, humidity and wind fields in the atmospheric boundary layer over the Siberian region

NASA Astrophysics Data System (ADS)

Lomakina, N. Ya.

2017-11-01

The work presents the results of the applied climatic division of the Siberian region into districts based on the methodology of objective classification of the atmospheric boundary layer climates by the "temperature-moisture-wind" complex realized with using the method of principal components and the special similarity criteria of average profiles and the eigen values of correlation matrices. On the territory of Siberia, it was identified 14 homogeneous regions for winter season and 10 regions were revealed for summer. The local statistical models were constructed for each region. These include vertical profiles of mean values, mean square deviations, and matrices of interlevel correlation of temperature, specific humidity, zonal and meridional wind velocity. The advantage of the obtained local statistical models over the regional models is shown.

Tolerant compressed sensing with partially coherent sensing matrices

NASA Astrophysics Data System (ADS)

Birnbaum, Tobias; Eldar, Yonina C.; Needell, Deanna

2017-08-01

Most of compressed sensing (CS) theory to date is focused on incoherent sensing, that is, columns from the sensing matrix are highly uncorrelated. However, sensing systems with naturally occurring correlations arise in many applications, such as signal detection, motion detection and radar. Moreover, in these applications it is often not necessary to know the support of the signal exactly, but instead small errors in the support and signal are tolerable. Despite the abundance of work utilizing incoherent sensing matrices, for this type of tolerant recovery we suggest that coherence is actually beneficial . We promote the use of coherent sampling when tolerant support recovery is acceptable, and demonstrate its advantages empirically. In addition, we provide a first step towards theoretical analysis by considering a specific reconstruction method for selected signal classes.

Symmetries at ultrahigh energies and searches for neutrino oscillations

NASA Astrophysics Data System (ADS)

Papageorgiu, E.

1995-02-01

Motivated by the possibility that new (gauge) symmetries which are broken at the grand- (string-) unification scale give rise to texture zeros in the fermion mass matrices which are at the origin of the hierarchy of masses and mixings we explore the effect of such zeros on the neutrino spectrum of SUSY-GUT models. We find that the quadratic-seesaw spectrum on which most expectations are focused is neither the only nor the most interesting possibility. Cases of strong νμ- ντ or νe- ντ mixing are present for a specific texture structure of the Yukawa matrices and experimental evidence can thus throw some light on the latter. In contrast if the quadratic-seesaw scenario should be confirmed very little could be said about the symmetries of the Yukawa sector.

Magnetic resonance microscopy for assessment of morphological changes in hydrating hydroxypropylmethylcellulose matrix tablets in situ-is it possible to detect phenomena related to drug dissolution within the hydrated matrices?

PubMed

Kulinowski, Piotr; Młynarczyk, Anna; Jasiński, Krzysztof; Talik, Przemysław; Gruwel, Marco L H; Tomanek, Bogusław; Węglarz, Władysław P; Dorożyński, Przemysław

2014-09-01

So far, the hydrated part of the HPMC matrix has commonly been denoted as a "gel" or "pseudogel" layer. No MRI-based results have been published regarding observation of internal phenomena related to drug dissolution inside swelling polymeric matrices during hydration. The purpose of the study was to detect such phenomena. Multiparametric, spatially and temporally resolved T2 MR relaxometry, in situ, was applied to study formation of the hydration progress in HPMC matrix tablets loaded with L-dopa and ketoprofen using a 11.7 T MRI system. Two spin-echo based pulse sequences were used, one of them specifically designed to study short T2 signals. Two components in the T2 decay envelope were estimated and spatial distributions of their parameters, i.e. amplitudes and T2 values, were obtained. Based on the data, different region formation patterns (i.e. multilayer structure) were registered depending on drug presence and solubility. Inside the matrix with incorporated sparingly soluble drug a specific layer formation due to drug dissolution was detected, whereas a matrix with very slightly soluble drug does not form distinct external "gel-like" layer. We have introduced a new paradigm in the characterization of hydrating matrices using (1)H MRI methods. It reflects molecular mobility and concentration of water inside the hydrated matrix. For the first time, drug dissolution related phenomena, i.e. particular front and region formation, were observed by MRI methods.

Using the MATRICS to guide development of a preclinical cognitive test battery for research in schizophrenia

PubMed Central

YOUNG, Jared W; POWELL, Susan; RISBROUGH, Victoria; MARSTON, Hugh M; GEYER, Mark A

2009-01-01

Cognitive deficits in schizophrenia are among the core symptoms of the disease, correlate with functional outcome, and are not well treated with current antipsychotic therapies. In order to bring together academic, industrial, and governmental bodies to address this great ‘unmet therapeutic need’, the NIMH sponsored the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) initiative. Through careful factor analysis and consensus of expert opinion, MATRICS identified seven domains of cognition that are deficient in schizophrenia (attention/vigilance, working memory, reasoning and problem solving, processing speed, visual learning and memory, verbal learning and memory, and social cognition) and recommended a specific neuropsychological test battery to probe these domains. In order to move the field forward and outline an approach for translational research, there is a need for a “preclinical MATRICS” to develop a rodent test battery that is appropriate for drug development. In this review, we outline such an approach and review current rodent tasks that target these seven domains of cognition. The rodent tasks are discussed in terms of their validity for probing each cognitive domain as well as a brief overview of the pharmacology and manipulations relevant to schizophrenia for each task. PMID:19269307

The use of multidimensional scaling for facilities layout - An application to the design of the Space Station

NASA Technical Reports Server (NTRS)

Tullis, Thomas S.; Bied Sperling, Barbra; Steinberg, A. L.

1986-01-01

Before an optimum layout of the facilities for the proposed Space Station can be designed, it is necessary to understand the functions that will be performed by the Space Station crew and the relationships among those functions. Five criteria for assessing functional relationships were identified. For each of these criteria, a matrix representing the degree of association of all pairs of functions was developed. The key to making inferences about the layout of the Space Station from these matrices was the use of multidimensional scaling (MDS). Applying MDS to these matrices resulted in spatial configurations of the crew functions in which smaller distances in the MDS configuration reflected closer associations. An MDS analysis of a composite matrix formed by combining the five individual matrices resulted in two dimensions that describe the configuration: a 'private-public' dimension and a 'group-individual' dimension. Seven specific recommendations for Space Station layout were derived from analyses of the MDS configurations. Although these techniques have been applied to the design of the Space Station, they can be applied to the design of any facility where people live or work.

Conventional and alternative matrices for driving under the influence of cannabis: recent progress and remaining challenges.

PubMed

Wille, Sarah M R; Ramírez-Fernandez, Maria Del Mar; Samyn, Nele; De Boeck, Gert

2010-04-01

In the past decade much research concerning the impact of cannabis use on road safety has been conducted. More specifically, studies on effects of cannabis smoking on driving performance, as well as epidemiological studies and cannabis-detection techniques have been published. As a result, several countries have adopted driving under the influence of drugs (DUID) legislations, with varying approaches worldwide. A wide variety of bodily fluids have been utilized to determine the presence of cannabis. Urine and blood are the most widely used matrices for DUID legislations. However, more and more publications focus on the usability of oral fluid testing for this purpose. Each matrix provides different information about time and extent of use and likelihood of impairment. This review will focus on the practical aspects of implying a DUID legislation. The pros and cons of the different biological matrices used for Δ(9)-tetrahydrocannabinol screening and quantification will be discussed. In addition, a literature overview concerning (roadside) cannabinoid detection, as well as laboratory confirmation techniques is given. Finally, we will discuss important issues influencing interpretation of these data, such as oral fluid collection, choice of cut-offs, stability and proficiency testing.

COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS.

PubMed

Regenbogen, Sam; Wilkins, Angela D; Lichtarge, Olivier

2016-01-01

Biomedicine produces copious information it cannot fully exploit. Specifically, there is considerable need to integrate knowledge from disparate studies to discover connections across domains. Here, we used a Collaborative Filtering approach, inspired by online recommendation algorithms, in which non-negative matrix factorization (NMF) predicts interactions among chemicals, genes, and diseases only from pairwise information about their interactions. Our approach, applied to matrices derived from the Comparative Toxicogenomics Database, successfully recovered Chemical-Disease, Chemical-Gene, and Disease-Gene networks in 10-fold cross-validation experiments. Additionally, we could predict each of these interaction matrices from the other two. Integrating all three CTD interaction matrices with NMF led to good predictions of STRING, an independent, external network of protein-protein interactions. Finally, this approach could integrate the CTD and STRING interaction data to improve Chemical-Gene cross-validation performance significantly, and, in a time-stamped study, it predicted information added to CTD after a given date, using only data prior to that date. We conclude that collaborative filtering can integrate information across multiple types of biological entities, and that as a first step towards precision medicine it can compute drug repurposing hypotheses.

COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS

PubMed Central

REGENBOGEN, SAM; WILKINS, ANGELA D.; LICHTARGE, OLIVIER

2015-01-01

Biomedicine produces copious information it cannot fully exploit. Specifically, there is considerable need to integrate knowledge from disparate studies to discover connections across domains. Here, we used a Collaborative Filtering approach, inspired by online recommendation algorithms, in which non-negative matrix factorization (NMF) predicts interactions among chemicals, genes, and diseases only from pairwise information about their interactions. Our approach, applied to matrices derived from the Comparative Toxicogenomics Database, successfully recovered Chemical-Disease, Chemical-Gene, and Disease-Gene networks in 10-fold cross-validation experiments. Additionally, we could predict each of these interaction matrices from the other two. Integrating all three CTD interaction matrices with NMF led to good predictions of STRING, an independent, external network of protein-protein interactions. Finally, this approach could integrate the CTD and STRING interaction data to improve Chemical-Gene cross-validation performance significantly, and, in a time-stamped study, it predicted information added to CTD after a given date, using only data prior to that date. We conclude that collaborative filtering can integrate information across multiple types of biological entities, and that as a first step towards precision medicine it can compute drug repurposing hypotheses. PMID:26776170

Numerical Aspects of Atomic Physics: Helium Basis Sets and Matrix Diagonalization

NASA Astrophysics Data System (ADS)

Jentschura, Ulrich; Noble, Jonathan

2014-03-01

We present a matrix diagonalization algorithm for complex symmetric matrices, which can be used in order to determine the resonance energies of auto-ionizing states of comparatively simple quantum many-body systems such as helium. The algorithm is based in multi-precision arithmetic and proceeds via a tridiagonalization of the complex symmetric (not necessarily Hermitian) input matrix using generalized Householder transformations. Example calculations involving so-called PT-symmetric quantum systems lead to reference values which pertain to the imaginary cubic perturbation (the imaginary cubic anharmonic oscillator). We then proceed to novel basis sets for the helium atom and present results for Bethe logarithms in hydrogen and helium, obtained using the enhanced numerical techniques. Some intricacies of ``canned'' algorithms such as those used in LAPACK will be discussed. Our algorithm, for complex symmetric matrices such as those describing cubic resonances after complex scaling, is faster than LAPACK's built-in routines, for specific classes of input matrices. It also offer flexibility in terms of the calculation of the so-called implicit shift, which is used in order to ``pivot'' the system toward the convergence to diagonal form. We conclude with a wider overview.

HS-SPME determination of volatile carbonyl and carboxylic compounds in different matrices.

PubMed

Stashenko, Elena E; Mora, Amanda L; Cervantes, Martha E; Martínez, Jairo R

2006-07-01

Specific chromatographic methodologies are developed for the analysis of carboxylic acids (C(2)-C(6), benzoic) and aldehydes (C(2)-C(10)) of low molecular weight in diverse matrices, such as air, automotive exhaust gases, human breath, and aqueous matrices. For carboxylic acids, the method is based on their reaction with pentafluorobenzyl bromide in aqueous solution, followed by the separation and identification of the resultant pentafluorobenzyl esters by means of headspace (HS)-solid-phase microextraction (SPME) combined with gas chromatography (GC) and electron capture detection (ECD). Detection limits in the microg/m(3) range are reached, with relative standard deviation (RSD) less than 10% and linear response (R(2) > 0.99) over two orders of magnitude. The analytical methodology for aldehydes is based on SPME with simultaneous derivatization of the analytes on the fiber, by reaction with pentafluorophenylhydrazine. The derivatization reagent is previously deposited on the SPME fiber, which is then exposed to the gaseous matrix or the HS of the sample solution. The pentafluorophenyl hydrazones formed on the fiber are analyzed selectively by means of GC-ECD, with detection limits in the ng/m(3) range, RSD less than 10%, and linear response (R(2) > 0.99) over two orders of magnitude.

A new preconditioner update strategy for the solution of sequences of linear systems in structural mechanics: application to saddle point problems in elasticity

NASA Astrophysics Data System (ADS)

Mercier, Sylvain; Gratton, Serge; Tardieu, Nicolas; Vasseur, Xavier

2017-12-01

Many applications in structural mechanics require the numerical solution of sequences of linear systems typically issued from a finite element discretization of the governing equations on fine meshes. The method of Lagrange multipliers is often used to take into account mechanical constraints. The resulting matrices then exhibit a saddle point structure and the iterative solution of such preconditioned linear systems is considered as challenging. A popular strategy is then to combine preconditioning and deflation to yield an efficient method. We propose an alternative that is applicable to the general case and not only to matrices with a saddle point structure. In this approach, we consider to update an existing algebraic or application-based preconditioner, using specific available information exploiting the knowledge of an approximate invariant subspace or of matrix-vector products. The resulting preconditioner has the form of a limited memory quasi-Newton matrix and requires a small number of linearly independent vectors. Numerical experiments performed on three large-scale applications in elasticity highlight the relevance of the new approach. We show that the proposed method outperforms the deflation method when considering sequences of linear systems with varying matrices.

A weighted adjustment of a similarity transformation between two point sets containing errors

NASA Astrophysics Data System (ADS)

Marx, C.

2017-10-01

For an adjustment of a similarity transformation, it is often appropriate to consider that both the source and the target coordinates of the transformation are affected by errors. For the least squares adjustment of this problem, a direct solution is possible in the cases of specific-weighing schemas of the coordinates. Such a problem is considered in the present contribution and a direct solution is generally derived for the m-dimensional space. The applied weighing schema allows (fully populated) point-wise weight matrices for the source and target coordinates, both weight matrices have to be proportional to each other. Additionally, the solutions of two borderline cases of this weighting schema are derived, which only consider errors in the source or target coordinates. The investigated solution of the rotation matrix of the adjustment is independent of the scaling between the weight matrices of the source and the target coordinates. The mentioned borderline cases, therefore, have the same solution of the rotation matrix. The direct solution method is successfully tested on an example of a 3D similarity transformation using a comparison with an iterative solution based on the Gauß-Helmert model.

Proactive interference and item similarity in working memory.

PubMed

Bunting, Michael

2006-03-01

Proactive interference (PI) may influence the predictive utility of working memory span tasks. Participants in one experiment (N=70) completed Ravens Advanced Progressive Matrices (RAPM) and multiple versions of operation span and probed recall, modified for the type of memoranda (digits or words). Changing memoranda within- or across-trials released PI, but not doing so permitted PI buildup. Scores from PI-build trials, but not PI-release trials, correlated with RAPM and accounted for as much variance in RAPM as unmodified tasks. These results are consistent with controlled attention and inhibition accounts of working memory, and they elucidate a fundamental component of working memory span tasks.

HAS AN IMPORTANT TEST BEEN OVERLOOKED?: CLOSURE FLEXIBILITY IN SCHIZOPHRENIA

PubMed Central

Butler, Pamela D.; Schechter, Isaac; Revheim, Nadine; Silipo, Gail; Javitt, Daniel C.

2010-01-01

Deficits in visual processing are now recognized as a core feature of schizophrenia. In the 1940’s, Louis Thurstone developed a series of tests designed to evaluate specific aspects of visual perceptual processing including the Closure Flexibility Test (CFT), which was designed to measure “the ability to hold a configuration in mind despite distraction.” The present study evaluated patients’ performance on this task and its relationship to other tests of neuropsychological function, particularly to a measure of sustained visual attention. Thirty-nine patients with schizophrenia or schizoaffective disorder and 40 controls participated. The CFT was administered both in its original form (10 min) and also in a briefer form (3 min) in which only a portion of stimuli were given. Patients showed highly significant large effect size deficits on both the original (d=1.6) and brief (d=1.2) CFT. Between-group deficits in performance survived covariation for IQ. In addition, the CFT score was significantly related to performance on the MATRICS measure of attention/vigilance, the Continuous Performance Test-Identical Pairs version (CPT-IP). This correlation remained significant even after controlling for non-specific intercorrelations among neurocognitive measures. Results confirm the severity of early visual processing deficits in schizophrenia. In addition, the CFT is a brief, easy to administer alphabet-independent, paper-and-pencil test with established psychometric properties that may be useful as an index of the sustained visual attention construct in schizophrenia. PMID:20110157

Impairments in proverb interpretation following focal frontal lobe lesions.

PubMed

Murphy, Patrick; Shallice, Tim; Robinson, Gail; MacPherson, Sarah E; Turner, Martha; Woollett, Katherine; Bozzali, Marco; Cipolotti, Lisa

2013-09-01

The proverb interpretation task (PIT) is often used in clinical settings to evaluate frontal "executive" dysfunction. However, only a relatively small number of studies have investigated the relationship between frontal lobe lesions and performance on the PIT. We compared 52 patients with unselected focal frontal lobe lesions with 52 closely matched healthy controls on a proverb interpretation task. Participants also completed a battery of neuropsychological tests, including a fluid intelligence task (Raven's Advanced Progressive Matrices). Lesions were firstly analysed according to a standard left/right sub-division. Secondly, a finer-grained analysis compared the performance of patients with medial, left lateral and right lateral lesions with healthy controls. Thirdly, a contrast of specific frontal subgroups compared the performance of patients with medial lesions with patients with lateral frontal lesions. The results showed that patients with left frontal lesions were significantly impaired on the PIT, while in patients with right frontal lesions the impairments approached significance. Medial frontal patients were the only frontal subgroup impaired on the PIT, relative to healthy controls and lateral frontal patients. Interestingly, an error analysis indicated that a significantly higher number of concrete responses were found in the left lateral subgroup compared to healthy controls. We found no correlation between scores on the PIT and on the fluid intelligence task. Overall our results suggest that specific regions of the frontal lobes contribute to the performance on the PIT. © 2013 The Authors. Published by Elsevier Ltd. All rights reserved.

Detection of pathogenic organisms in food, water, and body fluids

NASA Astrophysics Data System (ADS)

Wallace, William H.; Henley, Michael V.; Sayler, Gary S.

2002-06-01

The construction of specific bioluminescent bacteriophage for detection of pathogenic organism can be developed to overcome interferences in complex matrices such as food, water and body fluids. Detection and identification of bacteria often require several days and frequently weeks by standard methods of isolation, growth and biochemical test. Immunoassay detection often requires the expression of the bacterial toxin, which can lead to non-detection of cells that may express the toxin under conditions different from testing protocols. Immunoassays require production of a specific antibody to the agent for detection and interference by contaminants frequently affects results. PCR based detection may be inhibited by substances in complex matrices. Modified methods of the PCR technique, such as magnetic capture-hybridization PCR (MCH-PCR), appear to improve the technique by removing the DNA products away from the inhibitors. However, the techniques required for PCR-based detection are slow and the procedures require skilled personnel working with labile reagents. Our approach is based on transferring bioluminescence (lux) genes into a selected bacteriophage. Bacteriophages are bacterial viruses that are widespread in nature and often are genus and species specific. This specificity eliminates or reduces false positives in a bacteriophage assay. The phage recognizes a specific receptor molecule on the surface of a susceptible bacterium, attaches and then injects the viral nucleic acid into the cell. The injected viral genome is expressed and then replicated, generating numerous exact copies of the viral genetic material including the lux genes, often resulting in an increase in bioluminescence by several hundred fold.

Estimation of premorbid general fluid intelligence using traditional Chinese reading performance in Taiwanese samples.

PubMed

Chen, Ying-Jen; Ho, Meng-Yang; Chen, Kwan-Ju; Hsu, Chia-Fen; Ryu, Shan-Jin

2009-08-01

The aims of the present study were to (i) investigate if traditional Chinese word reading ability can be used for estimating premorbid general intelligence; and (ii) to provide multiple regression equations for estimating premorbid performance on Raven's Standard Progressive Matrices (RSPM), using age, years of education and Chinese Graded Word Reading Test (CGWRT) scores as predictor variables. Four hundred and twenty-six healthy volunteers (201 male, 225 female), aged 16-93 years (mean +/- SD, 41.92 +/- 18.19 years) undertook the tests individually under supervised conditions. Seventy percent of subjects were randomly allocated to the derivation group (n = 296), and the rest to the validation group (n = 130). RSPM score was positively correlated with CGWRT score and years of education. RSPM and CGWRT scores and years of education were also inversely correlated with age, but the declining trend for RSPM performance against age was steeper than that for CGWRT performance. Separate multiple regression equations were derived for estimating RSPM scores using different combinations of age, years of education, and CGWRT score for both groups. The multiple regression coefficient of each equation ranged from 0.71 to 0.80 with the standard error of estimate between 7 and 8 RSPM points. When fitting the data of one group to the equations derived from its counterpart group, the cross-validation multiple regression coefficients ranged from 0.71 to 0.79. There were no significant differences in the 'predicted-obtained' RSPM discrepancies between any equations. The regression equations derived in the present study may provide a basis for estimating premorbid RSPM performance.

Relationship between Intelligence Quotient and Musical Ability in Children with Cochlear Implantation.

PubMed

Soleimanifar, Simin; Jafari, Zahra; Motasaddi Zarandy, Masoud; Asadi, Houman; Haghani, Hamid

2016-09-01

Children with cochlear implants (CIs) may experience few opportunities for positive musical experiences, and musical perception is therefore often not sufficiently developed. This paper investigates and discusses the relationship between intelligence quotient (IQ) and musical ability in children with CIs compared with children with normal hearing. This was a comparative analytical study conducted in 48 children with unilateral CI and 48 normal-hearing children, 6-8 years of age, with 'normal' IQ and no formal music training. The average IQ score in the experimental and control groups were 105.41 and 106.31, respectively. No statistically significant differences were detected between Raven's IQ scores in both groups. Data were collected by administering Raven's Colored Progressive Matrices IQ Tests and the Montreal Battery of Evaluation of Musical Abilities (MBEMA) Test, consisting of scale, contour, interval, rhythm, and memory sections. Mean total MBEMA score in the experimental and control groups was 58.93 and 72.16 (out of 100), respectively. Significant differences were evident between scores of children with CIs in comparison with their normal-hearing peers (P≤0.001). A remarkable direct correlation between IQ and musical scores in both the control (r≥0.38) and experimental (r≥0.37) groups was observed. IQ has a noticeable effect on music processing and facilitates the perception of various musical elements. With regard to the mutual relationship between IQ and musical skills, this study illustrates the advantage of determining music perception scores and highlights the importance of appropriate musical intervention in order to enhance auditory neural plasticity, especially in children with cochlear implantation.

LANDSAT-D data format control book. Volume 6, appendix D: Thematic mapper Computer Compatible Tape (CCT-AT/PT)

NASA Technical Reports Server (NTRS)

Ahmed, H.

1981-01-01

The format of computer compatible tapes which contain LANDSAT 4 and D Prime thematic mapper data is defined. A complete specification of the CCT-AT (radiometric corrections applied and geometric matrices appended) and the CCT-PT (radiometric and geometric corrections) data formats is provided.

Mechanisms of deterioration of nutrients. [of freeze dried foods

NASA Technical Reports Server (NTRS)

Karel, M.; Flink, J. M.

1976-01-01

Methods which produce freeze dried foods of improved quality were examined with emphasis on storage stability. Specific topics discussed include: microstructure of freeze dried systems, investigation of structural changes in freeze dried systems, artificial food matrices, osmotic preconcentration to yield improved quality freeze dried fruits, and storage stability of osmotically preconcentrated freeze dried fruits.

THE IMPORTANCE OF ARSENIC SPECIES SPECIFIC MASS BALANCE ON THE EVALUATION OF ARSENIC SPECIATION RESULTS IN SEAFOOD MATRICES

EPA Science Inventory

The two predominant pathways to arsenic exposure are drinking water and dietary ingestion. A large percentage of the dietary exposure component is associated with a few food groups. For example, seafood alone represents over 50% of the total dietary exposure. From a daily dose...

DNA-based identification of spices: DNA isolation, whole genome amplification, and polymerase chain reaction.

PubMed

Focke, Felix; Haase, Ilka; Fischer, Markus

2011-01-26

Usually spices are identified morphologically using simple methods like magnifying glasses or microscopic instruments. On the other hand, molecular biological methods like the polymerase chain reaction (PCR) enable an accurate and specific detection also in complex matrices. Generally, the origins of spices are plants with diverse genetic backgrounds and relationships. The processing methods used for the production of spices are complex and individual. Consequently, the development of a reliable DNA-based method for spice analysis is a challenging intention. However, once established, this method will be easily adapted to less difficult food matrices. In the current study, several alternative methods for the isolation of DNA from spices have been developed and evaluated in detail with regard to (i) its purity (photometric), (ii) yield (fluorimetric methods), and (iii) its amplifiability (PCR). Whole genome amplification methods were used to preamplify isolates to improve the ratio between amplifiable DNA and inhibiting substances. Specific primer sets were designed, and the PCR conditions were optimized to detect 18 spices selectively. Assays of self-made spice mixtures were performed to proof the applicability of the developed methods.

Processing and properties of magnesium containing a dense uniform dispersion of nanoparticles.

PubMed

Chen, Lian-Yi; Xu, Jia-Quan; Choi, Hongseok; Pozuelo, Marta; Ma, Xiaolong; Bhowmick, Sanjit; Yang, Jenn-Ming; Mathaudhu, Suveen; Li, Xiao-Chun

2015-12-24

Magnesium is a light metal, with a density two-thirds that of aluminium, is abundant on Earth and is biocompatible; it thus has the potential to improve energy efficiency and system performance in aerospace, automobile, defence, mobile electronics and biomedical applications. However, conventional synthesis and processing methods (alloying and thermomechanical processing) have reached certain limits in further improving the properties of magnesium and other metals. Ceramic particles have been introduced into metal matrices to improve the strength of the metals, but unfortunately, ceramic microparticles severely degrade the plasticity and machinability of metals, and nanoparticles, although they have the potential to improve strength while maintaining or even improving the plasticity of metals, are difficult to disperse uniformly in metal matrices. Here we show that a dense uniform dispersion of silicon carbide nanoparticles (14 per cent by volume) in magnesium can be achieved through a nanoparticle self-stabilization mechanism in molten metal. An enhancement of strength, stiffness, plasticity and high-temperature stability is simultaneously achieved, delivering a higher specific yield strength and higher specific modulus than almost all structural metals.

Assessing the effects of cocaine dependence and pathological gambling using group-wise sparse representation of natural stimulus FMRI data.

PubMed

Ren, Yudan; Fang, Jun; Lv, Jinglei; Hu, Xintao; Guo, Cong Christine; Guo, Lei; Xu, Jiansong; Potenza, Marc N; Liu, Tianming

2017-08-01

Assessing functional brain activation patterns in neuropsychiatric disorders such as cocaine dependence (CD) or pathological gambling (PG) under naturalistic stimuli has received rising interest in recent years. In this paper, we propose and apply a novel group-wise sparse representation framework to assess differences in neural responses to naturalistic stimuli across multiple groups of participants (healthy control, cocaine dependence, pathological gambling). Specifically, natural stimulus fMRI (N-fMRI) signals from all three groups of subjects are aggregated into a big data matrix, which is then decomposed into a common signal basis dictionary and associated weight coefficient matrices via an effective online dictionary learning and sparse coding method. The coefficient matrices associated with each common dictionary atom are statistically assessed for each group separately. With the inter-group comparisons based on the group-wise correspondence established by the common dictionary, our experimental results demonstrated that the group-wise sparse coding and representation strategy can effectively and specifically detect brain networks/regions affected by different pathological conditions of the brain under naturalistic stimuli.

Influence of porosity and composition of supports on the methanogenic biofilm characteristics developed in a fixed bed anaerobic reactor.

PubMed

Picanço, A P; Vallero, M V; Gianotti, E P; Zaiat, M; Blundi, C E

2001-01-01

This paper reports on the influence of the material porosity on the anaerobic biomass adhesion on four different inert matrices: polyurethane foam, PVC, refractory brick and special ceramic. The biofilm development was performed in a fixed-bed anaerobic reactor containing all the support materials and fed with a synthetic wastewater containing protein, lipids and carbohydrates. The data obtained from microscopic analysis and kinetic assays indicated that the material porosity has a crucial importance in the retention of the anaerobic biomass. The polyurethane foam particles and the special ceramic were found to present better retentive properties than the PVC and the refractory brick. The large specific surface area, directly related to material porosity, is fundamental to provide a large amount of attached biomass. However, different supports can provide specific conditions for the adherence of distinct microorganism types. The microbiological exams revealed a distinction in the support colonization. A predominance of methanogenic archaeas resembling Methanosaeta was observed both in the refractory brick and the special ceramic. Methanosarcina-like microorganisms were predominant in the PVC and the polyurethane foam matrices.

Real-Time Cytotoxicity Assay for Rapid and Sensitive Detection of Ricin from Complex Matrices

PubMed Central

Pauly, Diana; Worbs, Sylvia; Kirchner, Sebastian; Shatohina, Olena; Dorner, Martin B.; Dorner, Brigitte G.

2012-01-01

Background In the context of a potential bioterrorist attack sensitive and fast detection of functionally active toxins such as ricin from complex matrices is necessary to be able to start timely countermeasures. One of the functional detection methods currently available for ricin is the endpoint cytotoxicity assay, which suffers from a number of technical deficits. Methodology/Findings This work describes a novel online cytotoxicity assay for the detection of active ricin and Ricinus communis agglutinin, that is based on a real-time cell electronic sensing system and impedance measurement. Characteristic growth parameters of Vero cells were monitored online and used as standardized viability control. Upon incubation with toxin the cell status and the cytotoxic effect were visualized using a characteristic cell index–time profile. For ricin, tested in concentrations of 0.06 ng/mL or above, a concentration-dependent decrease of cell index correlating with cytotoxicity was recorded between 3.5 h and 60 h. For ricin, sensitive detection was determined after 24 h, with an IC50 of 0.4 ng/mL (for agglutinin, an IC50 of 30 ng/mL was observed). Using functionally blocking antibodies, the specificity for ricin and agglutinin was shown. For detection from complex matrices, ricin was spiked into several food matrices, and an IC50 ranging from 5.6 to 200 ng/mL was observed. Additionally, the assay proved to be useful in detecting active ricin in environmental sample materials, as shown for organic fertilizer containing R. communis material. Conclusions/Significance The cell-electrode impedance measurement provides a sensitive online detection method for biologically active cytotoxins such as ricin. As the cell status is monitored online, the assay can be standardized more efficiently than previous approaches based on endpoint measurement. More importantly, the real-time cytotoxicity assay provides a fast and easy tool to detect active ricin in complex sample matrices. PMID:22532852

Validation of the Finnegan neonatal abstinence syndrome tool-short form.

PubMed

Maguire, Denise; Cline, Genieveve J; Parnell, Lisa; Tai, Chun-Yi

2013-12-01

The purpose of this study was to reduce the number of items in the Modified Finnegan Neonatal Abstinence Syndrome Tool (M-FNAST) to the minimum possible while retaining or improving its validity in a short version. All infants with a diagnosis of neonatal abstinence syndrome (171) who were admitted to a large neonatal intensive care unit in southwest Florida between September 2010 and October 2012 comprised the sample. This was a psychometric evaluation of 33 856 M-FNAST assessments that were downloaded from the electronic medical record. Principal axis factoring extraction with varimax rotation was performed on the M-FNAST data. Principal components extraction was used before principal factors extraction to estimate the number of factors with the scree test and factorability of the correlation matrices with Bartlett's chi-square test, and Kaiser-Meyer-Olkin Measure of Sampling Adequacy. The M-FNAST scores ranged from 0 to 29, with a mean of 3.5 (SD = 2.5). Less than 1% (21) of infants had scores of 17 or more. Nearly all (97.7%) scores fell between 0 and 9. Most subjects were full-term gestation, but 11 were preterm between 28 and 37 weeks' gestational age. The 2-factor solution explained 23.74% of the total variance and consists of 2 factors, mild/early and moderate/advanced signs. The 2-factor solution was significantly correlated with the total score on the MFNAST (r = 0.917; P < .001). Among infants who scored 8 or greater, the total score on the 2-factor solution short form FNAST was significantly correlated with the total score on the M-FNAST (r = 0.629; P < .001).

Investigating the mental abilities of rural Zulu primary school children in South Africa.

PubMed

Jinabhai, C C; Taylor, M; Rangongo, M F; Mkhize, N J; Anderson, S; Pillay, B J; Sullivan, K R

2004-02-01

Maximising the full potential of health and educational interventions in South African schools requires assessment of the current level of mental abilities of the school children as measured by cognitive and scholastic tests and the identification of any barriers to improved performance. This study reports on the application and interpretation of a selected battery of mental ability tests among Zulu school children and the methodological and analytical issues that need to be addressed. The test scores of 806 primary school children from a rural community are presented, based on four tests: Raven's Coloured Progressive Matrices (CPM), an Auditory Verbal Learning Test (AVLT), the Symbol Digit Modalities Test (SDMT) and Young's Group Mathematics Test (GMT). Significant gender differences were found in the test scores, and the mean scores of Zulu children in this study were lower than those reported in other studies. The results of this selected test battery provide data for the further development of appropriate test instruments for South African conditions. These results can contribute towards the development of a test battery for South African children that can be used to assess and improve their school performance.

Effect of gender and nutritional status on academic achievement and cognitive function among primary school children in a rural district in Malaysia.

PubMed

Hamid, Jan J M; Amal, Mitra K; Hasmiza, H; Pim, C D; Ng, L O; Wan, Manan W M

2011-08-01

The aim of this study was to investigate the relationship between gender, birth weight, nutritional status, and iron status of children with their academic performance and cognitive function. Two hundred and forty-nine children, seven to nine years of age, were recruited by systematic sampling from six primary schools in a rural area in Malaysia. Cognitive function was assessed by using Raven's Coloured Progressive Matrices (R-CPM). Academic performance of the children was recorded from their school final examination results in four subjects including Malay language, English, Mathematics, and Science. Birth weight was recorded from the birth certificate, and nutritional status was determined by weight-for-age z score and height-for-age z score. Girls had a significantly higher score in all the academic tests, but a lower cognitive score compared to boys. Nutritional status was found to be correlated significantly with academic performance. Academic and cognitive function scores were also found to be correlated significantly with birth weight, parents' education, and family income. In a multivariate analysis, gender remained the significant predictor of academic function, and iron status and haemoglobin were the significant predictors of cognitive function, after controlling for other variables. The study showed that girls performed better academically than boys in rural Malaysia. Nutritional status, parents' education and family income could be additional modifiable factors to improve academic performance of the children. More attention is needed to improve academic achievements of boys at their early school years.

Effects of transcranial direct current stimulation (tDCS) on cognition, symptoms, and smoking in schizophrenia: A randomized controlled study.

PubMed

Smith, Robert C; Boules, Sylvia; Mattiuz, Sanela; Youssef, Mary; Tobe, Russell H; Sershen, Henry; Lajtha, Abel; Nolan, Karen; Amiaz, Revital; Davis, John M

2015-10-01

Schizophrenia is characterized by cognitive deficits which persist after acute symptoms have been treated or resolved. Transcranial direct current stimulation (tDCS) has been reported to improve cognition and reduce smoking craving in healthy subjects but has not been as carefully evaluated in a randomized controlled study for these effects in schizophrenia. We conducted a randomized double-blind, sham-controlled study of the effects of 5 sessions of tDCS (2 milliamps for 20minutes) on cognition, psychiatric symptoms, and smoking and cigarette craving in 37 outpatients with schizophrenia or schizoaffective disorder who were current smokers. Thirty subjects provided evaluable data on the MATRICS Consensus Cognitive Battery (MCCB), with the primary outcome measure, the MCCB Composite score. Active compared to sham tDCS subjects showed significant improvements after the fifth tDCS session in MCCB Composite score (p=0.008) and on the MCCB Working Memory (p=0.002) and Attention-Vigilance (p=0.027) domain scores, with large effect sizes. MCCB Composite and Working Memory domain scores remained significant at Benjamini-Hochberg corrected significance levels (α=0.05). There were no statistically significant effects on secondary outcome measures of psychiatric symptoms (PANSS scores), hallucinations, cigarette craving, or cigarettes smoked. The positive effects of tDCS on cognitive performance suggest a potential efficacious treatment for cognitive deficits in partially recovered chronic schizophrenia outpatients that should be further investigated. Copyright © 2015 Elsevier B.V. All rights reserved.

Stochastic local operations and classical communication (SLOCC) and local unitary operations (LU) classifications of n qubits via ranks and singular values of the spin-flipping matrices

NASA Astrophysics Data System (ADS)

Li, Dafa

2018-06-01

We construct ℓ -spin-flipping matrices from the coefficient matrices of pure states of n qubits and show that the ℓ -spin-flipping matrices are congruent and unitary congruent whenever two pure states of n qubits are SLOCC and LU equivalent, respectively. The congruence implies the invariance of ranks of the ℓ -spin-flipping matrices under SLOCC and then permits a reduction of SLOCC classification of n qubits to calculation of ranks of the ℓ -spin-flipping matrices. The unitary congruence implies the invariance of singular values of the ℓ -spin-flipping matrices under LU and then permits a reduction of LU classification of n qubits to calculation of singular values of the ℓ -spin-flipping matrices. Furthermore, we show that the invariance of singular values of the ℓ -spin-flipping matrices Ω 1^{(n)} implies the invariance of the concurrence for even n qubits and the invariance of the n-tangle for odd n qubits. Thus, the concurrence and the n-tangle can be used for LU classification and computing the concurrence and the n-tangle only performs additions and multiplications of coefficients of states.

Quantitative Analysis of Microbicide Concentrations in Fluids, Gels and Tissues Using Confocal Raman Spectroscopy

PubMed Central

Chuchuen, Oranat; Henderson, Marcus H.; Sykes, Craig; Kim, Min Sung; Kashuba, Angela D. M.; Katz, David F.

2013-01-01

Topical vaginal anti-HIV microbicides are an important focus in female-based strategies to prevent the sexual transmission of HIV. Understanding microbicide pharmacokinetics is essential to development, characterization and implementation of efficacious microbicide drug delivery formulations. Current methods to measure drug concentrations in tissue (e.g., LC-MS/MS, liquid chromatography coupled with tandem mass spectrometry) are highly sensitive, but destructive and complex. This project explored the use of confocal Raman spectroscopy to detect microbicide drugs and to measure their local concentrations in fluids, drug delivery gels, and tissues. We evaluated three candidate microbicide drugs: tenofovir, Dapivirine and IQP-0528. Measurements were performed in freshly excised porcine buccal tissue specimens, gel vehicles and fluids using two Horiba Raman microscopes, one of which is confocal. Characteristic spectral peak calibrations for each drug were obtained using serial dilutions in the three matrices. These specific Raman bands demonstrated strong linear concentration dependences in the matrices and were characterized with respect to their unique vibrational signatures. At least one specific Raman feature was identified for each drug as a marker band for detection in tissue. Sensitivity of detection was evaluated in the three matrices. A specific peak was also identified for tenofovir diphosphate, the anti-HIV bioactive product of tenofovir after phosphorylation in host cells. Z-scans of drug concentrations vs. depth in excised tissue specimens, incubated under layers of tenofovir solution in a Transwell assay, showed decreasing concentration with depth from the surface into the tissue. Time-dependent concentration profiles were obtained from tissue samples incubated in the Transwell assay, for times ranging 30 minutes - 6 hours. Calibrations and measurements from tissue permeation studies for tenofovir showed good correlation with gold standard LC-MS/MS data. These results demonstrate that confocal Raman spectroscopy holds promise as a tool for practical, minimally invasive, label-free measurement of microbicide drug concentrations in fluids, gels and tissues. PMID:24386455

Matrix computations in MACSYMA

NASA Technical Reports Server (NTRS)

Wang, P. S.

1977-01-01

Facilities built into MACSYMA for manipulating matrices with numeric or symbolic entries are described. Computations will be done exactly, keeping symbols as symbols. Topics discussed include how to form a matrix and create other matrices by transforming existing matrices within MACSYMA; arithmetic and other computation with matrices; and user control of computational processes through the use of optional variables. Two algorithms designed for sparse matrices are given. The computing times of several different ways to compute the determinant of a matrix are compared.

Complex symmetric matrices with strongly stable iterates

NASA Technical Reports Server (NTRS)

Tadmor, E.

1985-01-01

Complex-valued symmetric matrices are studied. A simple expression for the spectral norm of such matrices is obtained, by utilizing a unitarily congruent invariant form. A sharp criterion is provided for identifying those symmetric matrices whose spectral norm is not exceeding one: such strongly stable matrices are usually sought in connection with convergent difference approximations to partial differential equations. As an example, the derived criterion is applied to conclude the strong stability of a Lax-Wendroff scheme.

Isolation and Identification of Proteins Secreted by Cells Cultured within Synthetic Hydrogel-Based Matrices

PubMed Central

2018-01-01

Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices. Specifically, human mesenchymal stem cells (hMSCs), a model primary cell type, were cultured within well-defined poly(ethylene glycol) (PEG)-peptide hydrogels, and these cell-matrix constructs were decellularized and degraded for subsequent isolation and analysis of deposited proteins. Shotgun proteomics using liquid chromatography and mass spectrometry identified a variety of proteins, including the large ECM proteins fibronectin and collagen VI. Immunostaining and confocal imaging confirmed these results and provided visualization of protein organization within the synthetic matrices. Additionally, culture medium was collected from the encapsulated hMSCs, and a Luminex assay was performed to identify secreted soluble factors, including vascular endothelial growth factor (VEGF), endothelial growth factor (EGF), basic fibroblast growth factor (FGF-2), interleukin 8 (IL-8), and tumor necrosis factor alpha (TNF-α). Together, these methods provide a unique approach for studying dynamic reciprocity between cells and synthetic microenvironments and have the potential to provide new biological insights into cell responses during three-dimensional (3D) controlled cell culture. PMID:29552635

Isolation and Identification of Proteins Secreted by Cells Cultured within Synthetic Hydrogel-Based Matrices.

PubMed

Sawicki, Lisa A; Choe, Leila H; Wiley, Katherine L; Lee, Kelvin H; Kloxin, April M

2018-03-12

Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices. Specifically, human mesenchymal stem cells (hMSCs), a model primary cell type, were cultured within well-defined poly(ethylene glycol) (PEG)-peptide hydrogels, and these cell-matrix constructs were decellularized and degraded for subsequent isolation and analysis of deposited proteins. Shotgun proteomics using liquid chromatography and mass spectrometry identified a variety of proteins, including the large ECM proteins fibronectin and collagen VI. Immunostaining and confocal imaging confirmed these results and provided visualization of protein organization within the synthetic matrices. Additionally, culture medium was collected from the encapsulated hMSCs, and a Luminex assay was performed to identify secreted soluble factors, including vascular endothelial growth factor (VEGF), endothelial growth factor (EGF), basic fibroblast growth factor (FGF-2), interleukin 8 (IL-8), and tumor necrosis factor alpha (TNF-α). Together, these methods provide a unique approach for studying dynamic reciprocity between cells and synthetic microenvironments and have the potential to provide new biological insights into cell responses during three-dimensional (3D) controlled cell culture.

A 10-minute measure of global cognition: Validation of the Brief Cognitive Assessment Tool for Schizophrenia (B-CATS).

PubMed

Hurford, Irene M; Ventura, Joseph; Marder, Stephen R; Reise, Steven P; Bilder, Robert M

2018-05-01

Schizophrenia is marked by a global cognitive impairment that contributes significantly to chronic disability and unemployment. As new treatments are developed for cognition in schizophrenia, clinicians require easily administered instruments to assess cognition. We previously developed a very brief cognitive battery (Bell et al., 2005). The Brief Cognitive Assessment Tool for Schizophrenia (B-CATS) was developed specifically to provide clinicians with a way to assess cognition in their patients with schizophrenia. Here, we report the results of a validity study comparing B-CATS to a larger neurocognitive battery, the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) battery. Outpatients with schizophrenia (N=91) were administered the B-CATS and the non-overlapping tests of the MATRICS battery at two time points separated by 1month. They were also administered the UCSD Performance-based Skills Assessment-Brief (UPSA-B), a measure of functional capacity. The B-CATS has an administration time of approximately 10min. It demonstrates good test-retest reliability and internal consistency. It correlates 0.76 (p<0.01) with the MATRICS battery. The shorter B-CATS and the MATRICS battery correlate with the UPSA-B at 0.50 and 0.58 respectively. A 10-minute version of the B-CATS correlates highly with the "gold standard" neurocognitive battery that has an administration time of over 60min. Both measures correlate moderately with a measure of functional capacity. This brief battery was designed to allow clinicians to monitor cognitive change and better inform treatment decisions. Copyright © 2017 Elsevier B.V. All rights reserved.

Graph Theoretic Foundations of Multibody Dynamics Part I: Structural Properties

PubMed Central

Jain, Abhinandan

2011-01-01

This is the first part of two papers that use concepts from graph theory to obtain a deeper understanding of the mathematical foundations of multibody dynamics. The key contribution is the development of a unifying framework that shows that key analytical results and computational algorithms in multibody dynamics are a direct consequence of structural properties and require minimal assumptions about the specific nature of the underlying multibody system. This first part focuses on identifying the abstract graph theoretic structural properties of spatial operator techniques in multibody dynamics. The second part paper exploits these structural properties to develop a broad spectrum of analytical results and computational algorithms. Towards this, we begin with the notion of graph adjacency matrices and generalize it to define block-weighted adjacency (BWA) matrices and their 1-resolvents. Previously developed spatial operators are shown to be special cases of such BWA matrices and their 1-resolvents. These properties are shown to hold broadly for serial and tree topology multibody systems. Specializations of the BWA and 1-resolvent matrices are referred to as spatial kernel operators (SKO) and spatial propagation operators (SPO). These operators and their special properties provide the foundation for the analytical and algorithmic techniques developed in the companion paper. We also use the graph theory concepts to study the topology induced sparsity structure of these operators and the system mass matrix. Similarity transformations of these operators are also studied. While the detailed development is done for the case of rigid-link multibody systems, the extension of these techniques to a broader class of systems (e.g. deformable links) are illustrated. PMID:22102790

Characterisation of crystal matrices and single pixels for nuclear medicine applications

NASA Astrophysics Data System (ADS)

Herbert, D. J.; Belcari, N.; Camarda, M.; Guerra, A. Del; Vaiano, A.

2005-01-01

Commercially constructed crystal matrices are characterised for use with PSPMT detectors for PET system developments and other nuclear medicine applications. The matrices of different scintillation materials were specified with pixel dimensions of 1.5×1.5 mm2 in cross-section and a length corresponding to one gamma ray interaction length at 511 keV. The materials used in this study were BGO, LSO, LYSO, YSO and CsI(Na). Each matrix was constructed using a white TiO loaded epoxy that forms a 0.2 mm septa between each pixel. The white epoxy is not the optimum choice in terms of the reflective properties, but represents a good compromise between cost and the need for optical isolation between pixels. We also tested a YAP matrix that consisted of pixels of the same size specification but was manufactured by a different company, who instead of white epoxy, used a thin aluminium reflective layer for optical isolation that resulted in a septal thickness of just 0.01 mm, resulting in a much higher packing fraction. The characteristics of the scintillation materials, such as the light output and energy resolution, were first studied in the form of individual crystal elements by using a single pixel HPD. A comparison of individual pixels with and without the epoxy/dielectric coatings was also performed. Then the matrices themselves were coupled to a PSPMT in order to study the imaging performance. In particular, the system pixel resolution and the peak to valley ratio were measured at 511 and 122 keV.

Calculation of controllability and observability matrices for special case of continuous-time multi-order fractional systems.

PubMed

Hassanzadeh, Iman; Tabatabaei, Mohammad

2017-03-28

In this paper, controllability and observability matrices for pseudo upper or lower triangular multi-order fractional systems are derived. It is demonstrated that these systems are controllable and observable if and only if their controllability and observability matrices are full rank. In other words, the rank of these matrices should be equal to the inner dimension of their corresponding state space realizations. To reduce the computational complexities, these matrices are converted to simplified matrices with smaller dimensions. Numerical examples are provided to show the usefulness of the mentioned matrices for controllability and observability analysis of this case of multi-order fractional systems. These examples clarify that the duality concept is not necessarily true for these special systems. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Mirroring co-evolving trees in the light of their topologies.

PubMed

Hajirasouliha, Iman; Schönhuth, Alexander; de Juan, David; Valencia, Alfonso; Sahinalp, S Cenk

2012-05-01

Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain families through maximizing the similarity between trimmed versions of their phylogenetic trees. Since maximization of any natural similarity score is computationally difficult, many approaches employ heuristics to evaluate the distance matrices corresponding to the tree topologies in question. In this article, we devise an efficient deterministic algorithm which directly maximizes the similarity between two leaf labeled trees with edge lengths, obtaining a score-optimal alignment of the two trees in question. Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 min on a single processor versus 730 h on a supercomputer. Furthermore, we outperform the current state-of-the-art exhaustive search approach in terms of precision, while incurring acceptable losses in recall. A C implementation of the method demonstrated in this article is available at http://compbio.cs.sfu.ca/mirrort.htm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parrado, G., E-mail: gparrado@sgc.gov.co; Cañón, Y.; Peña, M., E-mail: mlpena@sgc.gov.co

The Neutron Activation Analysis (NAA) laboratory at the Colombian Geological Survey has developed a technique for multi-elemental analysis of soil and plant matrices, based on Instrumental Neutron Activation Analysis (INAA) using the comparator method. In order to evaluate the analytical capabilities of the technique, the laboratory has been participating in inter-comparison tests organized by Wepal (Wageningen Evaluating Programs for Analytical Laboratories). In this work, the experimental procedure and results for the multi-elemental analysis of four soil and four plant samples during participation in the first round on 2015 of Wepal proficiency test are presented. Only elements with radioactive isotopes withmore » medium and long half-lives have been evaluated, 15 elements for soils (As, Ce, Co, Cr, Cs, Fe, K, La, Na, Rb, Sb, Sc, Th, U and Zn) and 7 elements for plants (Br, Co, Cr, Fe, K, Na and Zn). The performance assessment by Wepal based on Z-score distributions showed that most results obtained |Z-scores| ≤ 3.« less

Clusters of cultures: diversity in meaning of family value and gender role items across Europe.

PubMed

van Vlimmeren, Eva; Moors, Guy B D; Gelissen, John P T M

2017-01-01

Survey data are often used to map cultural diversity by aggregating scores of attitude and value items across countries. However, this procedure only makes sense if the same concept is measured in all countries. In this study we argue that when (co)variances among sets of items are similar across countries, these countries share a common way of assigning meaning to the items. Clusters of cultures can then be observed by doing a cluster analysis on the (co)variance matrices of sets of related items. This study focuses on family values and gender role attitudes. We find four clusters of cultures that assign a distinct meaning to these items, especially in the case of gender roles. Some of these differences reflect response style behavior in the form of acquiescence. Adjusting for this style effect impacts on country comparisons hence demonstrating the usefulness of investigating the patterns of meaning given to sets of items prior to aggregating scores into cultural characteristics.

Improvement of analytical capabilities of neutron activation analysis laboratory at the Colombian Geological Survey

NASA Astrophysics Data System (ADS)

Parrado, G.; Cañón, Y.; Peña, M.; Sierra, O.; Porras, A.; Alonso, D.; Herrera, D. C.; Orozco, J.

2016-07-01

The Neutron Activation Analysis (NAA) laboratory at the Colombian Geological Survey has developed a technique for multi-elemental analysis of soil and plant matrices, based on Instrumental Neutron Activation Analysis (INAA) using the comparator method. In order to evaluate the analytical capabilities of the technique, the laboratory has been participating in inter-comparison tests organized by Wepal (Wageningen Evaluating Programs for Analytical Laboratories). In this work, the experimental procedure and results for the multi-elemental analysis of four soil and four plant samples during participation in the first round on 2015 of Wepal proficiency test are presented. Only elements with radioactive isotopes with medium and long half-lives have been evaluated, 15 elements for soils (As, Ce, Co, Cr, Cs, Fe, K, La, Na, Rb, Sb, Sc, Th, U and Zn) and 7 elements for plants (Br, Co, Cr, Fe, K, Na and Zn). The performance assessment by Wepal based on Z-score distributions showed that most results obtained |Z-scores| ≤ 3.

The influence of the parents' educational level on the development of executive functions.

PubMed

Ardila, Alfredo; Rosselli, Monica; Matute, Esmeralda; Guajardo, Soledad

2005-01-01

Information about the influence of educational variables on the development of executive functions is limited. The aim of this study was to analyze the relation of the parents' educational level and the type of school the child attended (private or public school) to children's executive functioning test performance. Six hundred twenty-two participants, ages 5 to 14 years (276 boys, 346 girls) were selected from Colombia and Mexico and grouped according to three variables: age (5-6, 7-8, 9-10, 11-12, and 13-14 years), gender (boys and girls), and school type (private and public). Eight executive functioning tests taken from the Evaluacion Neuropsicologica Infantil; Matute, Rosselli, Ardila, & Ostrosky, (in press) were individually administered: Semantic Verbal Fluency, Phonemic Verbal Fluency, Semantic Graphic Fluency, Nonsemantic Graphic Fluency, Matrices, Similarities, Card Sorting, and the Mexican Pyramid. There was a significant effect of age on all the test scores and a significant effect of type of school attended on all but Semantic Verbal Fluency and Nonsemantic Graphic Fluency tests. Most children's test scores, particularly verbal test scores, significantly correlated with parents' educational level. Our results suggest that the differences in test scores between the public and private school children depended on some conditions existing outside the school, such as the parents' level of education. Implications of these findings for the understanding of the influence of environmental factors on the development of executive functions are presented.

Comparison of Measures of Ability in Adolescents with Intellectual Disability

PubMed Central

Mungkhetklang, Chantanee; Crewther, Sheila G.; Bavin, Edith L.; Goharpey, Nahal; Parsons, Carl

2016-01-01

Finding the most appropriate intelligence test for adolescents with Intellectual Disability (ID) is challenging given their limited language, attention, perceptual, and motor skills and ability to stay on task. The study compared performance of 23 adolescents with ID on the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV), one of the most widely used intelligence tests, and three non-verbal IQ tests, the Raven's Colored Progressive Matrices (RCPM), the Test of Non-verbal Intelligence-Fourth Edition and the Wechsler Non-verbal test of Ability. Results showed that the WISC-IV Full Scale IQ raw and scaled scores were highly correlated with total scores from the three non-verbal tests, although the correlations were higher for raw scores, suggesting they may lead to better understanding of within group differences and what individuals with ID can do at the time of assessment. All participants attempted more questions on the non-verbal tests than the verbal. A preliminary analysis showed that adolescents with ID without ASD (n = 15) achieved higher scores overall than those presenting with ID+ASD (n = 8). Our findings support the view that short non-verbal tests are more likely to give a similar IQ result as obtained from the WISC-IV. In terms of the time to administer and the stress for participants, they are more appropriate for assessing adolescents with ID. PMID:27242597

Comparison of Measures of Ability in Adolescents with Intellectual Disability.

PubMed

Mungkhetklang, Chantanee; Crewther, Sheila G; Bavin, Edith L; Goharpey, Nahal; Parsons, Carl

2016-01-01

Finding the most appropriate intelligence test for adolescents with Intellectual Disability (ID) is challenging given their limited language, attention, perceptual, and motor skills and ability to stay on task. The study compared performance of 23 adolescents with ID on the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV), one of the most widely used intelligence tests, and three non-verbal IQ tests, the Raven's Colored Progressive Matrices (RCPM), the Test of Non-verbal Intelligence-Fourth Edition and the Wechsler Non-verbal test of Ability. Results showed that the WISC-IV Full Scale IQ raw and scaled scores were highly correlated with total scores from the three non-verbal tests, although the correlations were higher for raw scores, suggesting they may lead to better understanding of within group differences and what individuals with ID can do at the time of assessment. All participants attempted more questions on the non-verbal tests than the verbal. A preliminary analysis showed that adolescents with ID without ASD (n = 15) achieved higher scores overall than those presenting with ID+ASD (n = 8). Our findings support the view that short non-verbal tests are more likely to give a similar IQ result as obtained from the WISC-IV. In terms of the time to administer and the stress for participants, they are more appropriate for assessing adolescents with ID.

Almost commuting self-adjoint matrices: The real and self-dual cases

NASA Astrophysics Data System (ADS)

Loring, Terry A.; Sørensen, Adam P. W.

2016-08-01

We show that a pair of almost commuting self-adjoint, symmetric matrices is close to a pair of commuting self-adjoint, symmetric matrices (in a uniform way). Moreover, we prove that the same holds with self-dual in place of symmetric and also for paths of self-adjoint matrices. Since a symmetric, self-adjoint matrix is real, we get a real version of Huaxin Lin’s famous theorem on almost commuting matrices. Similarly, the self-dual case gives a version for matrices over the quaternions. To prove these results, we develop a theory of semiprojectivity for real C*-algebras and also examine various definitions of low-rank for real C*-algebras.

Decision Matrices: Tools to Enhance Middle School Engineering Instruction

ERIC Educational Resources Information Center

Gonczi, Amanda L.; Bergman, Brenda G.; Huntoon, Jackie; Allen, Robin; McIntyre, Barb; Turner, Sheri; Davis, Jen; Handler, Rob

2017-01-01

Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an…

19 CFR 10.90 - Master records and metal matrices.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301, containing...

19 CFR 10.90 - Master records and metal matrices.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301, containing...

19 CFR 10.90 - Master records and metal matrices.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301, containing...

19 CFR 10.90 - Master records and metal matrices.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301, containing...

19 CFR 10.90 - Master records and metal matrices.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301, containing...

Geomagnetic modeling by optimal recursive filtering

NASA Technical Reports Server (NTRS)

Gibbs, B. P.; Estes, R. H.

1981-01-01

The results of a preliminary study to determine the feasibility of using Kalman filter techniques for geomagnetic field modeling are given. Specifically, five separate field models were computed using observatory annual means, satellite, survey and airborne data for the years 1950 to 1976. Each of the individual field models used approximately five years of data. These five models were combined using a recursive information filter (a Kalman filter written in terms of information matrices rather than covariance matrices.) The resulting estimate of the geomagnetic field and its secular variation was propogated four years past the data to the time of the MAGSAT data. The accuracy with which this field model matched the MAGSAT data was evaluated by comparisons with predictions from other pre-MAGSAT field models. The field estimate obtained by recursive estimation was found to be superior to all other models.

Rotational 3D printing of damage-tolerant composites with programmable mechanics

PubMed Central

Raney, Jordan R.; Compton, Brett G.; Ober, Thomas J.; Shea, Kristina; Lewis, Jennifer A.

2018-01-01

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber–epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. PMID:29348206

Crosslinked type II collagen matrices: preparation, characterization, and potential for cartilage engineering.

PubMed

Pieper, J S; van der Kraan, P M; Hafmans, T; Kamp, J; Buma, P; van Susante, J L C; van den Berg, W B; Veerkamp, J H; van Kuppevelt, T H

2002-08-01

The limited intrinsic repair capacity of articular cartilage has stimulated continuing efforts to develop tissue engineered analogues. Matrices composed of type II collagen and chondroitin sulfate (CS), the major constituents of hyaline cartilage, may create an appropriate environment for the generation of cartilage-like tissue. In this study, we prepared, characterized, and evaluated type 11 collagen matrices with and without CS. Type II collagen matrices were prepared using purified, pepsin-treated, type II collagen. Techniques applied to prepare type I collagen matrices were found unsuitable for type II collagen. Crosslinking of collagen and covalent attachment of CS was performed using 1-ethyl-3-(3-dimethyl aminopropyl)carbodiimide. Porous matrices were prepared by freezing and lyophilization, and their physico-chemical characteristics (degree of crosslinking, denaturing temperature, collagenase-resistance, amount of CS incorporated) established. Matrices were evaluated for their capacity to sustain chondrocyte proliferation and differentiation in vitro. After 7 d of culture, chondrocytes were mainly located at the periphery of the matrices. In contrast to type I collagen, type II collagen supported the distribution of cells throughout the matrix. After 14 d of culture, matrices were surfaced with a cartilagenous-like layer, and occasionally clusters of chondrocytes were present inside the matrix. Chondrocytes proliferated and differentiated as indicated by biochemical analyses, ultrastructural observations, and reverse transcriptase PCR for collagen types I, II and X. No major differences were observed with respect to the presence or absence of CS in the matrices.

Resources | Office of Cancer Genomics

Cancer.gov

OCG provides a variety of scientific and educational resources for both cancer researchers and members of the general public. These resources are divided into the following types: OCG-Supported Resources: Tools, databases, and reagents generated by initiated and completed OCG programs for researchers, educators, and students. (Note: Databases for current OCG programs are available through program-specific data matrices)

Land manager's guide to the birds of the South

Treesearch

Paul B. Hamel

1992-01-01

Forested habitats and their suitability for bird species in the South are described. For each species, a summary of biological knowledge regarding status, distribution, and habitat requirements is presented. General and specific habitat requirements for each species are given in the form of habitat relationship matrices. This information is designed to be used by land...

Matrices. New Topics for Secondary School Mathematics: Materials and Software.

ERIC Educational Resources Information Center

North Carolina School of Science and Mathematics. Dept. of Mathematics and Computer Science.

This material on matrices is part of "Introduction to College Mathematics" (ICM), designed to prepare high school students who have students who have completed algebra II for the variety of mathematics they will encounter in college and beyond. The concept goals of this unit are to use matrices to model real-world phenomena, to use matrices as…

Generalized matrix summability of a conjugate derived Fourier series.

PubMed

Mursaleen, M; Alotaibi, Abdullah

2017-01-01

The study of infinite matrices is important in the theory of summability and in approximation. In particular, Toeplitz matrices or regular matrices and almost regular matrices have been very useful in this context. In this paper, we propose to use a more general matrix method to obtain necessary and sufficient conditions to sum the conjugate derived Fourier series.

Rhotrix Vector Spaces

ERIC Educational Resources Information Center

Aminu, Abdulhadi

2010-01-01

By rhotrix we understand an object that lies in some way between (n x n)-dimensional matrices and (2n - 1) x (2n - 1)-dimensional matrices. Representation of vectors in rhotrices is different from the representation of vectors in matrices. A number of vector spaces in matrices and their properties are known. On the other hand, little seems to be…

Field matric potential sensor

DOEpatents

Hubbell, Joel M.; Sisson, James B.

2001-01-01

A method of determining matric potential of a sample, the method comprising placing the sample in a container, the container having an opening; and contacting the sample with a tensiometer via the opening. An apparatus for determining matric potential of a sample, the apparatus comprising a housing configured to receive a sample; a portable matric potential sensing device extending into the housing and having a porous member; and a wall closing the housing to insulate the sample and at least a portion of the matric potential sensing device including the porous member.

Small diameter electrospun silk fibroin vascular grafts: Mechanical properties, in vitro biodegradability, and in vivo biocompatibility.

PubMed

Catto, Valentina; Farè, Silvia; Cattaneo, Irene; Figliuzzi, Marina; Alessandrino, Antonio; Freddi, Giuliano; Remuzzi, Andrea; Tanzi, Maria Cristina

2015-09-01

To overcome the drawbacks of autologous grafts currently used in clinical practice, vascular tissue engineering represents an alternative approach for the replacement of small diameter blood vessels. In the present work, the production and characterization of small diameter tubular matrices (inner diameter (ID)=4.5 and 1.5 mm), obtained by electrospinning (ES) of Bombyx mori silk fibroin (SF), have been considered. ES-SF tubular scaffolds with ID=1.5 mm are original, and can be used as vascular grafts in pediatrics or in hand microsurgery. Axial and circumferential tensile tests on ES-SF tubes showed appropriate properties for the specific application. The burst pressure and the compliance of ES-SF tubes were estimated using the Laplace's law. Specifically, the estimated burst pressure was higher than the physiological pressures and the estimated compliance was similar or higher than that of native rat aorta and Goretex® prosthesis. Enzymatic in vitro degradation tests demonstrated a decrease of order and crystallinity of the SF outer surface as a consequence of the enzyme activity. The in vitro cytocompatibility of the ES-SF tubes was confirmed by the adhesion and growth of primary porcine smooth muscle cells. The in vivo subcutaneous implant into the rat dorsal tissue indicated that ES-SF matrices caused a mild host reaction. Thus, the results of this investigation, in which comprehensive morphological and mechanical aspects, in vitro degradation and in vitro and in vivo biocompatibility were considered, indicate the potential suitability of these ES-SF tubular matrices as scaffolds for the regeneration of small diameter blood vessels. Copyright © 2015 Elsevier B.V. All rights reserved.

The construction of next-generation matrices for compartmental epidemic models.

PubMed

Diekmann, O; Heesterbeek, J A P; Roberts, M G

2010-06-06

The basic reproduction number (0) is arguably the most important quantity in infectious disease epidemiology. The next-generation matrix (NGM) is the natural basis for the definition and calculation of (0) where finitely many different categories of individuals are recognized. We clear up confusion that has been around in the literature concerning the construction of this matrix, specifically for the most frequently used so-called compartmental models. We present a detailed easy recipe for the construction of the NGM from basic ingredients derived directly from the specifications of the model. We show that two related matrices exist which we define to be the NGM with large domain and the NGM with small domain. The three matrices together reflect the range of possibilities encountered in the literature for the characterization of (0). We show how they are connected and how their construction follows from the basic model ingredients, and establish that they have the same non-zero eigenvalues, the largest of which is the basic reproduction number (0). Although we present formal recipes based on linear algebra, we encourage the construction of the NGM by way of direct epidemiological reasoning, using the clear interpretation of the elements of the NGM and of the model ingredients. We present a selection of examples as a practical guide to our methods. In the appendix we present an elementary but complete proof that (0) defined as the dominant eigenvalue of the NGM for compartmental systems and the Malthusian parameter r, the real-time exponential growth rate in the early phase of an outbreak, are connected by the properties that (0) > 1 if and only if r > 0, and (0) = 1 if and only if r = 0.

The construction of next-generation matrices for compartmental epidemic models

PubMed Central

Diekmann, O.; Heesterbeek, J. A. P.; Roberts, M. G.

2010-01-01

The basic reproduction number ℛ0 is arguably the most important quantity in infectious disease epidemiology. The next-generation matrix (NGM) is the natural basis for the definition and calculation of ℛ0 where finitely many different categories of individuals are recognized. We clear up confusion that has been around in the literature concerning the construction of this matrix, specifically for the most frequently used so-called compartmental models. We present a detailed easy recipe for the construction of the NGM from basic ingredients derived directly from the specifications of the model. We show that two related matrices exist which we define to be the NGM with large domain and the NGM with small domain. The three matrices together reflect the range of possibilities encountered in the literature for the characterization of ℛ0. We show how they are connected and how their construction follows from the basic model ingredients, and establish that they have the same non-zero eigenvalues, the largest of which is the basic reproduction number ℛ0. Although we present formal recipes based on linear algebra, we encourage the construction of the NGM by way of direct epidemiological reasoning, using the clear interpretation of the elements of the NGM and of the model ingredients. We present a selection of examples as a practical guide to our methods. In the appendix we present an elementary but complete proof that ℛ0 defined as the dominant eigenvalue of the NGM for compartmental systems and the Malthusian parameter r, the real-time exponential growth rate in the early phase of an outbreak, are connected by the properties that ℛ0 > 1 if and only if r > 0, and ℛ0 = 1 if and only if r = 0. PMID:19892718

Exploring visuospatial abilities and their contribution to constructional abilities and nonverbal intelligence.

PubMed

Trojano, Luigi; Siciliano, Mattia; Cristinzio, Chiara; Grossi, Dario

2018-01-01

The present study aimed at exploring relationships among the visuospatial tasks included in the Battery for Visuospatial Abilities (BVA), and at assessing the relative contribution of different facets of visuospatial processing on tests tapping constructional abilities and nonverbal abstract reasoning. One hundred forty-four healthy subjects with a normal score on Mini Mental State Examination completed the BVA plus Raven's Coloured Progressive Matrices and Constructional Apraxia test. We used Principal Axis Factoring and Parallel Analysis to investigate relationships among the BVA visuospatial tasks, and performed regression analyses to assess the visuospatial contribution to constructional abilities and nonverbal abstract reasoning. Principal Axis Factoring and Parallel Analysis revealed two eigenvalues exceeding 1, accounting for about 60% of the variance. A 2-factor model provided the best fit. Factor 1 included sub-tests exploring "complex" visuospatial skills, whereas Factor 2 included two subtests tapping "simple" visuospatial skills. Regression analyses revealed that both Factor 1 and Factor 2 significantly affected performance on Raven's Coloured Progressive Matrices, whereas only the Factor 1 affected performance on Constructional Apraxia test. Our results supported functional segregation proposed by De Renzi, suggesting clinical caution to utilize a single test to assess visuospatial domain, and qualified the visuospatial contribution in drawing and non-verbal intelligence test.

Schizophrenia, smoking status, and performance on the matrics Cognitive Consensus Battery.

PubMed

Reed, Alexandra C; Harris, Josette G; Olincy, Ann

2016-12-30

Cognitive deficits and high rates of nicotine dependence are consistently documented in the schizophrenia literature. However, there is currently no consensus about how regular smoking influences cognition in schizophrenia or which cognitive domains are most affected by chronic smoking. Previous studies have also failed to disambiguate the effects of chronic nicotine from those of acute exposure. The current study uses a novel approach to testing nicotine addicted patients at a time-point between acute enhancement and withdrawal and implements the MATRICS Cognitive Consensus Battery (MCCB) to compare the overall cognitive performance of regular smokers (n=40) and nonsmokers (n=36) with schizophrenia. Controlling for age, gender, and education, smokers with schizophrenia were significantly more impaired on a visual learning task, the Brief Visuospatial Memory Test-Revised (BVMT-R), than their nonsmoking peers. Among smokers, smoking behavior (i.e., exhaled carbon monoxide levels of smokers) predicted BVMT-R T score; greater smoking was associated with more impaired visual learning. Negative symptom severity was not predictive of greater visual learning deficits in smokers or nonsmokers. Future longitudinal research will be required to determine if there is a dose-response relationship between chronic nicotine and visual learning impairment in patients at various stages of psychotic illness. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein⁻Protein Interaction Network.

PubMed

Cao, Buwen; Deng, Shuguang; Qin, Hua; Ding, Pingjian; Chen, Shaopeng; Li, Guanghui

2018-06-15

High-throughput technology has generated large-scale protein interaction data, which is crucial in our understanding of biological organisms. Many complex identification algorithms have been developed to determine protein complexes. However, these methods are only suitable for dense protein interaction networks, because their capabilities decrease rapidly when applied to sparse protein⁻protein interaction (PPI) networks. In this study, based on penalized matrix decomposition ( PMD ), a novel method of penalized matrix decomposition for the identification of protein complexes (i.e., PMD pc ) was developed to detect protein complexes in the human protein interaction network. This method mainly consists of three steps. First, the adjacent matrix of the protein interaction network is normalized. Second, the normalized matrix is decomposed into three factor matrices. The PMD pc method can detect protein complexes in sparse PPI networks by imposing appropriate constraints on factor matrices. Finally, the results of our method are compared with those of other methods in human PPI network. Experimental results show that our method can not only outperform classical algorithms, such as CFinder, ClusterONE, RRW, HC-PIN, and PCE-FR, but can also achieve an ideal overall performance in terms of a composite score consisting of F-measure, accuracy (ACC), and the maximum matching ratio (MMR).

Relationship between Intelligence Quotient and Musical Ability in Children with Cochlear Implantation

PubMed Central

Soleimanifar, Simin; Jafari, Zahra; Motasaddi Zarandy, Masoud; Asadi, Houman; Haghani, Hamid

2016-01-01

Introduction: Children with cochlear implants (CIs) may experience few opportunities for positive musical experiences, and musical perception is therefore often not sufficiently developed. This paper investigates and discusses the relationship between intelligence quotient (IQ) and musical ability in children with CIs compared with children with normal hearing. Materials and Methods: This was a comparative analytical study conducted in 48 children with unilateral CI and 48 normal-hearing children, 6–8 years of age, with ‘normal’ IQ and no formal music training. The average IQ score in the experimental and control groups were 105.41 and 106.31, respectively. No statistically significant differences were detected between Raven’s IQ scores in both groups. Data were collected by administering Raven's Colored Progressive Matrices IQ Tests and the Montreal Battery of Evaluation of Musical Abilities (MBEMA) Test, consisting of scale, contour, interval, rhythm, and memory sections. Results: Mean total MBEMA score in the experimental and control groups was 58.93 and 72.16 (out of 100), respectively. Significant differences were evident between scores of children with CIs in comparison with their normal-hearing peers (P≤0.001). A remarkable direct correlation between IQ and musical scores in both the control (r≥0.38) and experimental (r≥0.37) groups was observed. Conclusion: IQ has a noticeable effect on music processing and facilitates the perception of various musical elements. With regard to the mutual relationship between IQ and musical skills, this study illustrates the advantage of determining music perception scores and highlights the importance of appropriate musical intervention in order to enhance auditory neural plasticity, especially in children with cochlear implantation. PMID:27738611

Evaluation of the Efficacy, Safety, and Tolerability of BI 409306, a Novel Phosphodiesterase 9 Inhibitor, in Cognitive Impairment in Schizophrenia: A Randomized, Double-Blind, Placebo-Controlled, Phase II Trial.

PubMed

Brown, David; Nakagome, Kazuyuki; Cordes, Joachim; Brenner, Ronald; Gründer, Gerhard; Keefe, Richard S E; Riesenberg, Robert; Walling, David P; Daniels, Kristen; Wang, Lara; McGinniss, Jennifer; Sand, Michael

2018-05-01

Patients with cognitive impairment associated with schizophrenia may benefit from treatments targeting dysfunctional glutamatergic neurotransmission. BI 409306, a potent and selective phosphodiesterase 9 inhibitor, was assessed in patients with schizophrenia using a learn-and-confirm adaptive trial design. This double-blind, parallel-group trial randomized patients 2:1:1:1:1 to once-daily placebo or BI 409306 (10, 25, 50, or 100 mg) for 12 weeks. Stage 1 (learn) assessed change from baseline in Cambridge Neuropsychological Test Automated Battery (CANTAB) scores (week 12) to identify ≥1 meaningful endpoints for stage 2 (confirm). If no domains showed efficacy, change from baseline in Measurements and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) Consensus Cognitive Battery (MCCB) composite scores (week 12) was the primary endpoint. The key secondary endpoint was change from baseline in Schizophrenia Cognition Rating Scale (SCoRS) total score. Safety was monitored. Five hundred eighteen patients were randomized. In stage 1, CANTAB did not differentiate between BI 409306 and placebo (n = 120), so the primary endpoint of change from baseline in MCCB composite score was analyzed in 450 patients in stage 2. There was no significant difference between BI 409306 (1.2-2.8) and placebo (2.5) in MCCB composite score change. BI 409306 did not significantly improve change from baseline in SCoRS total score (-3.1 to -2.0) vs placebo (-2.5). Adverse events were dose-dependent, increasing from 33.3% (10 mg) to 53.5% (100 mg), vs 36.4% for placebo. The primary endpoint of cognitive function improvement was not met. BI 409306 was well-tolerated, with an acceptable safety profile.

THE COMPARISON OF INTELLIGENCE QUOTIENTS OF ATOPIC AND NONATOPIC CHILDREN IN IBADAN, NIGERIA

PubMed Central

Daramola, O O M; Ayoola, O O; Ogunbiyi, A O

2010-01-01

Background: Atopy-related illnesses such as atopic dermatitis and asthma are chronic illnesses, and children suffering from such illnesses are subjected to frequent absenteeism from school. Studies have shown that the performance of children with asthma was comparable to their healthy counterparts despite their absenteeism at school, in contrast to findings in other chronic illnesses like epilepsy. Aim: In the present study, we investigated the association between atopy and intelligence quotient (IQ) scores in a group of Nigerian children in Ibadan, a city in southwestern Nigeria. Materials and Methods: This is a cross-sectional study of children in an urban elementary school. Questionnaires to ascertain the presence of atopy-associated conditions such as hay fever, atopic dermatitis, asthma, allergic rhinitis, and allergic conjunctivitis were administered to the parents of 128 pupils in the 3rd to 6th grades of elementary school. Based on the responses to the questionnaire, pupils were categorized as being atopic and nonatopic. All the pupils underwent the Standard Progressive Matrices IQ test. The IQ scores were then compared among these two groups of children. Results: Out of the children studied, 26.6% were found to have atopy and after adjusting for factors such as age and sex, the IQ scores in this atopic group were not found to be statistically different from the scores in the nonatopic group (r = 2.122872, P = 0.009). Conclusion: IQ scores were not statistically significantly different for children with and without atopy. Thus, the presence of atopy does not appear to be associated with low IQ scores and hence, may not be related to poor school performance. PMID:21063510

Characterization of good teleoperators - What aptitudes, interests, and experience correlate with measures of teleoperator performance

NASA Technical Reports Server (NTRS)

Yorchak, J. P.; Hartley, C. S.; Hinman, E.

1985-01-01

The use of aptitude tests and questionnaries to evaluate an individuals aptitude for teleoperation is studied. The Raven Progressive Matrices Test and Differential Aptitude Tests, and a 16-item questionnaire for assessing the subject's interests, academic background, and previous experience are described. The Proto-Flight Manipulator Arm, cameras, console, hand controller, and task board utilized by the 17 engineers are examined. The correlation between aptitude scores and questionnaire responses, and operator performance is investigated. Multiple regression data reveal that the eight predictor variables are not individually significant for evaluating operator performance; however, the complete test battery is applicable for predicting 49 percent of subject variance on the criterion task.

Contentious relationships in phylogenomic studies can be driven by a handful of genes

PubMed Central

Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis

2017-01-01

Phylogenomic studies have resolved countless branches of the tree of life (ToL), but remain strongly contradictory on certain, contentious relationships. Here, we employ a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal, and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. Finally, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, where examination of the distributions of gene-wise and site-wise phylogenetic signal across 8 data matrices consistently supports ctenophores as sister group to all other metazoans. PMID:28812701

Inferring Causalities in Landscape Genetics: An Extension of Wright's Causal Modeling to Distance Matrices.

PubMed

Fourtune, Lisa; Prunier, Jérôme G; Paz-Vinas, Ivan; Loot, Géraldine; Veyssière, Charlotte; Blanchet, Simon

2018-04-01

Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods-that is, maximum-likelihood path analysis and the directional separation test-by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.

A Nanostructured Matrices Assessment to Study Drug Distribution in Solid Tumor Tissues by Mass Spectrometry Imaging

PubMed Central

Giordano, Silvia; Pifferi, Valentina; Morosi, Lavinia; Morelli, Melinda; Falciola, Luigi; Cappelletti, Giuseppe; Visentin, Sonja; Licandro, Simonetta A.; Frapolli, Roberta; Zucchetti, Massimo; Pastorelli, Roberta; Brunelli, Laura; D’Incalci, Maurizio; Davoli, Enrico

2017-01-01

The imaging of drugs inside tissues is pivotal in oncology to assess whether a drug reaches all cells in an adequate enough concentration to eradicate the tumor. Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) is one of the most promising imaging techniques that enables the simultaneous visualization of multiple compounds inside tissues. The choice of a suitable matrix constitutes a critical aspect during the development of a MALDI-MSI protocol since the matrix ionization efficiency changes depending on the analyte structure and its physico-chemical properties. The objective of this study is the improvement of the MALDI-MSI technique in the field of pharmacology; developing specifically designed nanostructured surfaces that allow the imaging of different drugs with high sensitivity and reproducibility. Among several nanomaterials, we tested the behavior of gold and titanium nanoparticles, and halloysites and carbon nanotubes as possible matrices. All nanomaterials were firstly screened by co-spotting them with drugs on a MALDI plate, evaluating the drug signal intensity and the signal-to-noise ratio. The best performing matrices were tested on control tumor slices, and were spotted with drugs to check the ion suppression effect of the biological matrix. Finally; the best nanomaterials were employed in a preliminary drug distribution study inside tumors from treated mice. PMID:28336905

A Robust Adaptive Unscented Kalman Filter for Nonlinear Estimation with Uncertain Noise Covariance.

PubMed

Zheng, Binqi; Fu, Pengcheng; Li, Baoqing; Yuan, Xiaobing

2018-03-07

The Unscented Kalman filter (UKF) may suffer from performance degradation and even divergence while mismatch between the noise distribution assumed as a priori by users and the actual ones in a real nonlinear system. To resolve this problem, this paper proposes a robust adaptive UKF (RAUKF) to improve the accuracy and robustness of state estimation with uncertain noise covariance. More specifically, at each timestep, a standard UKF will be implemented first to obtain the state estimations using the new acquired measurement data. Then an online fault-detection mechanism is adopted to judge if it is necessary to update current noise covariance. If necessary, innovation-based method and residual-based method are used to calculate the estimations of current noise covariance of process and measurement, respectively. By utilizing a weighting factor, the filter will combine the last noise covariance matrices with the estimations as the new noise covariance matrices. Finally, the state estimations will be corrected according to the new noise covariance matrices and previous state estimations. Compared with the standard UKF and other adaptive UKF algorithms, RAUKF converges faster to the actual noise covariance and thus achieves a better performance in terms of robustness, accuracy, and computation for nonlinear estimation with uncertain noise covariance, which is demonstrated by the simulation results.

A Robust Adaptive Unscented Kalman Filter for Nonlinear Estimation with Uncertain Noise Covariance

PubMed Central

Zheng, Binqi; Yuan, Xiaobing

2018-01-01

The Unscented Kalman filter (UKF) may suffer from performance degradation and even divergence while mismatch between the noise distribution assumed as a priori by users and the actual ones in a real nonlinear system. To resolve this problem, this paper proposes a robust adaptive UKF (RAUKF) to improve the accuracy and robustness of state estimation with uncertain noise covariance. More specifically, at each timestep, a standard UKF will be implemented first to obtain the state estimations using the new acquired measurement data. Then an online fault-detection mechanism is adopted to judge if it is necessary to update current noise covariance. If necessary, innovation-based method and residual-based method are used to calculate the estimations of current noise covariance of process and measurement, respectively. By utilizing a weighting factor, the filter will combine the last noise covariance matrices with the estimations as the new noise covariance matrices. Finally, the state estimations will be corrected according to the new noise covariance matrices and previous state estimations. Compared with the standard UKF and other adaptive UKF algorithms, RAUKF converges faster to the actual noise covariance and thus achieves a better performance in terms of robustness, accuracy, and computation for nonlinear estimation with uncertain noise covariance, which is demonstrated by the simulation results. PMID:29518960

Genipin crosslinking reduced the immunogenicity of xenogeneic decellularized porcine whole-liver matrices through regulation of immune cell proliferation and polarization

NASA Astrophysics Data System (ADS)

Wang, Yujia; Bao, Ji; Wu, Xiujuan; Wu, Qiong; Li, Yi; Zhou, Yongjie; Li, Li; Bu, Hong

2016-04-01

Decellularized xenogeneic whole-liver matrices are plausible biomedical materials for the bioengineering of liver transplantation. A common method to reduce the inflammatory potential of xenogeneic matrices is crosslinking. Nevertheless, a comprehensive analysis of the immunogenic features of cross-linked decellularized tissue is still lacking. We aimed to reduce the immunogenicity of decellularized porcine whole-liver matrix through crosslinking with glutaraldehyde or genipin, a new natural agent, and investigated the mechanism of the immune-mediated responses. The histologic assessment of the host’s immune reaction activated in response to these scaffolds, as well as the M1/M2 phenotypic polarization profile of macrophages, was studied in vivo. The genipin-fixed scaffold elicited a predominantly M2 phenotype response, while the glutaraldehyde-fixed scaffold resulted in disrupted host tissue remodeling and a mixed macrophage polarization profile. The specific subsets of immune cells involved in the responses to the scaffolds were identified in vitro. Crosslinking alleviated the host response by reducing the proliferation of lymphocytes and their subsets, accompanied by a decreased release of both Th1 and Th2 cytokines. Therefore, we conclude that the natural genipin crosslinking could lower the immunogenic potential of xenogeneic decellularized whole-liver scaffolds.

Optimum modulation and demodulation matrices for solar polarimetry.

PubMed

del Toro Iniesta, J C; Collados, M

2000-04-01

Both temporal and/or spatial modulation are mandatory in current solar polarimetry [Appl. Opt. 24, 3893 (1985); 26, 3838 (1987)]. The modulating and demodulating processes are mathematically described by matrices O and D, respectively, on whose structure the accuracy of Stokes parameter measurements depend. We demonstrate, based on the definition of polarimetric efficiency [Instituto de Astrofísica de Canarias Internal Report (1994); ASP Conf. Ser. 184, 3 (1999)], that the maximum efficiencies of an ideal polarimeter are unity for Stokes I and for (Q(2) + U(2) + V(2))(1/2) and that this occurs if and only if O(T)O is diagonal; given a general (possibly nonideal) modulation matrix O, the optimum demodulation matrix turns out to be D = (O(T)O)(-1)O(T); and the maximum efficiencies in the nonideal case are given by the rms value of the column elements of matrix O and are reached by modulation matrices such that O(T)O is diagonal. From these analytical results we distill two recipes useful in the practical design of polarimeters. Their usefulness is illustrated by discussing cases of currently available solar polarimeters. Although specifically devoted to solar polarimetry, the results here may be applied in practically all other branches of science for which polarimetric measurements are needed.

Pharmacological Interventions for the MATRICS Cognitive Domains in Schizophrenia: What’s the Evidence?

PubMed Central

Vingerhoets, Wilhelmina A. M.; Bloemen, Oswald J. N.; Bakker, Geor; van Amelsvoort, Therese A. M. J.

2013-01-01

Schizophrenia is a disabling, chronic psychiatric disorder with a prevalence rate of 0.5–1% in the general population. Symptoms include positive (e.g., delusions, hallucinations), negative (e.g., blunted affect, social withdrawal), as well as cognitive symptoms (e.g., memory and attention problems). Although 75–85% of patients with schizophrenia report cognitive impairments, the underlying neuropharmacological mechanisms are not well understood and currently no effective treatment is available for these impairments. This has led to the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) initiative, which established seven cognitive domains that are fundamentally impaired in schizophrenia. These domains include verbal learning and memory, visual learning and memory, working memory, attention and vigilance, processing speed, reasoning and problem solving, and social cognition. Recently, a growing number of studies have been conducted trying to identify the underlying neuropharmacological mechanisms of cognitive impairments in schizophrenia patients. Specific cognitive impairments seem to arise from different underlying neuropharmacological mechanisms. However, most review articles describe cognition in general and an overview of the mechanisms involved in these seven separate cognitive domains is currently lacking. Therefore, we reviewed the underlying neuropharmacological mechanisms focusing on the domains as established by the MATRICS initiative which are considered most crucial in schizophrenia. PMID:24363646

Nanoparticles prepared by the sol gel method and their use in the formation of nanocomposites with polypropylene

NASA Astrophysics Data System (ADS)

Moncada, E.; Quijada, R.; Retuert, J.

2007-08-01

Hybrid layered aluminosilicate nanoparticles (HLNP) containing octadecylamine (ODA) as the organic part, and silica nanoparticles with spherical morphology containing ODA (HSNP) or without ODA (SNP) were prepared by the sol-gel method and used for the formation of nanocomposites with polypropylene. The polypropylene matrices, of different molecular weight and polydispersity, were prepared using polymers obtained via Ziegler-Natta or metallocene catalysts. A strong influence of the morphology and the presence of ODA on the surface of the nanoparticles was found on the formation and characteristics of the nanocomposites. The mechanical properties and thermal stability of these materials were determined and compared with those of nanocomposites prepared with 2:1 phylosilicate clays such as montmorillonite and hectorite in similar polymer matrices. X-ray diffraction, transmission electron microscopy, and the study of mechanical properties showed that the use of HLNP allows nanocomposites with considerably improved mechanical properties to be obtained, compared with nanocomposites prepared with exfoliated clays. In the case of nanocomposites prepared with spherical particles functionalized with ODA (HSNP), materials with high specific strength combined with high elongation before rupture were obtained. The thermal stabilization of polypropylene matrices containing the synthesized nanoparticles (HLNP, HSNP or SNP) occurs about 50 °C higher than that attained with clays.

Electrospun Zein/PCL Fibrous Matrices Release Tetracycline in a Controlled Manner, Killing Staphylococcus aureus Both in Biofilms and Ex Vivo on Pig Skin, and are Compatible with Human Skin Cells.

PubMed

Alhusein, Nour; Blagbrough, Ian S; Beeton, Michael L; Bolhuis, Albert; De Bank, Paul A

2016-01-01

To investigate the destruction of clinically-relevant bacteria within biofilms via the sustained release of the antibiotic tetracycline from zein-based electrospun polymeric fibrous matrices and to demonstrate the compatibility of such wound dressing matrices with human skin cells. Zein/PCL triple layered fibrous dressings with entrapped tetracycline were electrospun. The successful entrapment of tetracycline in these dressings was validated. The successful release of bioactive tetracycline, the destruction of preformed biofilms, and the viability of fibroblast (FEK4) cells were investigated. The sustained release of tetracycline from these matrices led to the efficient destruction of preformed biofilms from Staphylococcus aureus MRSA252 in vitro, and of MRSA252 and ATCC 25923 bacteria in an ex vivo pig skin model using 1 × 1 cm square matrices containing tetracycline (30 μg). Human FEK4 cells grew normally in the presence of these matrices. The ability of the zein-based matrices to destroy bacteria within increasingly complex in vitro biofilm models was clearly established. An ex vivo pig skin assay showed that these matrices, with entrapped tetracycline, efficiently kill bacteria and this, combined with their compatibility with a human skin cell line suggest these matrices are well suited for applications in wound healing and infection control.

Novel value-added uses for sweet potato juice and flour in polyphenol- and protein-enriched functional food ingredients.

PubMed

Grace, Mary H; Truong, An N; Truong, Van-Den; Raskin, Ilya; Lila, Mary Ann

2015-09-01

Blackcurrant, blueberry, and muscadine grape juices were efficiently sorbed, concentrated, and stabilized into dry granular ingredient matrices which combined anti-inflammatory and antioxidant fruit polyphenols with sweet potato functional constituents (carotenoids, vitamins, polyphenols, fibers). Total phenolics were highest in blackcurrant-orange sweet potato ingredient matrices (34.03 mg/g), and lowest in muscadine grape-yellow sweet potato matrices (10.56 mg/g). Similarly, anthocyanins were most concentrated in blackcurrant-fortified orange and yellow sweet potato matrices (5.40 and 6.54 mg/g, respectively). Alternatively, other protein-rich edible matrices (defatted soy flour, light roasted peanut flour, and rice protein concentrate) efficiently captured polyphenols (6.09-9.46 mg/g) and anthocyanins (0.77-1.27 mg/g) from purple-fleshed sweet potato juice, with comparable efficiency. Antioxidant activity correlated well with total phenolic content. All formulated ingredient matrices stabilized and preserved polyphenols for up to 24 weeks, even when stored at 37°C. Complexation with juice-derived polyphenols did not significantly alter protein or carbohydrate profiles of the matrices. Sensory evaluation of the ingredient matrices suggested potential uses for a wide range of functional food products.

Inference for High-dimensional Differential Correlation Matrices.

PubMed

Cai, T Tony; Zhang, Anru

2016-01-01

Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical guarantees are given. Minimax rate of convergence is established and the proposed estimator is shown to be adaptively rate-optimal over collections of paired correlation matrices with approximately sparse differences. Simulation results show that the procedure significantly outperforms two other natural methods that are based on separate estimation of the individual correlation matrices. The procedure is also illustrated through an analysis of a breast cancer dataset, which provides evidence at the gene co-expression level that several genes, of which a subset has been previously verified, are associated with the breast cancer. Hypothesis testing on the differential correlation matrices is also considered. A test, which is particularly well suited for testing against sparse alternatives, is introduced. In addition, other related problems, including estimation of a single sparse correlation matrix, estimation of the differential covariance matrices, and estimation of the differential cross-correlation matrices, are also discussed.

On Fluctuations of Eigenvalues of Random Band Matrices

NASA Astrophysics Data System (ADS)

Shcherbina, M.

2015-10-01

We consider the fluctuations of linear eigenvalue statistics of random band matrices whose entries have the form with i.i.d. possessing the th moment, where the function u has a finite support , so that M has only nonzero diagonals. The parameter b (called the bandwidth) is assumed to grow with n in a way such that . Without any additional assumptions on the growth of b we prove CLT for linear eigenvalue statistics for a rather wide class of test functions. Thus we improve and generalize the results of the previous papers (Jana et al., arXiv:1412.2445; Li et al. Random Matrices 2:04, 2013), where CLT was proven under the assumption . Moreover, we develop a method which allows to prove automatically the CLT for linear eigenvalue statistics of the smooth test functions for almost all classical models of random matrix theory: deformed Wigner and sample covariance matrices, sparse matrices, diluted random matrices, matrices with heavy tales etc.

An Approximate Approach to Automatic Kernel Selection.

PubMed

Ding, Lizhong; Liao, Shizhong

2016-02-02

Kernel selection is a fundamental problem of kernel-based learning algorithms. In this paper, we propose an approximate approach to automatic kernel selection for regression from the perspective of kernel matrix approximation. We first introduce multilevel circulant matrices into automatic kernel selection, and develop two approximate kernel selection algorithms by exploiting the computational virtues of multilevel circulant matrices. The complexity of the proposed algorithms is quasi-linear in the number of data points. Then, we prove an approximation error bound to measure the effect of the approximation in kernel matrices by multilevel circulant matrices on the hypothesis and further show that the approximate hypothesis produced with multilevel circulant matrices converges to the accurate hypothesis produced with kernel matrices. Experimental evaluations on benchmark datasets demonstrate the effectiveness of approximate kernel selection.

E-Spun Composite Fibers of Collagen and Dragline Silk Protein: Fiber Mechanics, Biocompatibility, and Application in Stem Cell Differentiation

PubMed Central

2015-01-01

Biocomposite matrices with high mechanical strength, high stability, and the ability to direct matrix-specific stem cell differentiation are essential for the reconstruction of lesioned tissues in tissue engineering and cell therapeutics. Toward this end, we used the electrospinning technique to fabricate well-aligned composite fibers from collagen and spider dragline silk protein, obtained from the milk of transgenic goats, mimicking the native extracellular matrix (ECM) on a similar scale. Collagen and the dragline silk proteins were found to mix homogeneously at all ratios in the electrospun (E-spun) fibers. As a result, the ultimate tensile strength and elasticity of the fibers increased monotonically with silk percentage, whereas the stretchability was slightly reduced. Strikingly, we found that the incorporation of silk proteins to collagen dramatically increased the matrix stability against excessive fiber swelling and shape deformation in cell culture medium. When human decidua parietalis placental stem cells (hdpPSCs) were seeded on the collagen–silk matrices, the matrices were found to support cell proliferation at a similar rate as that of the pure collagen matrix, but they provided cell adhesion with reduced strengths and induced cell polarization at varied levels. Matrices containing 15 and 30 wt % silk in collagen (CS15, CS30) were found to induce a level of neural differentiation comparable to that of pure collagen. In particular, CS15 matrix induced the highest extent of cell polarization and promoted the development of extended 1D neural filaments strictly in-line with the aligned fibers. Taking the increased mechanical strength and fiber stability into consideration, CS15 and CS30 E-spun fibers offer better alternatives to pure collagen fibers as scaffolds that can be potentially utilized in neural tissue repair and the development of future nanobiodevices. PMID:25405355

In Situ β-Glucan Fortification of Cereal-Based Matrices by Pediococcus parvulus 2.6: Technological Aspects and Prebiotic Potential

PubMed Central

Mohedano, María Luz; Spano, Giuseppe; Fiocco, Daniela; Russo, Pasquale; Capozzi, Vittorio

2017-01-01

Bacterial exopolysaccharides produced by lactic acid bacteria are of increasing interest in the food industry, since they might enhance the technological and functional properties of some edible matrices. In this work, Pediococcus parvulus 2.6, which produces an O2-substituted (1,3)-β-d-glucan exopolysaccharide only synthesised by bacteria, was proposed as a starter culture for the production of three cereal-based fermented foods. The obtained fermented matrices were naturally bio-fortified in microbial β-glucans, and used to investigate the prebiotic potential of the bacterial exopolysaccharide by analysing the impact on the survival of a probiotic Lactobacillus plantarum strain under starvation and gastrointestinal simulated conditions. All of the assays were performed by using as control of the P. parvulus 2.6’s performance, the isogenic β-glucan non-producing 2.6NR strain. Our results showed a differential capability of P. parvulus to ferment the cereal flours. During the fermentation step, the β-glucans produced were specifically quantified and their concentration correlated with an increased viscosity of the products. The survival of the model probiotic L. plantarum WCFS1 was improved by the presence of the bacterial β-glucans in oat and rice fermented foods under starvation conditions. The probiotic bacteria showed a significantly higher viability when submitted to a simulated intestinal stress in the oat matrix fermented by the 2.6 strain. Therefore, the cereal flours were a suitable substrate for in situ bio-fortification with the bacterial β-glucan, and these matrices could be used as carriers to enhance the beneficial properties of probiotic bacteria. PMID:28754020

Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana*

PubMed Central

Kotzsch, Alexander; Pawolski, Damian; Milentyev, Alexander; Shevchenko, Anna; Scheffel, André; Poulsen, Nicole; Shevchenko, Andrej; Kröger, Nils

2016-01-01

The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis. PMID:26710847

A simple, rapid, cost-effective and sensitive method for detection of Salmonella in environmental and pecan samples.

PubMed

Dobhal, S; Zhang, G; Rohla, C; Smith, M W; Ma, L M

2014-10-01

PCR is widely used in the routine detection of foodborne human pathogens; however, challenges remain in overcoming PCR inhibitors present in some sample matrices. The objective of this study was to develop a simple, sensitive, cost-effective and rapid method for processing large numbers of environmental and pecan samples for Salmonella detection. This study was also aimed at validation of a new protocol for the detection of Salmonella from in-shell pecans. Different DNA template preparation methods, including direct boiling, prespin, multiple washing and commercial DNA extraction kits, were evaluated with pure cultures of Salmonella Typhimurium and with enriched soil, cattle feces and in-shell pecan each spiked individually with Salmonella Typhimurium. PCR detection of Salmonella was conducted using invA and 16S rRNA gene (internal amplification control) specific primers. The effect of amplification facilitators, including bovine serum albumin (BSA), polyvinylpyrrolidone (PVP), polyethylene glycol (PEG) and gelatin on PCR sensitivity, was also evaluated. Conducting a prespin of sample matrices in combination with the addition of 0·4% (w/v) BSA and 1% (w/v) PVP in PCR mix was the simplest, most rapid, cost-effective and sensitive method for PCR detection of Salmonella, with up to 40 CFU Salmonella per reaction detectable in the presence of over 10(9 ) CFU ml(-1) of background micro-organisms from enriched feces soil or pecan samples. The developed method is rapid, cost-effective and sensitive for detection of Salmonella from different matrices. This study provides a method with broad applicability for PCR detection of Salmonella in complex sample matrices. This method has a potential for its application in different research arenas and diagnostic laboratories. © 2014 The Society for Applied Microbiology.

Methods for Quantum Circuit Design and Simulation

DTIC Science & Technology

2010-03-01

cannot be deter- mined given the one output. Reversible gates, expressed mathematically, are unitary matrices. 16 3.3.1 PAULI Gates/Matrices Three...common single-qubit gates are expressed mathematically as Pauli matrices, which are 2x2 matrices. A 2x2 quantum gate can be applied to a single quantum...bit (a 2x1 column vector). The Pauli matrices are expressed as follows: X =   0 1 1 0   Y =   0 −i i 0   Z =   1 0 0 −1   (3.10) where i

An automated procedure for calculating system matrices from perturbation data generated by an EAI Pacer and 100 hybrid computer system

NASA Technical Reports Server (NTRS)

Milner, E. J.; Krosel, S. M.

1977-01-01

Techniques are presented for determining the elements of the A, B, C, and D state variable matrices for systems simulated on an EAI Pacer 100 hybrid computer. An automated procedure systematically generates disturbance data necessary to linearize the simulation model and stores these data on a floppy disk. A separate digital program verifies this data, calculates the elements of the system matrices, and prints these matrices appropriately labeled. The partial derivatives forming the elements of the state variable matrices are approximated by finite difference calculations.

Simple and Inexpensive but Highly Discriminating Method for Computer-Assisted DNA Fingerprinting of Pseudomonas aeruginosa

PubMed Central

Al-Samarrai, Taha H.; Zhang, Ningxin; Lamont, Iain L.; Martin, Lois; Kolbe, John; Wilsher, Margaret; Morris, Arthur J.; Schmid, Jan

2000-01-01

We describe here a method for computer-assisted fingerprinting of Pseudomonas aeruginosa. In this method, DNA is digested with SalI, and bands with molecular sizes of ≥9.7 kb are visually scored after electrophoresis on agarose gels. Pattern scores are entered into a Microsoft Excel database. In scoring, the number of bands within each of a set of molecular size ranges is scored, rather than the absolute molecular size of each band, substantially enhancing the speed and reproducibility of the method, while eliminating the need for using expensive gel scanning equipment and software. Pattern scores are used to generate matrices of genetic distance values, which can be visualized in neighbor-joining trees. The method reliably distinguishes two epidemiologically unrelated isolates in 99.3% of all comparisons. The genetic relationships between isolates observed with the method were consistent with those obtained by analysis of two P. aeruginosa genes, indicating that it provides valid estimates of genetic divergence between isolates. Using the method, respiratory tract isolates from cystic fibrosis patients in Green Lane Hospital in Auckland, New Zealand, were shown to be genetically less diverse than epidemiologically unrelated isolates from other patients. This finding was not due to the existence of clusters of related strains specialized toward colonization of the respiratory tract and thus was indicative of transmission between patients. Analysis of multiple isolates from individual cystic fibrosis patients suggested that up to five separate clusters of genetically related strains may simultaneously be present in a patient. The method described should significantly enhance our ability to investigate the epidemiology of P. aeruginosa. PMID:11101578

Substructure-based control of flexible structures

NASA Technical Reports Server (NTRS)

Babuska, Vit; Craig, Roy R., Jr.

1993-01-01

A decentralized procedure is presented for the design of controllers for flexible structures. Spatially significant components are created which approximate the response of a specific part of the complete structure. For each component, the controller and observer gain matrices which are used in a controller for the complete structure. The proposed method is illustrated on a model of NASA Langley's CSI testbed structure.

Examining the Utility of the Schoolwide Expectations Survey for Specific Settings (SESSS): A Data-Informed Approach to Developing Expectation Matrices

ERIC Educational Resources Information Center

Royer, David James

2017-01-01

To best support all students' academic, behavioral, and social needs, an integrated systems approach is necessary. In such systems, all faculty and staff ideally recognize student success is a shared responsibility and collaborate in a data-informed process to define common student behavioral expectations to facilitate success academically,…

Natural-based nanocomposites for bone tissue engineering and regenerative medicine: a review.

PubMed

Pina, Sandra; Oliveira, Joaquim M; Reis, Rui L

2015-02-18

Tissue engineering and regenerative medicine has been providing exciting technologies for the development of functional substitutes aimed to repair and regenerate damaged tissues and organs. Inspired by the hierarchical nature of bone, nanostructured biomaterials are gaining a singular attention for tissue engineering, owing their ability to promote cell adhesion and proliferation, and hence new bone growth, compared with conventional microsized materials. Of particular interest are nanocomposites involving biopolymeric matrices and bioactive nanosized fillers. Biodegradability, high mechanical strength, and osteointegration and formation of ligamentous tissue are properties required for such materials. Biopolymers are advantageous due to their similarities with extracellular matrices, specific degradation rates, and good biological performance. By its turn, calcium phosphates possess favorable osteoconductivity, resorbability, and biocompatibility. Herein, an overview on the available natural polymer/calcium phosphate nanocomposite materials, their design, and properties is presented. Scaffolds, hydrogels, and fibers as biomimetic strategies for tissue engineering, and processing methodologies are described. The specific biological properties of the nanocomposites, as well as their interaction with cells, including the use of bioactive molecules, are highlighted. Nanocomposites in vivo studies using animal models are also reviewed and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Focused Multiple Reaction Monitoring (MRM) Quantitative Method for Bioactive Grapevine Stilbenes by Ultra-High-Performance Liquid Chromatography Coupled to Triple-Quadrupole Mass Spectrometry (UHPLC-QqQ).

PubMed

Hurtado-Gaitán, Elías; Sellés-Marchart, Susana; Martínez-Márquez, Ascensión; Samper-Herrero, Antonio; Bru-Martínez, Roque

2017-03-07

Grapevine stilbenes are a family of polyphenols which derive from trans -resveratrol having antifungal and antimicrobial properties, thus being considered as phytoalexins. In addition to their diverse bioactive properties in animal models, they highlight a strong potential in human health maintenance and promotion. Due to this relevance, highly-specific qualitative and quantitative methods of analysis are necessary to accurately analyze stilbenes in different matrices derived from grapevine. Here, we developed a rapid, sensitive, and specific analysis method using ultra-high-performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC-QqQ) in MRM mode to detect and quantify five grapevine stilbenes, trans -resveratrol, trans -piceid, trans -piceatannol, trans -pterostilbene, and trans -ε-viniferin, whose interest in relation to human health is continuously growing. The method was optimized to minimize in-source fragmentation of piceid and to avoid co-elution of cis -piceid and trans -resveratrol, as both are detected with resveratrol transitions. The applicability of the developed method of stilbene analysis was tested successfully in different complex matrices including cellular extracts of Vitis vinifera cell cultures, reaction media of biotransformation assays, and red wine.

Hydrolytically degradable poly(ethylene glycol) hydrogel scaffolds with tunable degradation and mechanical properties

PubMed Central

Zustiak, Silviya P.

2011-01-01

The objective of this work was to create three-dimensional (3D) hydrogel matrices with defined mechanical properties, as well as tunable degradability for use in applications involving protein delivery and cell encapsulation. Thus, we report the synthesis and characterization of a novel hydrolytically degradable poly(ethylene glycol) (PEG) hydrogel composed of PEG vinyl sulfone (PEG-VS) cross-linked with PEG-diester-dithiol. Unlike previously reported degradable PEG-based hydrogels, these materials are homogeneous in structure, fully hydrophilic and have highly specific cross-linking chemistry. We characterized hydrogel degradation and associated trends in mechanical properties, i.e., storage modulus (G′), swelling ratio (QM), and mesh size (ξ). Degradation time and the monitored mechanical properties of the hydrogel correlated with cross-linker molecular weight, cross-linker functionality, and total polymer density; these properties changed predictably as degradation proceeded (G′ decreased, whereas QM and ξ increased) until the gels reached complete degradation. Balb/3T3 fibroblast adhesion and proliferation within the 3D hydrogel matrices were also verified. In sum, these unique properties indicate that the reported degradable PEG hydrogels are well poised for specific applications in protein and cell delivery to repair soft tissue. PMID:20355705

New Surface-Enhanced Raman Sensing Chip Designed for On-Site Detection of Active Ricin in Complex Matrices Based on Specific Depurination.

PubMed

Tang, Ji-Jun; Sun, Jie-Fang; Lui, Rui; Zhang, Zong-Mian; Liu, Jing-Fu; Xie, Jian-Wei

2016-01-27

Quick and accurate on-site detection of active ricin has very important realistic significance in view of national security and defense. In this paper, optimized single-stranded oligodeoxynucleotides named poly(21dA), which function as a depurination substrate of active ricin, were screened and chemically attached on gold nanoparticles (AuNPs, ∼100 nm) via the Au-S bond [poly(21dA)-AuNPs]. Subsequently, poly(21dA)-AuNPs were assembled on a dihydrogen lipoic-acid-modified Si wafer (SH-Si), thus forming the specific surface-enhanced Raman spectroscopy (SERS) chip [poly(21dA)-AuNPs@SH-Si] for depurination of active ricin. Under optimized conditions, active ricin could specifically hydrolyze multiple adenines from poly(21dA) on the chip. This depurination-induced composition change could be conveniently monitored by measuring the distinct attenuation of the SERS signature corresponding to adenine. To improve sensitivity of this method, a silver nanoshell was deposited on post-reacted poly(21dA)-AuNPs, which lowered the limit of detection to 8.9 ng mL(-1). The utility of this well-controlled SERS chip was successfully demonstrated in food and biological matrices spiked with different concentrations of active ricin, thus showing to be very promising assay for reliable and rapid on-site detection of active ricin.

Poor Auditory Task Scores in Children with Specific Reading and Language Difficulties: Some Poor Scores Are More Equal than Others

ERIC Educational Resources Information Center

McArthur, Genevieve M.; Hogben, John H.

2012-01-01

Children with specific reading disability (SRD) or specific language impairment (SLI), who scored poorly on an auditory discrimination task, did up to 140 runs on the failed task. Forty-one percent of the children produced widely fluctuating scores that did not improve across runs (untrainable errant performance), 23% produced widely fluctuating…

Combination of STOP-Bang Score with Mallampati Score fails to improve specificity in the prediction of sleep-disordered breathing.

PubMed

Dette, Frank G; Graf, Juergen; Cassel, Werner; Lloyd-Jones, Carla; Boehm, Stefan; Zoremba, Martin; Schramm, Patrick; Pestel, Gunther; Thal, Serge C

2016-06-01

Sleep-disordered breathing (SDB) is closely associated with perioperative complications. STOP-Bang score was validated for preoperative screening of SDB. However, STOP-Bang Score lacks adequately high specificity. We aimed to improve it by combining it with the Mallampati Score. The study included 347 patients, in which we assessed both STOP-Bang and Mallampati scores. Overnight oxygen saturation was measured to calculate ODI4%. We calculated the sensitivity and specificity for AHI and ODI4% of both scores separately and in combination. We found that STOP-Bang Score ≥3 was present in 71%, ODI≥5/h (AHI ≥5/h) in 42.6% (39.3%) and ODI≥15/h (AHI ≥15/h) in 13.5% (17.8%). For ODI4%≥5/h (AHI ≥5/h) we observed in men a response rate for sensitivity and specificity of STOP-Bang of 94.5% and 17.1% (90.9% and 12.5%) and in women 66% and 51% (57.8% and 46.9%). For ODI4%≥15/h (AHI≥15/h) it was 92% and 12% (84.6% and 10.3%) and 93% and 49% (75% and 49.2%). For ODI4%≥5 (AHI≥5) sensitivity and specificity of Mallampati score were in men 38.4% and 78.6% (27.3% and 68.2%) and in women 25% and 82.7% (21.9% and 81.3%), for ODI≥15 (AHI ≥15/h) 38.5% and 71.8% (26.9% and 69.2%) and 33.3% and 81.4% (17.9% and 79.6%). In combination, for ODI4%≥15/h, we found sensitivity in men to be 92.3% and in women 93.3%, specificity 10.3% and 41.4%. STOP-Bang Score combined with Mallampati Score fails to increase specificity. Low specificity should be considered when using both scores for preoperative screening of SDB.

A progress report on estuary modeling by the finite-element method

USGS Publications Warehouse

Gray, William G.

1978-01-01

Various schemes are investigated for finite-element modeling of two-dimensional surface-water flows. The first schemes investigated combine finite-element spatial discretization with split-step time stepping schemes that have been found useful in finite-difference computations. Because of the large number of numerical integrations performed in space and the large sparse matrices solved, these finite-element schemes were found to be economically uncompetitive with finite-difference schemes. A very promising leapfrog scheme is proposed which, when combined with a novel very fast spatial integration procedure, eliminates the need to solve any matrices at all. Additional problems attacked included proper propagation of waves and proper specification of the normal flow-boundary condition. This report indicates work in progress and does not come to a definitive conclusion as to the best approach for finite-element modeling of surface-water problems. The results presented represent findings obtained between September 1973 and July 1976. (Woodard-USGS)

Underground coal mining section data

NASA Technical Reports Server (NTRS)

Gabrill, C. P.; Urie, J. T.

1981-01-01

A set of tables which display the allocation of time for ten personnel and eight pieces of underground coal mining equipment to ten function categories is provided. Data from 125 full shift time studies contained in the KETRON database was utilized as the primary source data. The KETRON activity and delay codes were mapped onto JPL equipment, personnel and function categories. Computer processing was then performed to aggregate the shift level data and generate the matrices. Additional, documented time study data were analyzed and used to supplement the KETRON databased. The source data including the number of shifts are described. Specific parameters of the mines from which there data were extracted are presented. The result of the data processing including the required JPL matrices is presented. A brief comparison with a time study analysis of continuous mining systems is presented. The procedures used for processing the source data are described.

Matrices and scaffolds for drug delivery in dental, oral and craniofacial tissue engineering☆

PubMed Central

Moioli, Eduardo K.; Clark, Paul A.; Xin, Xuejun; Lal, Shan; Mao, Jeremy J.

2010-01-01

Current treatments for diseases and trauma of dental, oral and craniofacial (DOC) structures rely on durable materials such as amalgam and synthetic materials, or autologous tissue grafts. A paradigm shift has taken place to utilize tissue engineering and drug delivery approaches towards the regeneration of these structures. Several prototypes of DOC structures have been regenerated such as temporomandibular joint (TMJ) condyle, cranial sutures, tooth structures and periodontium components. However, many challenges remain when taking in consideration the high demand for esthetics of DOC structures, the complex environment and yet minimal scar formation in the oral cavity, and the need for accommodating multiple tissue phenotypes. This review highlights recent advances in the regeneration of DOC structures, including the tooth, periodontium, TMJ, cranial sutures and implant dentistry, with specific emphasis on controlled release of signaling cues for stem cells, biomaterial matrices and scaffolds, and integrated tissue engineering approaches. PMID:17499385

Scattering matrix elements of biological particles measured in a flow through system: theory and practice.

PubMed

Sloot, P M; Hoekstra, A G; van der Liet, H; Figdor, C G

1989-05-15

Light scattering techniques (including depolarization experiments) applied to biological cells provide a fast nondestructive probe that is very sensitive to small morphological differences. Until now quantitative measurement of these scatter phenomena were only described for particles in suspension. In this paper we discuss the symmetry conditions applicable to the scattering matrices of monodisperse biological cells in a flow cytometer and provide evidence that quantitative measurement of the elements of these scattering matrices is possible in flow through systems. Two fundamental extensions to the theoretical description of conventional scattering experiments are introduced: large cone integration of scattering signals and simultaneous implementation of the localization principle to account for scattering by a sharply focused laser beam. In addition, a specific calibration technique is proposed to account for depolarization effects of the highly specialized optics applied in flow through equipment.

Disposable and removable nucleic acid extraction and purification cartridges for automated flow-through systems

DOEpatents

Regan, John Frederick

2014-09-09

Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

Camera-Model Identification Using Markovian Transition Probability Matrix

NASA Astrophysics Data System (ADS)

Xu, Guanshuo; Gao, Shang; Shi, Yun Qing; Hu, Ruimin; Su, Wei

Detecting the (brands and) models of digital cameras from given digital images has become a popular research topic in the field of digital forensics. As most of images are JPEG compressed before they are output from cameras, we propose to use an effective image statistical model to characterize the difference JPEG 2-D arrays of Y and Cb components from the JPEG images taken by various camera models. Specifically, the transition probability matrices derived from four different directional Markov processes applied to the image difference JPEG 2-D arrays are used to identify statistical difference caused by image formation pipelines inside different camera models. All elements of the transition probability matrices, after a thresholding technique, are directly used as features for classification purpose. Multi-class support vector machines (SVM) are used as the classification tool. The effectiveness of our proposed statistical model is demonstrated by large-scale experimental results.

Ureasil-polyether hybrid film-forming materials.

PubMed

Souza, L K; Bruno, C H; Lopes, L; Pulcinelli, S H; Santilli, C V; Chiavacci, L A

2013-01-01

The objectives of this work were to study the suitability and highlight the advantages of the use of cross-linked ureasil-polyether hybrid matrices as film-forming systems. The results revealed that ureasil-polyethers are excellent film-forming systems due to specific properties, such as their biocompatibility, their cosmetic attractiveness for being able to form thin and transparent films, their short drying time to form films and their excellent bioadhesion compared to the commercial products known as strong adhesives. Rheological measurements have demonstrated the ability of these hybrid matrices to form a film in only a few seconds and Water Vapor Transmitting Rate (WVTR) showed adequate semi-occlusive properties suggesting that these films could be used as skin and wound protectors. Both the high skin bioadhesion and non-cytotoxic character seems to be improved by the presence of multiple amine groups in the hybrid molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Earth orbital experiment program and requirements study, volume 1, sections 1 - 6

NASA Technical Reports Server (NTRS)

1971-01-01

A reference manual for planners of manned earth-orbital research activity is presented. The manual serves as a systems approach to experiment and mission planning based on an integrated consideration of candidate research programs and the appropriate vehicle, mission, and technology development requirements. Long range goals and objectives for NASA activities during the 1970 to 1980 time period are analyzed. The useful and proper roles of manned and automated spacecraft for implementing NASA experiments are described. An integrated consideration of NASA long range goals and objectives, the system and mission requirements, and the alternative implementation plans are developed. Specific areas of investigation are: (1) manned space flight requirements, (2) space biology, (3) spaceborne astronomy, (4) space communications and navigation, (5) earth observation, (6) supporting technology development requirements, (7) data management system matrices, (8) instrumentation matrices, and (9) biotechnology laboratory experiments.

A systematic investigation of PET Radionuclide Specific Activity on Miniaturization of Radiochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeanne M Link, PhD

2012-03-08

The PET radionuclides, 18F and 11C consist of very high radiation to mass amounts and should be easily adapted to new technologies such as chip chemistry with nanofluidics. However, environmental contamination with nonradioactive fluorine, carbon and other trace contaminants add sufficient mass, micrograms to milligrams, to prevent adapting PET radiochemistry to the nanochip technologies. In addition, the large volumes of material required for beam irradiation make it necessary to also remove the 18F and 11C from their chemical matrices. These steps add contaminants. The work described in this report was a systematic investigation of sources of these contaminants and methodsmore » to reduce these contaminants and the reaction volumes for radiochemical synthesis. Several methods were found to lower the contaminants and matrices to within a factor of 2 to 100 of those needed to fully implement chip technology but further improvements are needed.« less

Rotational 3D printing of damage-tolerant composites with programmable mechanics.

PubMed

Raney, Jordan R; Compton, Brett G; Mueller, Jochen; Ober, Thomas J; Shea, Kristina; Lewis, Jennifer A

2018-02-06

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber-epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. Copyright © 2018 the Author(s). Published by PNAS.

Invertible flexible matrices

NASA Astrophysics Data System (ADS)

Justino, Júlia

2017-06-01

Matrices with coefficients having uncertainties of type o (.) or O (.), called flexible matrices, are studied from the point of view of nonstandard analysis. The uncertainties of the afore-mentioned kind will be given in the form of the so-called neutrices, for instance the set of all infinitesimals. Since flexible matrices have uncertainties in their coefficients, it is not possible to define the identity matrix in an unique way and so the notion of spectral identity matrix arises. Not all nonsingular flexible matrices can be turned into a spectral identity matrix using Gauss-Jordan elimination method, implying that that not all nonsingular flexible matrices have the inverse matrix. Under certain conditions upon the size of the uncertainties appearing in a nonsingular flexible matrix, a general theorem concerning the boundaries of its minors is presented which guarantees the existence of the inverse matrix of a nonsingular flexible matrix.

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

PubMed

Tan, Yen Hock; Huang, He; Kihara, Daisuke

2006-08-15

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

The Development of Novel Nanodiamond Based MALDI Matrices for the Analysis of Small Organic Pharmaceuticals

NASA Astrophysics Data System (ADS)

Chitanda, Jackson M.; Zhang, Haixia; Pahl, Erica; Purves, Randy W.; El-Aneed, Anas

2016-10-01

The utility of novel functionalized nanodiamonds (NDs) as matrices for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) is described herein. MALDI-MS analysis of small organic compounds (<1000 Da) is typically complex because of interferences from numerous cluster ions formed when using conventional matrices. To expand the use of MALDI for the analysis of small molecules, novel matrices were designed by covalently linking conventional matrices (or a lysine moiety) to detonated NDs. Four new functionalized NDs were evaluated for their ionization capabilities using five pharmaceuticals with varying molecular structures. Two ND matrices were able to ionize all tested pharmaceuticals in the negative ion mode, producing the deprotonated ions [M - H]-. Ion intensity for target analytes was generally strong with enhanced signal-to-noise ratios compared with conventional matrices. The negative ion mode is of great importance for biological samples as interference from endogenous compounds is inherently minimized in the negative ion mode. Since the molecular structures of the tested pharmaceuticals did not suggest that negative ion mode would be preferable, this result magnifies the importance of these findings. On the other hand, conventional matrices primarily facilitated the ionization as expected in the positive ion mode, producing either the protonated molecules [M + H]+ or cationic adducts (typically producing complex spectra with numerous adduct peaks). The data presented in this study suggests that these matrices may offer advantages for the analysis of low molecular weight pharmaceuticals/metabolites.

The Development of Novel Nanodiamond Based MALDI Matrices for the Analysis of Small Organic Pharmaceuticals.

PubMed

Chitanda, Jackson M; Zhang, Haixia; Pahl, Erica; Purves, Randy W; El-Aneed, Anas

2016-10-01

The utility of novel functionalized nanodiamonds (NDs) as matrices for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) is described herein. MALDI-MS analysis of small organic compounds (<1000 Da) is typically complex because of interferences from numerous cluster ions formed when using conventional matrices. To expand the use of MALDI for the analysis of small molecules, novel matrices were designed by covalently linking conventional matrices (or a lysine moiety) to detonated NDs. Four new functionalized NDs were evaluated for their ionization capabilities using five pharmaceuticals with varying molecular structures. Two ND matrices were able to ionize all tested pharmaceuticals in the negative ion mode, producing the deprotonated ions [M - H](-). Ion intensity for target analytes was generally strong with enhanced signal-to-noise ratios compared with conventional matrices. The negative ion mode is of great importance for biological samples as interference from endogenous compounds is inherently minimized in the negative ion mode. Since the molecular structures of the tested pharmaceuticals did not suggest that negative ion mode would be preferable, this result magnifies the importance of these findings. On the other hand, conventional matrices primarily facilitated the ionization as expected in the positive ion mode, producing either the protonated molecules [M + H](+) or cationic adducts (typically producing complex spectra with numerous adduct peaks). The data presented in this study suggests that these matrices may offer advantages for the analysis of low molecular weight pharmaceuticals/metabolites. Graphical Abstract ᅟ.

A highly sensitive and specific combined clinical and sonographic score to diagnose appendicitis.

PubMed

Reddy, Swathi B; Kelleher, Michael; Bokhari, S A Jamal; Davis, Kimberly A; Schuster, Kevin M

2017-10-01

Computed tomography (CT) scanning reduces the negative appendectomy rate however it exposes the patient to ionizing radiation. Ultrasound (US) does not carry this risk but may be nondiagnostic. We hypothesized that a clinical-US scoring system would improve diagnostic accuracy. We conducted a retrospective review of all patients (age, >15 years) who presented through the emergency department with suspected appendicitis and underwent initial US. A US score was developed using odds ratios for appendicitis given appendiceal diameter, compressibility, hyperemia, free fluid, and focal or diffuse tenderness. The US score was then combined with the Alvarado score. Final diagnosis of appendicitis was assigned by pathology reports. Three hundred patients who underwent US as initial imaging were identified. Thirty-two patients with evident nonappendiceal pathology on US were excluded. In 114 (38%), the appendix was not visualized and partially visualized in 36 (12%). Fifty-seven (21.3%) had an appendectomy with 1 (1.7%) negative. Six nonvisualized appendicies underwent appendectomy, with no negative cases. Sensitivity and specificity for the sonographic score were 86% and 90%, respectively, at a score of 1.5. The combined score demonstrated 98% sensitivity and 82% specificity at 6.5, and 95% sensitivity, and 87% specificity at a score of 7.5. Sensitivity and specificity were confirmed by bootstrap resampling for validation. Area under receiver operating characteristic (ROC) curves for our new US score were similar to the ROC curve for the Alvarado score (91.9 and 91.1, p = 0.8). The combined US and Alvarado score yielded an area under the ROC curve of 97.1, significantly better than either score alone (p = 0.017 and p < 0.001, respectively). Our scoring system based entirely on US findings was highly sensitive and specific for appendicitis, and it significantly improved when combined with the Alvarado score. After prospective evaluation, the combined US-Alvarado score might replace the need for computed tomography imaging in a majority of patients. Diagnostic Test, Level III.

Extraction and Analysis of Sulfur Mustard (HD) from Various Food Matrices by Gas ChromatographyMass Spectrometry

DTIC Science & Technology

2016-01-01

EXTRACTION AND ANALYSIS OF SULFUR MUSTARD (HD) FROM VARIOUS FOOD MATRICES BY GAS CHROMATOGRAPHY–MASS...Sulfur Mustard (HD) from Various Food Matrices by Gas Chromatography–Mass Spectrometry 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...spectrometry was used to analyze sulfur mustard (HD) in various food matrices. The development of a solid-phase extraction method using a normal

Novel value-added uses for sweet potato juice and flour in polyphenol- and protein-enriched functional food ingredients

PubMed Central

Grace, Mary H; Truong, An N; Truong, Van-Den; Raskin, Ilya; Lila, Mary Ann

2015-01-01

Blackcurrant, blueberry, and muscadine grape juices were efficiently sorbed, concentrated, and stabilized into dry granular ingredient matrices which combined anti-inflammatory and antioxidant fruit polyphenols with sweet potato functional constituents (carotenoids, vitamins, polyphenols, fibers). Total phenolics were highest in blackcurrant-orange sweet potato ingredient matrices (34.03 mg/g), and lowest in muscadine grape-yellow sweet potato matrices (10.56 mg/g). Similarly, anthocyanins were most concentrated in blackcurrant-fortified orange and yellow sweet potato matrices (5.40 and 6.54 mg/g, respectively). Alternatively, other protein-rich edible matrices (defatted soy flour, light roasted peanut flour, and rice protein concentrate) efficiently captured polyphenols (6.09–9.46 mg/g) and anthocyanins (0.77–1.27 mg/g) from purple-fleshed sweet potato juice, with comparable efficiency. Antioxidant activity correlated well with total phenolic content. All formulated ingredient matrices stabilized and preserved polyphenols for up to 24 weeks, even when stored at 37°C. Complexation with juice-derived polyphenols did not significantly alter protein or carbohydrate profiles of the matrices. Sensory evaluation of the ingredient matrices suggested potential uses for a wide range of functional food products. PMID:26405527

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

PubMed Central

2011-01-01

Background CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions. Results Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. Conclusions Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously. PMID:21388552

Virial expansion for almost diagonal random matrices

NASA Astrophysics Data System (ADS)

Yevtushenko, Oleg; Kravtsov, Vladimir E.

2003-08-01

Energy level statistics of Hermitian random matrices hat H with Gaussian independent random entries Higeqj is studied for a generic ensemble of almost diagonal random matrices with langle|Hii|2rangle ~ 1 and langle|Hi\

Aberrant topology of striatum's connectivity is associated with the number of episodes in depression.

PubMed

Meng, Chun; Brandl, Felix; Tahmasian, Masoud; Shao, Junming; Manoliu, Andrei; Scherr, Martin; Schwerthöffer, Dirk; Bäuml, Josef; Förstl, Hans; Zimmer, Claus; Wohlschläger, Afra M; Riedl, Valentin; Sorg, Christian

2014-02-01

In major depressive disorder, depressive episodes reoccur in ∼60% of cases; however, neural mechanisms of depressive relapse are poorly understood. Depressive episodes are characterized by aberrant topology of the brain's intrinsic functional connectivity network, and the number of episodes is one of the most important predictors for depressive relapse. In this study we hypothesized that specific changes of the topology of intrinsic connectivity interact with the course of episodes in recurrent depressive disorder. To address this hypothesis, we investigated which changes of connectivity topology are associated with the number of episodes in patients, independently of current symptoms and disease duration. Fifty subjects were recruited including 25 depressive patients (two to 10 episodes) and 25 gender- and age-matched control subjects. Resting-state functional magnetic resonance imaging, Harvard-Oxford brain atlas, wavelet-transformation of atlas-shaped regional time-series, and their pairwise Pearson's correlation were used to define individual connectivity matrices. Matrices were analysed by graph-based methods, resulting in outcome measures that were used as surrogates of intrinsic network topology. Topological scores were subsequently compared across groups, and, for patients only, related with the number of depressive episodes and current symptoms by partial correlation analysis. Concerning the whole brain connectivity network of patients, small-world topology was preserved but global efficiency was reduced and global betweenness-centrality increased. Aberrant nodal efficiency and centrality of regional connectivity was found in the dorsal striatum, inferior frontal and orbitofrontal cortex as well as in the occipital and somatosensory cortex. Inferior frontal changes were associated with current symptoms, whereas aberrant right putamen network topology was associated with the number of episodes. Results were controlled for effects of total grey matter volume, medication, and total disease duration. This finding provides first evidence that in major depressive disorder aberrant topology of the right putamen's intrinsic connectivity pattern is associated with the course of depressive episodes, independently of current symptoms, medication status and disease duration. Data suggest that the reorganization of striatal connectivity may interact with the course of episodes in depression thereby contributing to depressive relapse risk.

Inference for High-dimensional Differential Correlation Matrices *

PubMed Central

Cai, T. Tony; Zhang, Anru

2015-01-01

Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical guarantees are given. Minimax rate of convergence is established and the proposed estimator is shown to be adaptively rate-optimal over collections of paired correlation matrices with approximately sparse differences. Simulation results show that the procedure significantly outperforms two other natural methods that are based on separate estimation of the individual correlation matrices. The procedure is also illustrated through an analysis of a breast cancer dataset, which provides evidence at the gene co-expression level that several genes, of which a subset has been previously verified, are associated with the breast cancer. Hypothesis testing on the differential correlation matrices is also considered. A test, which is particularly well suited for testing against sparse alternatives, is introduced. In addition, other related problems, including estimation of a single sparse correlation matrix, estimation of the differential covariance matrices, and estimation of the differential cross-correlation matrices, are also discussed. PMID:26500380

Deterministic matrices matching the compressed sensing phase transitions of Gaussian random matrices

PubMed Central

Monajemi, Hatef; Jafarpour, Sina; Gavish, Matan; Donoho, David L.; Ambikasaran, Sivaram; Bacallado, Sergio; Bharadia, Dinesh; Chen, Yuxin; Choi, Young; Chowdhury, Mainak; Chowdhury, Soham; Damle, Anil; Fithian, Will; Goetz, Georges; Grosenick, Logan; Gross, Sam; Hills, Gage; Hornstein, Michael; Lakkam, Milinda; Lee, Jason; Li, Jian; Liu, Linxi; Sing-Long, Carlos; Marx, Mike; Mittal, Akshay; Monajemi, Hatef; No, Albert; Omrani, Reza; Pekelis, Leonid; Qin, Junjie; Raines, Kevin; Ryu, Ernest; Saxe, Andrew; Shi, Dai; Siilats, Keith; Strauss, David; Tang, Gary; Wang, Chaojun; Zhou, Zoey; Zhu, Zhen

2013-01-01

In compressed sensing, one takes samples of an N-dimensional vector using an matrix A, obtaining undersampled measurements . For random matrices with independent standard Gaussian entries, it is known that, when is k-sparse, there is a precisely determined phase transition: for a certain region in the (,)-phase diagram, convex optimization typically finds the sparsest solution, whereas outside that region, it typically fails. It has been shown empirically that the same property—with the same phase transition location—holds for a wide range of non-Gaussian random matrix ensembles. We report extensive experiments showing that the Gaussian phase transition also describes numerous deterministic matrices, including Spikes and Sines, Spikes and Noiselets, Paley Frames, Delsarte-Goethals Frames, Chirp Sensing Matrices, and Grassmannian Frames. Namely, for each of these deterministic matrices in turn, for a typical k-sparse object, we observe that convex optimization is successful over a region of the phase diagram that coincides with the region known for Gaussian random matrices. Our experiments considered coefficients constrained to for four different sets , and the results establish our finding for each of the four associated phase transitions. PMID:23277588

Amino acid "little Big Bang": representing amino acid substitution matrices as dot products of Euclidian vectors.

PubMed

Zimmermann, Karel; Gibrat, Jean-François

2010-01-04

Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

A study on different forms of intelligence in Indian school-going children.

PubMed

Singh, Yashpal; Makharia, Archita; Sharma, Abhilasha; Agrawal, Kruti; Varma, Gowtham; Yadav, Tarun

2017-01-01

Most definitions of intelligence focus on capabilities that are relevant to scholastic performances. However, there are seven forms of intelligences. There is a lack of data on multiple intelligences in Indian children. Hence, this study was conducted to assess different forms of intelligences in students and compared these diverse intelligences with intelligence quotient (IQ) scores. In this cross-sectional observational study, we recruited 1065 school children between the age of 12 and 16 years from two government and 13 private schools in five towns, six cities, and two villages across India. All the children were administered multiple intelligences questionnaire by Armstrong, consisting of thirty true/false types of questions to assess the intelligences of a child in seven domains including linguistic skills, logical/mathematical abilities, musical skills, spatial intelligence, bodily-kinesthetic skills, intrapersonal intelligence, and interpersonal intelligence. IQ scores were assessed by Ravens Standard Progressive Matrices. We found that different students possessed different forms of intelligences and most students had more than one forms of intelligence. Of seven forms of intelligence, only three forms of intelligence such as logical/mathematical, musical, and spatial were positively correlated with the IQ score. Even in the children with low IQ, many students had other forms of intelligences. The IQ scores correlated with only logical/mathematical, spatial, and musical intelligence. Hence, tapping the intelligences of students can help enhance their learning process. Our curriculum should have an amalgamation of teaching for all kinds of intelligences for maximum productivity.

Relating streamflow characteristics to specialized insectivores in the Tennessee River Valley: a regional approach

USGS Publications Warehouse

Knight, Rodney R.; Gregory, M. Brian; Wales, Amy K.

2008-01-01

Analysis of hydrologic time series and fish community data across the Tennessee River Valley identified three hydrologic metrics essential to habitat suitability and food availability for insectivorous fish communities in streams of the Tennessee River Valley: constancy (flow stability or temporal invariance), frequency of moderate flooding (frequency of habitat disturbance), and rate of streamflow recession. Initial datasets included 1100 fish community sites and 300 streamgages. Reduction of these datasets to sites with coexisting data yielded 33 sites with streamflow and fish community data for analysis. Identification of critical hydrologic metrics was completed using a multivariate correlation procedure that maximizes the rank correlation between the hydrologic metrics and fish community resemblance matrices. Quantile regression was used to define thresholds of potential ranges of insectivore scores for given values of the hydrologic metrics. Increased values of constancy and insectivore scores were positively correlated. Constancy of streamflow maintains wetted perimeter, which is important for providing habitat for fish spawning and increased surface area for invertebrate colonization and reproduction. Site scores for insectivorous fish increased as the frequency of moderate flooding (3 times the median annual streamflow) decreased, suggesting that insectivorous fish communities respond positively to less frequent disturbance and a more stable habitat. Increased streamflow recession rates were associated with decreased insectivore scores. Increased streamflow recession can strand fish in pools and other areas that are disconnected from flowing water and remove invertebrates as food sources that were suspended during high-streamflow events.

Significantly improved neurocognitive function in major depressive disorders 6 weeks after ECT.

PubMed

Mohn, Christine; Rund, Bjørn Rishovd

2016-09-15

Cognitive side effects may occur after electroconvulsive treatment (ECT) in depressive disorder patients. Previous studies have been limited by small numbers of cognitive functions assessed. The present study reports the first results from a prospective project monitoring cognitive effects of ECT using a comprehensive neuropsychological test battery and subjective report of everyday cognitive function. Thirty-one patients with major depressive disorder were assessed with the MATRICS Consensus Cognitive Battery (MCCB). Subjective cognitive complaints were described with the Everyday Memory Questionnaire (EMQ). Severity of depression symptoms were assessed with the Montgomery-Åsberg Depression Rating Scale (MADRS). These assessments were performed prior to and 6 weeks after non-standardized ECT. Compared to baseline, the mean depression severity level was nearly halved and there were significant improvements in mean levels of Speed of Processing, Attention/Vigilance, and Visual Learning 6 weeks after ECT. The other cognitive domains were not altered from baseline. There was no significant change in subjective cognitive complaints. At baseline, there were several significant correlations between the MADRS and MCCB scores. There was no strong association between the EMQ and MCCB scores at either assessment point, but the post-ECT EMQ score was significantly correlated with depression severity. Major limitations were low N and lack of uniform ECT procedure. There was significant improvement in Speed of Processing, Attention/Vigilance, and Visual Learning 6 weeks after ECT. Cognitive tests scores were related to severity of depression, but not to subjective memory complaints. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantification of VX Nerve Agent in Various Food Matrices by Solid-Phase Extraction Ultra-Performance Liquid ChromatographyTime-of-Flight Mass Spectrometry

DTIC Science & Technology

2016-04-01

QUANTIFICATION OF VX NERVE AGENT IN VARIOUS FOOD MATRICES BY SOLID-PHASE EXTRACTION ULTRA-PERFORMANCE...TITLE AND SUBTITLE Quantification of VX Nerve Agent in Various Food Matrices by Solid-Phase Extraction Ultra-Performance Liquid Chromatography... food matrices. The mixed-mode cation exchange (MCX) sorbent and Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) methods were used for

Novel image compression-encryption hybrid algorithm based on key-controlled measurement matrix in compressive sensing

NASA Astrophysics Data System (ADS)

Zhou, Nanrun; Zhang, Aidi; Zheng, Fen; Gong, Lihua

2014-10-01

The existing ways to encrypt images based on compressive sensing usually treat the whole measurement matrix as the key, which renders the key too large to distribute and memorize or store. To solve this problem, a new image compression-encryption hybrid algorithm is proposed to realize compression and encryption simultaneously, where the key is easily distributed, stored or memorized. The input image is divided into 4 blocks to compress and encrypt, then the pixels of the two adjacent blocks are exchanged randomly by random matrices. The measurement matrices in compressive sensing are constructed by utilizing the circulant matrices and controlling the original row vectors of the circulant matrices with logistic map. And the random matrices used in random pixel exchanging are bound with the measurement matrices. Simulation results verify the effectiveness, security of the proposed algorithm and the acceptable compression performance.

Intrinsic character of Stokes matrices

NASA Astrophysics Data System (ADS)

Gagnon, Jean-François; Rousseau, Christiane

2017-02-01

Two germs of linear analytic differential systems x k + 1Y‧ = A (x) Y with a non-resonant irregular singularity are analytically equivalent if and only if they have the same eigenvalues and equivalent collections of Stokes matrices. The Stokes matrices are the transition matrices between sectors on which the system is analytically equivalent to its formal normal form. Each sector contains exactly one separating ray for each pair of eigenvalues. A rotation in S allows supposing that R+ lies in the intersection of two sectors. Reordering of the coordinates of Y allows ordering the real parts of the eigenvalues, thus yielding triangular Stokes matrices. However, the choice of the rotation in x is not canonical. In this paper we establish how the collection of Stokes matrices depends on this rotation, and hence on a chosen order of the projection of the eigenvalues on a line through the origin.

Sensitivity and Specificity of Fenyö-Lindberg and Teicher Scores in the Diagnosis of Acute Appendicitis in Women

PubMed

Madžar, Zrinko; Kopljar, Mario; Madžar, Tomislav; Mesić, Marko; Mužina Mišić, Dubravka; Čiček, Slaven; Zovak, Mario

2016-12-01

The aim of the study was to assess diagnostic accuracy (sensitivity and specificity) of Fenyö-Lindberg and Teicher scores for distinguishing patients that need immediate surgical treatment from the others, in a female population from an urban setting. The study prospectively included 130 female patients admitted to the emergency department with abdominal pain indicating acute appendicitis. The scores and parameters of validity were calculated and compared to definitive diagnosis. For Fenyö-Lindberg score of -17 or less, 84.5% sensitivity, 55.6% specificity, 87.9% positive predictive value (PPV) and 48.4% negative predictive value (NPV) were recorded. For cut-off value greater or equal to -2, there was 59.2% sensitivity, 77.8% specificity, 91% PPV and 33.3% NPV. The Receiver Operating Characteristic (ROC) curve analysis of Fenyö-Lindberg score showed that the best single cut-off value for discriminating acute appendicitis in the study population was -15. For Teicher score, values greater than -3 yielded 89.3% sensitivity and 22.2% specificity, 81.4% PPV and 35.3% NPV. In conclusion, Fenyö-Lindberg score could be used as an additional tool to exclude appendicitis and avoid unnecessary appendectomies. Teicher score may help in recognizing patients with appendicitis. None of the two scores can indicate or decline appendectomy in all cases. Scoring systems may be useful for pointing to important clinical signs and symptoms in specific subpopulations.

Efficient linear algebra routines for symmetric matrices stored in packed form.

PubMed

Ahlrichs, Reinhart; Tsereteli, Kakha

2002-01-30

Quantum chemistry methods require various linear algebra routines for symmetric matrices, for example, diagonalization or Cholesky decomposition for positive matrices. We present a small set of these basic routines that are efficient and minimize memory requirements.

Evaluation of modified Alvarado scoring system and RIPASA scoring system as diagnostic tools of acute appendicitis.

PubMed

Shuaib, Abdullah; Shuaib, Ali; Fakhra, Zainab; Marafi, Bader; Alsharaf, Khalid; Behbehani, Abdullah

2017-01-01

Acute appendicitis is the most common surgical condition presented in emergency departments worldwide. Clinical scoring systems, such as the Alvarado and modified Alvarado scoring systems, were developed with the goal of reducing the negative appendectomy rate to 5%-10%. The Raja Isteri Pengiran Anak Saleha Appendicitis (RIPASA) scoring system was established in 2008 specifically for Asian populations. The aim of this study was to compare the modified Alvarado with the RIPASA scoring system in Kuwait population. This study included 180 patients who underwent appendectomies and were documented as having "acute appendicitis" or "abdominal pain" in the operating theatre logbook (unit B) from November 2014 to March 2016. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy, predicted negative appendectomy and receiver operating characteristic (ROC) curve of the modified Alvarado and RIPASA scoring systems were derived using SPSS statistical software. A total of 136 patients were included in this study according to our criteria. The cut-off threshold point of the modified Alvarado score was set at 7.0, which yielded a sensitivity of 82.8% and a specificity of 56%. The PPV was 89.3% and the NPV was 42.4%. The cut-off threshold point of the RIPASA score was set at 7.5, which yielded a 94.5% sensitivity and an 88% specificity. The PPV was 97.2% and the NPV was 78.5%. The predicted negative appendectomy rates were 10.7% and 2.2% for the modified Alvarado and RIPASA scoring systems, respectively. The negative appendectomy rate decreased significantly, from 18.4% to 10.7% for the modified Alvarado, and to 2.2% for the RIPASA scoring system, which was a significant difference (P<0.001) for both scoring systems. Based on the results of this study, the RIPASA score is a simple scoring system with better sensitivity and specificity than the modified Alvarado scoring system in Asian populations. It consists of 14 clinical parameters that can be obtained from a good patient history, clinical examination and laboratory investigations. The RIPASA scoring system is more accurate and specific than the modified Alvarado scoring system for Kuwait population.

Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

NASA Astrophysics Data System (ADS)

Jepsen, Morten Leth; Harmsen, Charlotte; Godbole, Adwait Anand; Nagaraja, Valakunja; Knudsen, Birgitta R.; Ho, Yi-Ping

2015-12-01

We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes. Electronic supplementary information (ESI) available: Characterization of the QD-based DNA Nanosensor. See DOI: 10.1039/c5nr06326d

Analytical validation of BRAF mutation testing from circulating free DNA using the amplification refractory mutation testing system.

PubMed

Aung, Kyaw L; Donald, Emma; Ellison, Gillian; Bujac, Sarah; Fletcher, Lynn; Cantarini, Mireille; Brady, Ged; Orr, Maria; Clack, Glen; Ranson, Malcolm; Dive, Caroline; Hughes, Andrew

2014-05-01

BRAF mutation testing from circulating free DNA (cfDNA) using the amplification refractory mutation testing system (ARMS) holds potential as a surrogate for tumor mutation testing. Robust assay validation is needed to establish the optimal clinical matrix for measurement and cfDNA-specific mutation calling criteria. Plasma- and serum-derived cfDNA samples from 221 advanced melanoma patients were analyzed for BRAF c.1799T>A (p.V600E) mutation using ARMS in two stages in a blinded fashion. cfDNA-specific mutation calling criteria were defined in stage 1 and validated in stage 2. cfDNA concentrations in serum and plasma, and the sensitivities and specificities of BRAF mutation detection in these two clinical matrices were compared. Sensitivity of BRAF c.1799T>A (p.V600E) mutation detection in cfDNA was increased by using mutation calling criteria optimized for cfDNA (these criteria were adjusted from those used for archival tumor biopsies) without compromising specificity. Sensitivity of BRAF mutation detection in serum was 44% (95% CI, 35% to 53%) and in plasma 52% (95% CI, 43% to 61%). Specificity was 96% (95% CI, 90% to 99%) in both matrices. Serum contains significantly higher total cfDNA than plasma, whereas the proportion of tumor-derived mutant DNA was significantly higher in plasma. Using mutation calling criteria optimized for cfDNA improves sensitivity of BRAF c.1799T>A (p.V600E) mutation detection. The proportion of tumor-derived cfDNA in plasma was significantly higher than in serum. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Stroke is predicted by low visuospatial in relation to other intellectual abilities and coronary heart disease by low general intelligence.

PubMed

Kajantie, Eero; Räikkönen, Katri; Henriksson, Markus; Leskinen, Jukka T; Forsén, Tom; Heinonen, Kati; Pesonen, Anu-Katriina; Osmond, Clive; Barker, David J P; Eriksson, Johan G

2012-01-01

Low intellectual ability is associated with an increased risk of coronary heart disease and stroke. Most studies have used a general intelligence score. We studied whether three different subscores of intellectual ability predict these disorders. We studied 2,786 men, born between 1934 and 1944 in Helsinki, Finland, who as conscripts at age 20 underwent an intellectual ability test comprising verbal, visuospatial (analogous to Raven's progressive matrices) and arithmetic reasoning subtests. We ascertained the later occurrence of coronary heart disease and stroke from validated national hospital discharge and death registers. 281 men (10.1%) had experienced a coronary heart disease event and 131 (4.7%) a stroke event. Coronary heart disease was predicted by low scores in all subtests, hazard ratios for each standard deviation (SD) lower score ranging from 1.21 to 1.30 (confidence intervals 1.08 to 1.46). Stroke was predicted by a low visuospatial reasoning score, the corresponding hazard ratio being 1.23 (95% confidence interval 1.04 to 1.46), adjusted for year and age at testing. Adjusted in addition for the two other scores, the hazard ratio was 1.40 (1.10 to 1.79). This hazard ratio was little affected by adjustment for socioeconomic status in childhood and adult life, whereas the same adjustments attenuated the associations between intellectual ability and coronary heart disease. The associations with stroke were also unchanged when adjusted for systolic blood pressure at 20 years and reimbursement for adult antihypertensive medication. Stroke is predicted by low visuospatial reasoning scores in relation to scores in the two other subtests. This association may be mediated by common underlying causes such as impaired brain development, rather than by mechanisms associated with risk factors shared by stroke and coronary heart disease, such as socio-economic status, hypertension and atherosclerosis.

Investigation into Text Classification With Kernel Based Schemes

DTIC Science & Technology

2010-03-01

Document Matrix TDMs Term-Document Matrices TMG Text to Matrix Generator TN True Negative TP True Positive VSM Vector Space Model xxii THIS PAGE...are represented as a term-document matrix, common evaluation metrics, and the software package Text to Matrix Generator ( TMG ). The classifier...AND METRICS This chapter introduces the indexing capabilities of the Text to Matrix Generator ( TMG ) Toolbox. Specific attention is placed on the

Stimulating effect of graphene oxide on myogenesis of C2C12 myoblasts on RGD peptide-decorated PLGA nanofiber matrices.

PubMed

Shin, Yong Cheol; Lee, Jong Ho; Kim, Min Jeong; Hong, Suck Won; Kim, Bongju; Hyun, Jung Keun; Choi, Yu Suk; Park, Jong-Chul; Han, Dong-Wook

2015-01-01

In the field of biomedical engineering, many studies have focused on the possible applications of graphene and related nanomaterials due to their potential for use as scaffolds, coating materials and delivery carriers. On the other hand, electrospun nanofiber matrices composed of diverse biocompatible polymers have attracted tremendous attention for tissue engineering and regenerative medicine. However, their combination is intriguing and still challenging. In the present study, we fabricated nanofiber matrices composed of M13 bacteriophage with RGD peptide displayed on its surface (RGD-M13 phage) and poly(lactic-co-glycolic acid, PLGA) and characterized their physicochemical properties. In addition, the effect of graphene oxide (GO) on the cellular behaviors of C2C12 myoblasts, which were cultured on PLGA decorated with RGD-M13 phage (RGD/PLGA) nanofiber matrices, was investigated. Our results revealed that the RGD/PLGA nanofiber matrices have suitable physicochemical properties as a tissue engineering scaffold and the growth of C2C12 myoblasts were significantly enhanced on the matrices. Moreover, the myogenic differentiation of C2C12 myoblasts was substantially stimulated when they were cultured on the RGD/PLGA matrices in the presence of GO. In conclusion, these findings propose that the combination of RGD/PLGA nanofiber matrices and GO can be used as a promising strategy for skeletal tissue engineering and regeneration.

Electrospun Poly(lactic acid-co-glycolic acid) Scaffolds for Skin Tissue Engineering

PubMed Central

Kumbar, Sangamesh G.; Nukavarapu, Syam Prasad; James, Roshan; Nair, Lakshmi S.; Laurencin, Cato T.

2008-01-01

Electrospun fiber matrices composed of scaffolds of varying fiber diameters were investigated for potential application of severe skin loss. Few systematic studies have been performed to examine the effect of varying fiber diameter electrospun fiber matrices for skin regeneration. The present study reports the fabrication of poly[lactic acid-co-glycolic acid] (PLAGA) matrices with fiber diameters of 150–225, 200–300, 250–467, 500–900, 600–1200, 2500–3000 and 3250–6000 nm via electrospinning. All fiber matrices found to have a tensile modulus from 39.23 ± 8.15 to 79.21 ± 13.71 MPa which falls in the range for normal human skin. Further, the porous fiber matrices have porosity between 38–60 % and average pore diameters between 10–14µm. We evaluated the efficacy of these biodegradable fiber matrices as skin substitutes by seeding them with human skin fibroblasts (hSF). Human skin fibroblasts acquired a well spread morphology and showed significant progressive growth on fiber matrices in the 350–1100 nm diameter range. Collagen type III gene expression was significantly up-regulated in hSF seeded on matrices with fiber diameters in the range of 350–1100 nm. Based on the need, the proposed fiber skin substitutes can be successfully fabricated and optimized for skin fibroblast attachment and growth. PMID:18639927

Redistribution of Sr and rare earth elements in the matrices of CV3 carbonaceous chondrites during aqueous alteration in their parent body

NASA Astrophysics Data System (ADS)

Jogo, Kaori; Ito, Motoo; Nakamura, Tomoki; Kobayashi, Sachio; Lee, Jong Ik

2018-03-01

We measured the abundances of Sr and rare earth elements (REEs) in the matrices of five CV3 carbonaceous chondrites: Meteorite Hills (MET) 00430, MET 01070, La Paz ice field (LAP) 02206, Asuka (A) 881317 and Roberts Massif (RBT) 04143. In the MET 00430 and MET 01074 matrices, the Sr/CI and light REE (LREE, La-Nd)/CI ratios positively correlate with the amounts of Ca-rich secondary minerals, which formed during aqueous alteration in the CV3 chondrite parent body. In contrast, in the LAP 02206 and RBT 04143 matrices, although the Sr/CI ratios correlate with the amounts of Ca-rich secondary minerals, the LREE/CI ratios vary independently from the amounts of any secondary minerals. This suggests that the LREE/CI ratios in these matrices were produced prior to the parent body alteration, probably in the solar nebula. The LREE/CI ratios of the LAP 02206 and RBT 04143 matrices reveal the mixing process of matrix minerals prior to the accretion of the CV3 chondrite parent body. The mixing degrees of matrix minerals might be different between these two matrices. Because solid materials would be mixed over time according to the radial diffusion model of a turbulent disk, the matrix minerals consisting of LAP 02206 and RBT 04143 matrices might be incorporated into their parent body with different timing.

A dissonant scale: stress recognition in the SAQ.

PubMed

Taylor, Jennifer A; Pandian, Ravi

2013-07-31

Our previous analyses using the Stress Recognition subscale of the Safety Attitudes Questionnaire (SAQ) resulted in significant effect estimates with equally opposing explanations. We suspected construct validity issues and investigated such using our own data and correlation matrices of previous published studies. The correlation matrices for each of the SAQ subscales from two previous studies by Speroff and Taylor were replicated and compared. The SAS Proc Factor procedure and the PRIORS = SMC option were used to perform Common Factor Analysis. The correlation matrices of both studies were very similar. Teamwork, Safety Climate, Job Satisfaction, Perceptions of Management and Working Conditions were well-correlated. The correlations ranged from 0.53 to 0.76. For Stress Recognition correlations ranged from -0.15 to 0.03. Common Factor Analysis confirmed the isolation of Stress Recognition. CFA returned a strong one-factor model that explained virtually all of the communal variance. Stress Recognition loaded poorly on this factor in both instances, and the CFA indicated that 96.4-100.0% of the variance associated with Stress Recognition was unique to that subscale, and not shared with the other 5 subscales. We conclude that the Stress Recognition subscale does not fit into the overall safety climate construct the SAQ intended to reflect. We recommend that this domain be omitted from overall safety climate scale score calculations, and clearly identified as an important yet distinct organizational construct. We suggest that this subscale be investigated for its true meaning, characterized as such, and findings conveyed to SAQ end users. We make no argument against Stress Recognition as an important organizational metric, rather we suggest that as a stand-alone construct its current packaging within the SAQ may be misleading for those intent on intervention development and evaluation in healthcare settings if they interpret Stress Recognition results as emblematic of safety climate.

Gender-related decrease in raven`s progressive matrices scores in children prenatally exposed to polychlorinated biphenyls and related contaminants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Y.L.; Lai, T.J.; Chen, S.J.

1995-07-01

Polychlorinated biphenyls (PCBs) and industrial mixtures that have been widely used throughout the world. PCBs have long environmental half lives and bioconcentrate, therefore contaminating soil, water, wild life, and human tissues. Typical human exposures come from environmental contamination of food supply, especially fresh water fish and meat, and occupational exposures. In certain uses, PCBs can partially oxidize and themselves become contaminated by extremely toxic compounds such as polychlorinated dibenzofurans (PCDFs). Two episodes of intoxication with heat-degraded PCBs have occurred, in Japan and Taiwan respectively. In 1979, over 2000 persons in Taiwan were intoxicated by heat-degraded PCBs that had contaminated theirmore » cooking oil. Kaneclor 500 (a Japanese PCB mixture) contained in the heating pipe was used as the heat transmitter. Leakage of the pipe introduced PCBs and heat-degraded products such as polychlorinated dibenzofurans (PCDFs) and polychlorinated quaterphenyls (PCQs) into the rice oil. Exposed victims developed chloracne, hyperpigmentation, peripheral neuropathy, and other signs and symptoms which were later called Yu-Cheng ({open_quotes}oil disease{close_quotes}) in Taiwan. These symptoms were caused not only by PCBs but by their heat degraded products, PCDFs. PCBs, PCDFs and PCDDs also can cross the placenta to affect the fetus and cause significant neurodevelopmental toxicity. Raven`s Colored Progressive Matrices (CPM) and Standarized Progressive Matrices (SPM) test spatial rather than verbal capabilities in children. These test are useful for determining whether prenatal exposure to PCBs/PCDFs cause differential effects on boys and girls. This paper reports results of CPM and SPM from age six to nine year in Yu-Cheng children and their matched controls. Cognative deficits up to 9 years of age were detected n children with prenatal exposure to PCBs and PCDFs, and boys were more affected than girls. 26 refs., 1 fig., 2 tabs.« less

Sex Differences in Task Distribution and Task Exposures among Danish House Painters: An Observational Study Combining Questionnaire Data with Biomechanical Measurements

PubMed Central

Heilskov-Hansen, Thomas; Wulff Svendsen, Susanne; Frølund Thomsen, Jane; Mikkelsen, Sigurd; Hansson, Gert-Åke

2014-01-01

Objectives Sex differences in occupational biomechanical exposures may be part of the explanation why musculoskeletal complaints and disorders tend to be more common among women than among men. We aimed to determine possible sex differences in task distribution and task-specific postures and movements of the upper extremities among Danish house painters, and to establish sex-specific task exposure matrices. Methods To obtain task distributions, we sent out a questionnaire to all members of the Painters' Union in Denmark (N = 9364), of whom 53% responded. Respondents reported their task distributions in a typical week. To obtain task exposures, postures and movements were measured in 25 male and 25 female house painters for one whole working day per person. We used goniometers on the wrists, and inclinometers on the forehead and the upper arms. Participants filled in a logbook allowing task-specific exposures to be identified. Percentiles and % time with non-neutral postures were used to characterise postures. Velocity, range of motion, repetitiveness, and variation were used as measures of movement. Cochran-Mantel-Haenszel statistics and unpaired double-sided t-tests with post-hoc Bonferroni correction were used to evaluate sex differences. Results Statistically significant (p<0.05) sex differences were revealed in task proportions, but the proportions differed by less than 4%. For task exposures, no statistically significant sex differences were found. Conclusions Only minor sex differences were found in task distribution and task exposures regarding postures and movements among Danish house painters. Sex-specific task exposure matrices were established. PMID:25365301

Improving Consumer Satisfaction with Addiction Treatment: An Analysis of Alumni Preferences.

PubMed

Sanghani, Ruchi M; Moler, Alexander K

2015-01-01

Objective. The primary objective of this investigation is to determine which individual and aggregate factors of residential addiction treatment centers are most significant influencers of alumni satisfaction. Design. Survey targeted alumni of residential addiction treatment facilities. Alumni were queried through a survey, which utilized Likert-scale matrices and binary response options: 379 respondents met the completion threshold. Alumni rated amenities and individual and group counseling factors; additionally, respondents provided feedback on two satisfaction proxies: cost worthiness and future recommendations. Descriptive and relational analyses were conducted, with the latter utilizing logistic regression models. Results. Individual factors' scores of group counseling, and overall aggregate group counseling score, are most enthusiastically positive. Group counseling is also the most significant influencer of satisfaction. Other significant influencers of satisfaction are met expectations for individual counseling and psychiatric care offerings. Conclusions. While individual counseling and facility amenities should not be ignored, group counseling may be the most significant influencer of alumni satisfaction. Long-term outcomes are not single-faceted; however, treatment providers should be encouraged to invest in high-quality group counseling offerings in order to best satisfy, and thereby empower, clients.

Does WISC-IV Underestimate the Intelligence of Autistic Children?

PubMed

Nader, Anne-Marie; Courchesne, Valérie; Dawson, Michelle; Soulières, Isabelle

2016-05-01

Wechsler Intelligence Scale for Children (WISC) is widely used to estimate autistic intelligence (Joseph in The neuropsychology of autism. Oxford University Press, Oxford, 2011; Goldstein et al. in Assessment of autism spectrum disorders. Guilford Press, New York, 2008; Mottron in J Autism Dev Disord 34(1):19-27, 2004). However, previous studies suggest that while WISC-III and Raven's Progressive Matrices (RPM) provide similar estimates of non-autistic intelligence, autistic children perform significantly better on RPM (Dawson et al. in Psychol Sci 18(8):657-662, doi: 10.1111/j.1467-9280.2007.01954.x , 2007). The latest WISC version introduces substantial changes in subtests and index scores; thus, we asked whether WISC-IV still underestimates autistic intelligence. Twenty-five autistic and 22 typical children completed WISC-IV and RPM. Autistic children's RPM scores were significantly higher than their WISC-IV FSIQ, but there was no significant difference in typical children. Further, autistic children showed a distinctively uneven WISC-IV index profile, with a "peak" in the new Perceptual Reasoning Index. In spite of major changes, WISC-IV FSIQ continues to underestimate autistic intelligence.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Detecting cis-regulatory binding sites for cooperatively binding proteins

PubMed Central

van Oeffelen, Liesbeth; Cornelis, Pierre; Van Delm, Wouter; De Ridder, Fedor; De Moor, Bart; Moreau, Yves

2008-01-01

Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM-based methods where biophysical cooperativity is not taken into account. PMID:18400778

Improving Consumer Satisfaction with Addiction Treatment: An Analysis of Alumni Preferences

PubMed Central

Sanghani, Ruchi M.; Moler, Alexander K.

2015-01-01

Objective. The primary objective of this investigation is to determine which individual and aggregate factors of residential addiction treatment centers are most significant influencers of alumni satisfaction. Design. Survey targeted alumni of residential addiction treatment facilities. Alumni were queried through a survey, which utilized Likert-scale matrices and binary response options: 379 respondents met the completion threshold. Alumni rated amenities and individual and group counseling factors; additionally, respondents provided feedback on two satisfaction proxies: cost worthiness and future recommendations. Descriptive and relational analyses were conducted, with the latter utilizing logistic regression models. Results. Individual factors' scores of group counseling, and overall aggregate group counseling score, are most enthusiastically positive. Group counseling is also the most significant influencer of satisfaction. Other significant influencers of satisfaction are met expectations for individual counseling and psychiatric care offerings. Conclusions. While individual counseling and facility amenities should not be ignored, group counseling may be the most significant influencer of alumni satisfaction. Long-term outcomes are not single-faceted; however, treatment providers should be encouraged to invest in high-quality group counseling offerings in order to best satisfy, and thereby empower, clients. PMID:26483986

Analysing generator matrices G of similar state but varying minimum determinants

NASA Astrophysics Data System (ADS)

Harun, H.; Razali, M. F.; Rahman, N. A. Abdul

2016-10-01

Since Tarokh discovered Space-Time Trellis Code (STTC) in 1998, a considerable effort has been done to improve the performance of the original STTC. One way of achieving enhancement is by focusing on the generator matrix G, which represents the encoder structure for STTC. Until now, researchers have only concentrated on STTCs of different states in analyzing the performance of generator matrix G. No effort has been made on different generator matrices G of similar state. The reason being, it is difficult to produce a wide variety of generator matrices G with diverse minimum determinants. In this paper a number of generator matrices G with minimum determinant of four (4), eight (8) and sixteen (16) of the same state (i.e., 4-PSK) have been successfully produced. The performance of different generator matrices G in term of their bit error rate and signal-to-noise ratio for a Rayleigh fading environment are compared and evaluated. It is found from the MATLAB simulation that at low SNR (<8), the BER of generator matrices G with smaller minimum determinant is comparatively lower than those of higher minimum determinant. However, at high SNR (>14) there is no significant difference between the BER of these generator matrices G.

Determination of glyoxal and methylglyoxal in environmental and biological matrices by stir bar sorptive extraction with in-situ derivatization.

PubMed

Neng, N R; Cordeiro, C A A; Freire, A P; Nogueira, J M F

2007-10-26

Stir bar sorptive extraction with in-situ derivatization using 2,3-diaminonaphthalene (DAN) followed by liquid desorption and high performance liquid chromatography with diode array detection (SBSE(DAN)in-situ-LD-HPLC-DAD) was developed for the determination of glyoxal (Gly) and methylglyoxal (MGly) in environmental and biological matrices. DAN proved very good specificity as in-situ derivatising agent for Gly and MGly in aqueous media, allowing the formation of adducts with remarkable sensitivity, selectivity and the absence of photodegradation. Assays performed on spiked (1.0 microg L(-1)) water samples, under convenient experimental conditions, yielded recoveries of 96.2+/-7.9% for Gly and 96.1+/-6.4% for MGly. The analytical performance showed good accuracy, suitable precision (<12.0%), low detection limits (15 ng L(-1) for Gly and 25 ng L(-1) for MGly adducts) and excellent linear dynamic ranges (r2>0.99) from 0.1 to 120.0 microg L(-1). By using the standard addition method, the application of the present method to tap and swimming-pool water, beer, yeast cells suspension and urine samples allowed very good performance at the trace level. The proposed methodology proved to be a feasible alternative for routine quality control analysis, showing to be easy to implement, reliable, sensitive and with a low sample volume requirement to monitor Gly and MGly in environmental and biological matrices.

Simultaneous detection of the protozoan parasites Toxoplasma, Cryptosporidium and Giardia in food matrices and their persistence on basil leaves.

PubMed

Hohweyer, Jeanne; Cazeaux, Catherine; Travaillé, Emmanuelle; Languet, Emilie; Dumètre, Aurélien; Aubert, Dominique; Terryn, Christine; Dubey, Jitender P; Azas, Nadine; Houssin, Maryline; Loïc, Favennec; Villena, Isabelle; La Carbona, Stéphanie

2016-08-01

Toxoplasma gondii, Cryptosporidium spp. and Giardia intestinalis are emerging pathogen parasites in the food domain. However, without standardized methods for their detection in food matrices, parasitic foodborne outbreaks remain neglected. In this study, a new immunomagnetic separation assay (IMS Toxo) targeting the oocyst's wall of T. gondii was developed using a specific purified monoclonal antibody. Performance of this IMS Toxo coupled to microscopic and qPCR analyses was evaluated in terms of limit of detection (LOD) and recovery rate (RR) on: i) simple matrix (LOD = 5 oocysts; RR between 5 and 56%); ii) raspberries and basil (LOD = 33 oocysts/g; RR between 0.2 and 35%). Finally, to simultaneously extract the three protozoa from these food matrices, T. gondii oocysts were directly concentrated (without IMS Toxo) from the supernatant of the IMS of Cryptosporidium and Giardia (oo)cysts. This strategy associated to qPCR detection led to LOD <1 to 3 (oo)cysts/g and RR between 2 and 35%. This procedure was coupled to RT-qPCR analyses and showed that the three protozoa persisted on the leaves of basil and remained viable following storage at 4 °C for 8 days. These data strengthen the need to consider these protozoa in food safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.

PubMed

Kim, Tane; Hao, Weilong

2014-09-27

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data. DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

NMR Quantification of Carbohydrates in Complex Mixtures. A Challenge on Honey.

PubMed

Schievano, Elisabetta; Tonoli, Marco; Rastrelli, Federico

2017-12-19

The knowledge of carbohydrate composition is greatly important to determine the properties of natural matrices such as foodstuff and food ingredients. However, because of the structural similarity and the multiple isomeric forms of carbohydrates in solution, their analysis is often a complex task. Here we propose an NMR analytical procedure based on highly selective chemical shift filters followed by TOCSY, which allows us to acquire specific background-free signals for each sugar. The method was tested on raw honey samples dissolved in water with no other pretreatment. In total, 22 sugars typically found in honey were quantified: 4 monosaccharides (glucose, fructose, mannose, rhamnose), 11 disaccharides (sucrose, trehalose, turanose, maltose, maltulose, palatinose, melibiose and melezitose, isomaltose, gentiobiose nigerose, and kojibiose), and 7 trisaccharides (raffinose, isomaltotriose, erlose, melezitose, maltotriose, panose, and 1-kestose). Satisfactory results in terms of limit of quantification (0.03-0.4 g/100g honey), precision (% RSD: 0.99-4.03), trueness (bias % 0.4-4.2), and recovery (97-104%) were obtained. An accurate control of the instrumental temperature and of the sample pH endows an optimal chemical shift reproducibility, making the procedure amenable to automation and suitable to routine analysis. While validated on honey, which is one of the most complex natural matrices in terms of saccharides composition, this innovative approach can be easily transferred to other natural matrices.

Spectrophotometric versus NIR-MIR assessments of cowpea pods for discriminating the impact of freezing.

PubMed

Machado, Nelson; Domínguez-Perles, Raúl; Ramos, Ana; Rosa, Eduardo As; Barros, Ana Irna

2017-10-01

Freezing represents an important storage method for vegetal foodstuffs, such as cowpea pods, and thus the impact of this process on the chemical composition of these matrices arises as a prominent issue. In this sense, the phytochemical contents in frozen cowpea pods (i.e. at 6 and 9 months) have been compared with fresh cowpea pods material, with the samples being concomitantly assessed by Fourier-transform infrared spectroscopy (FTIR), both mid-infrared (MIR) and near infrared (NIR), aiming to evaluate the potential of these techniques as a rapid tool for the traceability of these matrices. A decrease in phytochemical contents during freezing was observed, allowing the classification of samples according to the freezing period based on such variations. Also, MIR and NIR allowed discrimination of samples: the use of the first derivative demonstrated a better performance for this purpose, whereas the use of the normalized spectra gave the best correlations between the spectra and specific contents. In both cases, NIR displayed the best performance. Freezing of cowpea pods leads to a decrease of phytochemical contents, which can be monitored by FTIR spectroscopy, both within the MIR and NIR ranges, whereas the use of this technique, in tandem with chemometrics, constitutes a suitable methodology for the traceability of these matrices. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Effects of Pressure-shift Freezing on the Structural and Physical Properties of Gelatin Hydrogel Matrices

PubMed Central

Kim, Byeongsoo; Gil, Hyung Bae; Min, Sang-Gi; Lee, Si-Kyung; Choi, Mi-Jung

2014-01-01

This study investigates the effects of the gelatin concentration (10-40%, w/v), freezing temperatures (from -20℃ to -50℃) and freezing methods on the structural and physical properties of gelatin matrices. To freeze gelatin, the pressure-shift freezing (PSF) is being applied at 0.1 (under atmospheric control), 50 and 100 MPa, respectively. The freezing point of gelatin solutions decrease with increasing gelatin concentrations, from -0.2℃ (10% gelatin) to -6.7℃ (40% gelatin), while the extent of supercooling did not show any specific trends. The rheological properties of the gelatin indicate that both the storage (G') and loss (G") moduli were steady in the strain amplitude range of 0.1-10%. To characterize gelatin matrices formed by the various freezing methods, the ice crystal sizes which were being determined by the scanning electron microscopy (SEM) are affected by the gelatin concentrations. The ice crystal sizes are affected by gelatin concentrations and freezing temperature, while the size distributions of ice crystals depend on the freezing methods. Smaller ice crystals are being formed with PSF rather than under the atmospheric control where the freezing temperature is above -40℃. Thus, the results of this study indicate that the PSF processing at a very low freezing temperature (-50℃) offers a potential advantage over commercial atmospheric freezing points for the formation of small ice crystals. PMID:26760743

Extraction Methodological Contributions Toward Ultra-Performance Liquid ChromatographyTime-of-Flight Mass Spectrometry: Quantification of Free GB from Various Food Matrices

DTIC Science & Technology

2016-02-01

SPECTROMETRY: QUANTIFICATION OF FREE GB FROM VARIOUS FOOD MATRICES ECBC-TR-1351 Sue Y. Bae Mark D. Winemiller RESEARCH AND TECHNOLOGY DIRECTORATE...Flight Mass Spectrometry: Quantification of Free GB from Various Food Matrices 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...methylphosphonofluoridate (sarin, GB) in various food matrices. The development of a solid-phase extraction method using a normal-phase silica gel column for

Bunch-Kaufman factorization for real symmetric indefinite banded matrices

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1989-01-01

The Bunch-Kaufman algorithm for factoring symmetric indefinite matrices was rejected for banded matrices because it destroys the banded structure of the matrix. Herein, it is shown that for a subclass of real symmetric matrices which arise in solving the generalized eigenvalue problem using Lanczos's method, the Bunch-Kaufman algorithm does not result in major destruction of the bandwidth. Space time complexities of the algorithm are given and used to show that the Bunch-Kaufman algorithm is a significant improvement over LU factorization.

Fluorescent fingerprints of edible oils and biodiesel by means total synchronous fluorescence and Tucker3 modeling

NASA Astrophysics Data System (ADS)

Insausti, Matías; de Araújo Gomes, Adriano; Camiña, José Manuel; de Araújo, Mario Cesar Ugulino; Band, Beatriz Susana Fernández

2017-03-01

The present work proposes the use of total synchronous fluorescence spectroscopy (TSFS) as a discrimination methodology for fluorescent compounds in edible oils, which are preserved after the transesterification processes in the biodiesel production. In the same way, a similar study is presented to identify fluorophores that do not change in expired vegetal oils, to associate physicochemical parameters to fluorescent measures, as contribution to a fingerprint for increasing the chemical knowledge of these products. The fluorescent fingerprints were obtained by Tucker3 decomposition of a three-way array of the total synchronous fluorescence matrices. This chemometric method presents the ability for modeling non-bilinear data, as Total Synchronous Fluorescence Spectra data, and consists in the decomposition of the three way data arrays (samples × Δλ × λ excitation), into four new data matrices: A (scores), B (profile in Δλ mode), C (profile in spectra mode) and G (relationships between A, B and C). In this study, 50 samples of oil from soybean, corn and sunflower seeds before and after its expiration time, as well as 50 biodiesel samples obtained by transesterification of the same oils were measured by TSFS. This study represents an immediate application of chemical fingerprint for the discrimination of non-expired and expired edible oils and biodiesel. This method does not require the use of reagents or laborious procedures for the chemical characterization of samples.

New approach for rapid assessment of trophic status of Yellow Sea and East China Sea using easy-to-measure parameters

NASA Astrophysics Data System (ADS)

Kong, Xianyu; Liu, Yanfang; Jian, Huimin; Su, Rongguo; Yao, Qingzhen; Shi, Xiaoyong

2017-10-01

To realize potential cost savings in coastal monitoring programs and provide timely advice for marine management, there is an urgent need for efficient evaluation tools based on easily measured variables for the rapid and timely assessment of estuarine and offshore eutrophication. In this study, using parallel factor analysis (PARAFAC), principal component analysis (PCA), and discriminant function analysis (DFA) with the trophic index (TRIX) for reference, we developed an approach for rapidly assessing the eutrophication status of coastal waters using easy-to-measure parameters, including chromophoric dissolved organic matter (CDOM), fluorescence excitation-emission matrices, CDOM UV-Vis absorbance, and other water-quality parameters (turbidity, chlorophyll a, and dissolved oxygen). First, we decomposed CDOM excitation-emission matrices (EEMs) by PARAFAC to identify three components. Then, we applied PCA to simplify the complexity of the relationships between the water-quality parameters. Finally, we used the PCA score values as independent variables in DFA to develop a eutrophication assessment model. The developed model yielded classification accuracy rates of 97.1%, 80.5%, 90.3%, and 89.1% for good, moderate, and poor water qualities, and for the overall data sets, respectively. Our results suggest that these easy-to-measure parameters could be used to develop a simple approach for rapid in-situ assessment and monitoring of the eutrophication of estuarine and offshore areas.

Biodegradable organic acid-crosslinked alkali-treated gelatins with anti-thrombogenic and endothelialization properties

PubMed Central

Inoue, Motoki; Sasaki, Makoto; Taguchi, Tetsushi

2012-01-01

Gelatins were crosslinked with organic acids and treated with alkali to impart to them endothelialization and anti-thrombogenic properties. These matrices were characterized by biochemical and physicochemical techniques. The amounts of residual amino groups in the matrices decreased with increasing crosslinker concentration. The matrices with the highest crosslinking densities showed excellent endothelial cell adhesion and proliferation. In addition, the adhesion of platelets and formation of fibrin networks on the matrices were suppressed with increasing crosslinker concentration. The matrices also exhibited excellent biodegradability, and the degradation rate decreased with increasing crosslinking density. All the organic acid-crosslinked alkali-treated gelatins showed excellent anti-thrombogenic and endothelialization properties, superior to those of glutaraldehyde-crosslinked alkali-treated gelatins. PMID:27877542

Grades of undernutrition and socioeconomic status influence cognitive development in school children of Kolkata.

PubMed

Ghosh, Satabdi; Chowdhury, Sutanu Dutta; Chandra, Ananga Mohan; Ghosh, Tusharkanti

2015-02-01

Cognitive development of children is influenced by different environmental factors like nutritional and socio-economic status. The objectives of the present study were to determine the influence of grades of undernutrition and socio-economic status (SES) on the cognitive development of school children of Kolkata. Five hundred sixty six (566) school children having 5-12 years of age were selected from different schools of Kolkata. The cognitive development was measured by the scores of Raven's colored progressive matrices (RCPM). The chronic and acute nutritional statuses were measured from height-for-age (HAZ) and weight-for-age (WAZ) Z scores respectively with reference to the values of WHO. SES was determined by updated Kuppuswamy scale. The prevalences of undernutrition in the observed children were 57.95% (according to HAZ) and 52.82% (according to WAZ). The age dependent growth curve of RCPM scores of the observed children remains in between the 10th and 25th centile of British children. The children belonging to superior and intellectual deficit IQ classes were 21.55 and 36.40%, respectively of the total subjects. Most of the subjects belong to lower middle (39.93%) and upper middle (36.40%) class of SES. RCPM scores of school children were gradually decreased with the grades of undernutrition and SES. RCPM scores were significantly correlated with HAZ, WAZ, SES, age, and sex (P < 0.001) and strongly associated with HAZ, SES, age, and sex (P < 0.001, P < 0.05). Present study indicates that cognitive development of school children of Kolkata is influenced by the grade of undernutrition and SES. © 2015 Wiley Periodicals, Inc.

Emotion perception, non-social cognition and symptoms as predictors of theory of mind in schizophrenia.

PubMed

Vaskinn, Anja; Andersson, Stein; Østefjells, Tiril; Andreassen, Ole A; Sundet, Kjetil

2018-06-05

Theory of mind (ToM) can be divided into cognitive and affective ToM, and a distinction can be made between overmentalizing and undermentalizing errors. Research has shown that ToM in schizophrenia is associated with non-social and social cognition, and with clinical symptoms. In this study, we investigate cognitive and clinical predictors of different ToM processes. Ninety-one individuals with schizophrenia participated. ToM was measured with the Movie for the Assessment of Social Cognition (MASC) yielding six scores (total ToM, cognitive ToM, affective ToM, overmentalizing errors, undermentalizing errors and no mentalizing errors). Neurocognition was indexed by a composite score based on the non-social cognitive tests in the MATRICS Consensus Cognitive Battery (MCCB). Emotion perception was measured with Emotion in Biological Motion (EmoBio), a point-light walker task. Clinical symptoms were assessed with the Positive and Negative Syndrome Scale (PANSS). Seventy-one healthy control (HC) participants completed the MASC. Individuals with schizophrenia showed large impairments compared to HC for all MASC scores, except overmentalizing errors. Hierarchical regression analyses with the six different MASC scores as dependent variables revealed that MCCB was a significant predictor of all MASC scores, explaining 8-18% of the variance. EmoBio increased the explained variance significantly, to 17-28%, except for overmentalizing errors. PANSS excited symptoms increased explained variance for total ToM, affective ToM and no mentalizing errors. Both social and non-social cognition were significant predictors of ToM. Overmentalizing was only predicted by non-social cognition. Excited symptoms contributed to overall and affective ToM, and to no mentalizing errors. Copyright © 2018 Elsevier Inc. All rights reserved.

The food matrix affects the anthocyanin profile of fortified egg and dairy matrices during processing and in vitro digestion.

PubMed

Pineda-Vadillo, Carlos; Nau, Françoise; Guerin-Dubiard, Catherin; Jardin, Julien; Lechevalier, Valérie; Sanz-Buenhombre, Marisa; Guadarrama, Alberto; Tóth, Tamás; Csavajda, Éva; Hingyi, Hajnalka; Karakaya, Sibel; Sibakov, Juhani; Capozzi, Francesco; Bordoni, Alessandra; Dupont, Didier

2017-01-01

The aim of the present study was to understand to what extent the inclusion of anthocyanins into dairy and egg matrices could affect their stability after processing and their release and solubility during digestion. For this purpose, individual and total anthocyanin content of four different enriched matrices, namely custard dessert, milkshake, pancake and omelettete, was determined after their manufacturing and during in vitro digestion. Results showed that anthocyanin recovery after processing largely varied among matrices, mainly due to the treatments applied and the interactions developed with other food components. In terms of digestion, the present study showed that the inclusion of anthocyanins into food matrices could be an effective way to protect them against intestinal degradation, and also the incorporation of anthocyanins into matrices with different compositions and structures could represent an interesting and effective method to control the delivery of anthocyanins within the different compartments of the digestive tract. Copyright © 2016 Elsevier Ltd. All rights reserved.

Time series, correlation matrices and random matrix models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vinayak; Seligman, Thomas H.

2014-01-08

In this set of five lectures the authors have presented techniques to analyze open classical and quantum systems using correlation matrices. For diverse reasons we shall see that random matrices play an important role to describe a null hypothesis or a minimum information hypothesis for the description of a quantum system or subsystem. In the former case various forms of correlation matrices of time series associated with the classical observables of some system. The fact that such series are necessarily finite, inevitably introduces noise and this finite time influence lead to a random or stochastic component in these time series.more » By consequence random correlation matrices have a random component, and corresponding ensembles are used. In the latter we use random matrices to describe high temperature environment or uncontrolled perturbations, ensembles of differing chaotic systems etc. The common theme of the lectures is thus the importance of random matrix theory in a wide range of fields in and around physics.« less

RGD peptide-displaying M13 bacteriophage/PLGA nanofibers as cell-adhesive matrices for smooth muscle cells

NASA Astrophysics Data System (ADS)

Shin, Yong Cheol; Lee, Jong Ho; Jin, Oh Seong; Lee, Eun Ji; Jin, Lin Hua; Kim, Chang-Seok; Hong, Suck Won; Han, Dong-Wook; Kim, Chuntae; Oh, Jin-Woo

2015-01-01

Extracellular matrices (ECMs) are network structures that play an essential role in regulating cellular growth and differentiation. In this study, novel nanofibrous matrices were fabricated by electrospinning M13 bacteriophage and poly(lactic- co-glycolic acid) (PLGA) and were shown to be structurally and functionally similar to natural ECMs. A genetically-engineered M13 bacteriophage was constructed to display Arg-Gly-Asp (RGD) peptides on its surface. The physicochemical properties of RGD peptide-displaying M13 bacteriophage (RGD-M13 phage)/PLGA nanofibers were characterized by using scanning electron microscopy and Fourier-transform infrared spectroscopy. We used immunofluorescence staining to confirm that M13 bacteriophages were homogenously distributed in RGD-M13 phage/PLGA matrices. Furthermore, RGD-M13 phage/PLGA nanofibrous matrices, having excellent biocompatibility, can enhance the behaviors of vascular smooth muscle cells. This result suggests that RGD-M13 phage/PLGA nanofibrous matrices have potentials to serve as tissue engineering scaffolds.

Reductions in finite-dimensional integrable systems and special points of classical r-matrices

NASA Astrophysics Data System (ADS)

Skrypnyk, T.

2016-12-01

For a given 𝔤 ⊗ 𝔤-valued non-skew-symmetric non-dynamical classical r-matrices r(u, v) with spectral parameters, we construct the general form of 𝔤-valued Lax matrices of finite-dimensional integrable systems satisfying linear r-matrix algebra. We show that the reduction in the corresponding finite-dimensional integrable systems is connected with "the special points" of the classical r-matrices in which they become degenerated. We also propose a systematic way of the construction of additional integrals of the Lax-integrable systems associated with the symmetries of the corresponding r-matrices. We consider examples of the Lax matrices and integrable systems that are obtained in the framework of the general scheme. Among them there are such physically important systems as generalized Gaudin systems in an external magnetic field, ultimate integrable generalization of Toda-type chains (including "modified" or "deformed" Toda chains), generalized integrable Jaynes-Cummings-Dicke models, integrable boson models generalizing Bose-Hubbard dimer models, etc.

PERFORMANCE OF TWO DIFFERENT CLINICAL SCORING SYSTEMS IN DIAGNOSING DISTAL SENSORY POLYNEUROPATHY IN PATIENTS WITH TYPE-2 DIABETES.

PubMed

Khan, Fehmeda Farrukh; Numan, Ahsan; Khawaja, Khadija Irfan; Atif, Ali; Fatima, Aziz; Masud, Faisal

2015-01-01

Early diagnosis of distal peripheral neuropathy (DSPN) the commonest diabetes complications, helps prevent significant morbidity. Clinical parameters are useful for detection, but subjectivity and lack of operator proficiency often results in inaccuracies. Comparative diagnostic accuracy of Diabetic Neuropathy Symptom (DNS) score and Diabetic Neuropathy Examination (DNE) score in detecting DSPN confirmed by nerve conduction studies (NCS) has not been evaluated. This study compares the performance of these scores in predicting the presence of electro physiologically proven DSPN. The objective of this, study was to compare the diagnostic accuracy of DNS and DNE scores in detecting NCS proven DSPN in type-2 diabetics, and to determine the frequency of sub-clinical DSPN among type-2 diabetics. In this cross-sectional study the DNS score and DNE score were determined in 110 diagnosed type-2 diabetic patients. NCS were carried out and amplitudes, velocities and latencies of sensory and motor nerves in lower limb were recorded. Comparison between the two clinical diagnostic modalities and NCS using Pearson's chi square test showed a significant association between NCS and DNE scores (p-value =.003, specificity 93%). The DNS score performed poorly in comparison (p-value = .068, specificity 77%). When the two scores were taken in combination the specificity in diagnosing DSPN was greater (p-value = .018, specificity 96%) than either alone. 33% of patients had subclinical neuropathy. DNE score alone and in combination with DNS score is reliable in predicting DSPN and is more specific than DNS score in evaluating DSPN. Both tests lack sensitivity. Patients without any evidence of clinical neuropathy manifest abnormalities on NCS.

Condition number estimation of preconditioned matrices.

PubMed

Kushida, Noriyuki

2015-01-01

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager's method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei's matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei's matrix, and matrices generated with the finite element method.

The asymptotic spectra of banded Toeplitz and quasi-Toeplitz matrices

NASA Technical Reports Server (NTRS)

Beam, Richard M.; Warming, Robert F.

1991-01-01

Toeplitz matrices occur in many mathematical, as well as, scientific and engineering investigations. This paper considers the spectra of banded Toeplitz and quasi-Toeplitz matrices with emphasis on non-normal matrices of arbitrarily large order and relatively small bandwidth. These are the type of matrices that appear in the investigation of stability and convergence of difference approximations to partial differential equations. Quasi-Toeplitz matrices are the result of non-Dirichlet boundary conditions for the difference approximations. The eigenvalue problem for a banded Toeplitz or quasi-Toeplitz matrix of large order is, in general, analytically intractable and (for non-normal matrices) numerically unreliable. An asymptotic (matrix order approaches infinity) approach partitions the eigenvalue analysis of a quasi-Toeplitz matrix into two parts, namely the analysis for the boundary condition independent spectrum and the analysis for the boundary condition dependent spectrum. The boundary condition independent spectrum is the same as the pure Toeplitz matrix spectrum. Algorithms for computing both parts of the spectrum are presented. Examples are used to demonstrate the utility of the algorithms, to present some interesting spectra, and to point out some of the numerical difficulties encountered when conventional matrix eigenvalue routines are employed for non-normal matrices of large order. The analysis for the Toeplitz spectrum also leads to a diagonal similarity transformation that improves conventional numerical eigenvalue computations. Finally, the algorithm for the asymptotic spectrum is extended to the Toeplitz generalized eigenvalue problem which occurs, for example, in the stability of Pade type difference approximations to differential equations.

Fibronectin alters the rate of formation and structure of the fibrin matrix.

PubMed

Ramanathan, Anand; Karuri, Nancy

2014-01-10

Plasma fibronectin is a vital component of the fibrin clot; however its role on clot structure is not clearly understood. The goal of this study was to examine the influence of fibronectin on the kinetics of formation, structural characteristics and composition of reconstituted fibrin clots or fibrin matrices. Fibrin matrices were formed by adding thrombin to 1, 2 or 4 mg/ml fibrinogen supplemented with 0-0.4 mg/ml fibronectin. The rate of fibrin matrix formation was then monitored by measuring light absorbance properties at different time points. Confocal microscopy of fluorescein conjugated fibrinogen was used to visualize the structural characteristics of fibrin matrices. The amount of fibronectin in fibrin matrices was determined through electrophoresis and immunoblotting of solubilized matrices. Fibronectin concentration positively correlated with the initial rate of fibrin matrix formation and with steady state light absorbance values of fibrin matrices. An increase in fibronectin concentration resulted in thinner and denser fibers in the fibrin matrices. Electrophoresis and immunoblotting showed that fibronectin was covalently and non-covalently bound to fibrin matrices and in the form of high molecular weight multimers. The formation of fibronectin multimers was attributed to cross-linking of fibronectin by trace amounts Factor XIIIa. These findings are novel because they link results from light absorbance studies to microcopy analyses and demonstrate an influence of fibronectin on fibrin matrix structural characteristics. This data is important in developing therapies that destabilize fibrin clots. Copyright © 2014. Published by Elsevier Inc.

The Modern Origin of Matrices and Their Applications

ERIC Educational Resources Information Center

Debnath, L.

2014-01-01

This paper deals with the modern development of matrices, linear transformations, quadratic forms and their applications to geometry and mechanics, eigenvalues, eigenvectors and characteristic equations with applications. Included are the representations of real and complex numbers, and quaternions by matrices, and isomorphism in order to show…

Enhancing Understanding of Transformation Matrices

ERIC Educational Resources Information Center

Dick, Jonathan; Childrey, Maria

2012-01-01

With the Common Core State Standards' emphasis on transformations, teachers need a variety of approaches to increase student understanding. Teaching matrix transformations by focusing on row vectors gives students tools to create matrices to perform transformations. This empowerment opens many doors: Students are able to create the matrices for…

The utility of covariance of combining ability in plant breeding.

PubMed

Arunachalam, V

1976-11-01

The definition of covariances of half- and full sibs, and hence that of variances of general and specific combining ability with regard to a quantitative character, is extended to take into account the respective covariances between a pair of characters. The interpretation of the dispersion and correlation matrices of general and specific combining ability is discussed by considering a set of single, three- and four-way crosses, made using diallel and line × tester mating systems in Pennisetum typhoides. The general implications of the concept of covariance of combining ability in plant breeding are discussed.

The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

NASA Astrophysics Data System (ADS)

Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

2012-05-01

The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

Non-localization and localization ROC analyses using clinically based scoring

NASA Astrophysics Data System (ADS)

Paquerault, Sophie; Samuelson, Frank W.; Myers, Kyle J.; Smith, Robert C.

2009-02-01

We are investigating the potential for differences in study conclusions when assessing the estimated impact of a computer-aided detection (CAD) system on readers' performance. The data utilized in this investigation were derived from a multi-reader multi-case observer study involving one hundred mammographic background images to which fixed-size and fixed-intensity Gaussian signals were added, generating a low- and high-intensity signal sets. The study setting allowed CAD assessment in two situations: when CAD sensitivity was 1) superior or 2) lower than the average reader. Seven readers were asked to review each set in the unaided and CAD-aided reading modes, mark and rate their findings. Using this data, we studied the effect on study conclusion of three clinically-based receiver operating characteristic (ROC) scoring definitions. These scoring definitions included both location-specific and non-location-specific rules. The results showed agreement in the estimated impact of CAD on the overall reader performance. In the study setting where CAD sensitivity is superior to the average reader, the mean difference in AUC between the CAD-aided read and unaided read was 0.049 (95%CIs: -0.027; 0.130) for the image scoring definition that is based on non-location-specific rules, and 0.104 (95%CIs: 0.036; 0.174) and 0.090 (95%CIs: 0.031; 0.155) for image scoring definitions that are based on location-specific rules. The increases in AUC were statistically significant for the location-specific scoring definitions. It was further observed that the variance on these estimates was reduced when using the location-specific scoring definitions compared to that using a non-location-specific scoring definition. In the study setting where CAD sensitivity is equivalent or lower than the average reader, the mean differences in AUC are slightly above 0.01 for all image scoring definitions. These increases in AUC were not statistical significant for any of the image scoring definitions. The results on the variance analysis differed from those observed in the other study setting. This investigation furthers our understanding of the relationships between non-localization-specific and localization-specific ROC assessment methodologies and their relevance to clinical practice.

Detection of organic compounds with whole-cell bioluminescent bioassays.

PubMed

Xu, Tingting; Close, Dan; Smartt, Abby; Ripp, Steven; Sayler, Gary

2014-01-01

Natural and manmade organic chemicals are widely deposited across a diverse range of ecosystems including air, surface water, groundwater, wastewater, soil, sediment, and marine environments. Some organic compounds, despite their industrial values, are toxic to living organisms and pose significant health risks to humans and wildlife. Detection and monitoring of these organic pollutants in environmental matrices therefore is of great interest and need for remediation and health risk assessment. Although these detections have traditionally been performed using analytical chemical approaches that offer highly sensitive and specific identification of target compounds, these methods require specialized equipment and trained operators, and fail to describe potential bioavailable effects on living organisms. Alternatively, the integration of bioluminescent systems into whole-cell bioreporters presents a new capacity for organic compound detection. These bioreporters are constructed by incorporating reporter genes into catabolic or signaling pathways that are present within living cells and emit a bioluminescent signal that can be detected upon exposure to target chemicals. Although relatively less specific compared to analytical methods, bioluminescent bioassays are more cost-effective, more rapid, can be scaled to higher throughput, and can be designed to report not only the presence but also the bioavailability of target substances. This chapter reviews available bacterial and eukaryotic whole-cell bioreporters for sensing organic pollutants and their applications in a variety of sample matrices.

Processed xenogenic cartilage as innovative biomatrix for cartilage tissue engineering: effects on chondrocyte differentiation and function.

PubMed

Schwarz, Silke; Elsaesser, Alexander F; Koerber, Ludwig; Goldberg-Bockhorn, Eva; Seitz, Andreas M; Bermueller, Christian; Dürselen, Lutz; Ignatius, Anita; Breiter, Roman; Rotter, Nicole

2015-12-01

One key point in the development of new bioimplant matrices for the reconstruction and replacement of cartilage defects is to provide an adequate microenvironment to ensure chondrocyte migration and de novo synthesis of cartilage-specific extracellular matrix (ECM). A recently developed decellularization and sterilization process maintains the three-dimensional (3D) collagen structure of native septal cartilage while increasing matrix porosity, which is considered to be crucial for cartilage tissue engineering. Human primary nasal septal chondrocytes were amplified in monolayer culture and 3D-cultured on processed porcine nasal septal cartilage scaffolds. The influence of chondrogenic growth factors on neosynthesis of ECM proteins was examined at the protein and gene expression levels. Seeding experiments demonstrated that processed xenogenic cartilage matrices provide excellent environmental properties for human nasal septal chondrocytes with respect to cell adhesion, migration into the matrix and neosynthesis of cartilage-specific ECM proteins, such as collagen type II and aggrecan. Matrix biomechanical stability indicated that the constructs retrieve full stability and function during 3D culture for up to 42 days, proportional to collagen type II and GAG production. Thus, processed xenogenic cartilage offers a suitable environment for human nasal chondrocytes and has promising potential for cartilage tissue engineering in the head and neck region. Copyright © 2012 John Wiley & Sons, Ltd.

Multi-dimensional Fokker-Planck equation analysis using the modified finite element method

NASA Astrophysics Data System (ADS)

Náprstek, J.; Král, R.

2016-09-01

The Fokker-Planck equation (FPE) is a frequently used tool for the solution of cross probability density function (PDF) of a dynamic system response excited by a vector of random processes. FEM represents a very effective solution possibility, particularly when transition processes are investigated or a more detailed solution is needed. Actual papers deal with single degree of freedom (SDOF) systems only. So the respective FPE includes two independent space variables only. Stepping over this limit into MDOF systems a number of specific problems related to a true multi-dimensionality must be overcome. Unlike earlier studies, multi-dimensional simplex elements in any arbitrary dimension should be deployed and rectangular (multi-brick) elements abandoned. Simple closed formulae of integration in multi-dimension domain have been derived. Another specific problem represents the generation of multi-dimensional finite element mesh. Assembling of system global matrices should be subjected to newly composed algorithms due to multi-dimensionality. The system matrices are quite full and no advantages following from their sparse character can be profited from, as is commonly used in conventional FEM applications in 2D/3D problems. After verification of partial algorithms, an illustrative example dealing with a 2DOF non-linear aeroelastic system in combination with random and deterministic excitations is discussed.

FISHing for bacteria in food--a promising tool for the reliable detection of pathogenic bacteria?

PubMed

Rohde, Alexander; Hammerl, Jens Andre; Appel, Bernd; Dieckmann, Ralf; Al Dahouk, Sascha

2015-04-01

Foodborne pathogens cause millions of infections every year and are responsible for considerable economic losses worldwide. The current gold standard for the detection of bacterial pathogens in food is still the conventional cultivation following standardized and generally accepted protocols. However, these methods are time-consuming and do not provide fast information about food contaminations and thus are limited in their ability to protect consumers in time from potential microbial hazards. Fluorescence in situ hybridization (FISH) represents a rapid and highly specific technique for whole-cell detection. This review aims to summarize the current data on FISH-testing for the detection of pathogenic bacteria in different food matrices and to evaluate its suitability for the implementation in routine testing. In this context, the use of FISH in different matrices and their pretreatment will be presented, the sensitivity and specificity of FISH tests will be considered and the need for automation shall be discussed as well as the use of technological improvements to overcome current hurdles for a broad application in monitoring food safety. In addition, the overall economical feasibility will be assessed in a rough calculation of costs, and strengths and weaknesses of FISH are considered in comparison with traditional and well-established detection methods. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Dlx homeobox gene family expression in osteoclasts.

PubMed

Lézot, F; Thomas, B L; Blin-Wakkach, C; Castaneda, B; Bolanos, A; Hotton, D; Sharpe, P T; Heymann, D; Carles, G F; Grigoriadis, A E; Berdal, A

2010-06-01

Skeletal growth and homeostasis require the finely orchestrated secretion of mineralized tissue matrices by highly specialized cells, balanced with their degradation by osteoclasts. Time- and site-specific expression of Dlx and Msx homeobox genes in the cells secreting these matrices have been identified as important elements in the regulation of skeletal morphology. Such specific expression patterns have also been reported in osteoclasts for Msx genes. The aim of the present study was to establish the expression patterns of Dlx genes in osteoclasts and identify their function in regulating skeletal morphology. The expression patterns of all Dlx genes were examined during the whole osteoclastogenesis using different in vitro models. The results revealed that Dlx1 and Dlx2 are the only Dlx family members with a possible function in osteoclastogenesis as well as in mature osteoclasts. Dlx5 and Dlx6 were detected in the cultures but appear to be markers of monocytes and their derivatives. In vivo, Dlx2 expression in osteoclasts was examined using a Dlx2/LacZ transgenic mouse. Dlx2 is expressed in a subpopulation of osteoclasts in association with tooth, brain, nerve, and bone marrow volumetric growths. Altogether the present data suggest a role for Dlx2 in regulation of skeletal morphogenesis via functions within osteoclasts. (c) 2010 Wiley-Liss, Inc.

Development of damage probability matrices based on Greek earthquake damage data

NASA Astrophysics Data System (ADS)

Eleftheriadou, Anastasia K.; Karabinis, Athanasios I.

2011-03-01

A comprehensive study is presented for empirical seismic vulnerability assessment of typical structural types, representative of the building stock of Southern Europe, based on a large set of damage statistics. The observational database was obtained from post-earthquake surveys carried out in the area struck by the September 7, 1999 Athens earthquake. After analysis of the collected observational data, a unified damage database has been created which comprises 180,945 damaged buildings from/after the near-field area of the earthquake. The damaged buildings are classified in specific structural types, according to the materials, seismic codes and construction techniques in Southern Europe. The seismic demand is described in terms of both the regional macroseismic intensity and the ratio α g/ a o, where α g is the maximum peak ground acceleration (PGA) of the earthquake event and a o is the unique value PGA that characterizes each municipality shown on the Greek hazard map. The relative and cumulative frequencies of the different damage states for each structural type and each intensity level are computed in terms of damage ratio. Damage probability matrices (DPMs) and vulnerability curves are obtained for specific structural types. A comparison analysis is fulfilled between the produced and the existing vulnerability models.

Theory of quark mixing matrix and invariant functions of mass matrices

NASA Astrophysics Data System (ADS)

Jarloskog, C.

1987-10-01

The origin of the quark mixing matrix; super elementary theory of flavor projection operators; equivalences and invariances; the commutator formalism and CP violation; CP conditions for any number of families; the angle between the quark mass matrices; and application to Fritzsch and Stech mass matrices are discussed.

Analyzing Matrices of Meta-Analytic Correlations: Current Practices and Recommendations

ERIC Educational Resources Information Center

Sheng, Zitong; Kong, Wenmo; Cortina, Jose M.; Hou, Shuofei

2016-01-01

Researchers have become increasingly interested in conducting analyses on meta-analytic correlation matrices. Methodologists have provided guidance and recommended practices for the application of this technique. The purpose of this article is to review current practices regarding analyzing meta-analytic correlation matrices, to identify the gaps…

Simplicity and Typical Rank Results for Three-Way Arrays

ERIC Educational Resources Information Center

ten Berge, Jos M. F.

2011-01-01

Matrices can be diagonalized by singular vectors or, when they are symmetric, by eigenvectors. Pairs of square matrices often admit simultaneous diagonalization, and always admit block wise simultaneous diagonalization. Generalizing these possibilities to more than two (non-square) matrices leads to methods of simplifying three-way arrays by…

76 FR 31356 - Notice of Proposed Information Collection for Public Comment; Technical Assistance Experience...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-31

... Matrices AGENCY: Office of the Community Planning and Development. ACTION: Notice of proposed information..., Expertise, and Awards Received Matrices. Description of the need for the information proposed: The Technical Assistance Experience, Expertise, and Awards Received Matrices will allow the Office of Special Needs...

76 FR 35231 - Notice of Proposed Information Collection for Public Comment; McKinney-Vento Technical Assistance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-16

... Information Collection for Public Comment; McKinney-Vento Technical Assistance Narrative, Matrices, and... Narrative, Matrices, and Reporting Requirements. Description of the need for the information proposed: McKinney- Vento Technical Assistance (MV-TA) Narrative, Matrices, and Reporting Requirements will allow the...

Random matrices with external source and the asymptotic behaviour of multiple orthogonal polynomials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aptekarev, Alexander I; Lysov, Vladimir G; Tulyakov, Dmitrii N

2011-02-28

Ensembles of random Hermitian matrices with a distribution measure defined by an anharmonic potential perturbed by an external source are considered. The limiting characteristics of the eigenvalue distribution of the matrices in these ensembles are related to the asymptotic behaviour of a certain system of multiple orthogonal polynomials. Strong asymptotic formulae are derived for this system. As a consequence, for matrices in this ensemble the limit mean eigenvalue density is found, and a variational principle is proposed to characterize this density. Bibliography: 35 titles.

Use of Mueller and non-Mueller matrices to describe polarization properties of telescope-based polarimeters

NASA Astrophysics Data System (ADS)

Seagraves, P. H.; Elmore, David F.

1994-09-01

Systems using optical elements such as linear polarizers, retarders, and mirrors can be represented by Mueller matrices. Some polarimeters include elements with time-varying polarization properties, multiple light beams, light detectors, and signal processing equipment. Standard Mueller matrix forms describing time-varying retarders, and beam splitters are presented, as well as non-Mueller matrices which describe detection and signal processing. These matrices provide a compact and intuitive mathematical description of polarimeter response which can aid in the refining of instrument designs.

Estimation for the Linear Model With Uncertain Covariance Matrices

NASA Astrophysics Data System (ADS)

Zachariah, Dave; Shariati, Nafiseh; Bengtsson, Mats; Jansson, Magnus; Chatterjee, Saikat

2014-03-01

We derive a maximum a posteriori estimator for the linear observation model, where the signal and noise covariance matrices are both uncertain. The uncertainties are treated probabilistically by modeling the covariance matrices with prior inverse-Wishart distributions. The nonconvex problem of jointly estimating the signal of interest and the covariance matrices is tackled by a computationally efficient fixed-point iteration as well as an approximate variational Bayes solution. The statistical performance of estimators is compared numerically to state-of-the-art estimators from the literature and shown to perform favorably.

Schur Complement Inequalities for Covariance Matrices and Monogamy of Quantum Correlations

NASA Astrophysics Data System (ADS)

Lami, Ludovico; Hirche, Christoph; Adesso, Gerardo; Winter, Andreas

2016-11-01

We derive fundamental constraints for the Schur complement of positive matrices, which provide an operator strengthening to recently established information inequalities for quantum covariance matrices, including strong subadditivity. This allows us to prove general results on the monogamy of entanglement and steering quantifiers in continuous variable systems with an arbitrary number of modes per party. A powerful hierarchical relation for correlation measures based on the log-determinant of covariance matrices is further established for all Gaussian states, which has no counterpart among quantities based on the conventional von Neumann entropy.

Schur Complement Inequalities for Covariance Matrices and Monogamy of Quantum Correlations.

PubMed

Lami, Ludovico; Hirche, Christoph; Adesso, Gerardo; Winter, Andreas

2016-11-25

We derive fundamental constraints for the Schur complement of positive matrices, which provide an operator strengthening to recently established information inequalities for quantum covariance matrices, including strong subadditivity. This allows us to prove general results on the monogamy of entanglement and steering quantifiers in continuous variable systems with an arbitrary number of modes per party. A powerful hierarchical relation for correlation measures based on the log-determinant of covariance matrices is further established for all Gaussian states, which has no counterpart among quantities based on the conventional von Neumann entropy.

Fidelity under isospectral perturbations: a random matrix study

NASA Astrophysics Data System (ADS)

Leyvraz, F.; García, A.; Kohler, H.; Seligman, T. H.

2013-07-01

The set of Hamiltonians generated by all unitary transformations from a single Hamiltonian is the largest set of isospectral Hamiltonians we can form. Taking advantage of the fact that the unitary group can be generated from Hermitian matrices we can take the ones generated by the Gaussian unitary ensemble with a small parameter as small perturbations. Similarly, the transformations generated by Hermitian antisymmetric matrices from orthogonal matrices form isospectral transformations among symmetric matrices. Based on this concept we can obtain the fidelity decay of a system that decays under a random isospectral perturbation with well-defined properties regarding time-reversal invariance. If we choose the Hamiltonian itself also from a classical random matrix ensemble, then we obtain solutions in terms of form factors in the limit of large matrices.

Retrieval of the non-depolarizing components of depolarizing Mueller matrices by using symmetry conditions and least squares minimization

NASA Astrophysics Data System (ADS)

Kuntman, Ertan; Canillas, Adolf; Arteaga, Oriol

2017-11-01

Experimental Mueller matrices contain certain amount of uncertainty in their elements and these uncertainties can create difficulties for decomposition methods based on analytic solutions. In an earlier paper [1], we proposed a decomposition method for depolarizing Mueller matrices by using certain symmetry conditions. However, because of the experimental error, that method creates over-determined systems with non-unique solutions. Here we propose to use least squares minimization approach in order to improve the accuracy of our results. In this method, we are taking into account the number of independent parameters of the corresponding symmetry and the rank constraints on the component matrices to decide on our fitting model. This approach is illustrated with experimental Mueller matrices that include material media with different Mueller symmetries.

Angiogenic response induced by acellular femoral matrix in vivo

PubMed Central

Conconi, Maria Teresa; Nico, Beatrice; Rebuffat, Piera; Crivellato, Enrico; Parnigotto, Pier Paolo; Nussdorfer, Gastone G; Ribatti, Domenico

2005-01-01

We investigated the angiogenic response induced by acellular femoral matrices implanted in vivo on to the chick embryo chorioallantoic membrane (CAM), a useful model for such investigation. The results showed that acellular matrices were able to induce a strong angiogenic response, comparable with that of fibroblast growth factor-2 (FGF-2), a well-known angiogenic cytokine. The angiogenic response was further increased when exogenous FGF-2 or transforming growth factor beta-1 (TGF-β1) was added to the matrices and inhibited by the addition of anti-FGF-2 or anti-TGF-β1 antibodies. The response may be considered to be dependent on a direct angiogenic effect exerted by the matrices, and also in part by the presence of FGF-2 and TGF-β1 in the acellular matrices. PMID:16011546

Introduction of organic/hydro-organic matrices in inductively coupled plasma optical emission spectrometry and mass spectrometry: a tutorial review. Part I. Theoretical considerations.

PubMed

Leclercq, Amélie; Nonell, Anthony; Todolí Torró, José Luis; Bresson, Carole; Vio, Laurent; Vercouter, Thomas; Chartier, Frédéric

2015-07-23

Due to their outstanding analytical performances, inductively coupled plasma optical emission spectrometry (ICP-OES) and mass spectrometry (ICP-MS) are widely used for multi-elemental measurements and also for isotopic characterization in the case of ICP-MS. While most studies are carried out in aqueous matrices, applications involving organic/hydro-organic matrices become increasingly widespread. This kind of matrices is introduced in ICP based instruments when classical "matrix removal" approaches such as acid digestion or extraction procedures cannot be implemented. Due to the physico-chemical properties of organic/hydro-organic matrices and their associated effects on instrumentation and analytical performances, their introduction into ICP sources is particularly challenging and has become a full topic. In this framework, numerous theoretical and phenomenological studies of these effects have been performed in the past, mainly by ICP-OES, while recent literature is more focused on applications and associated instrumental developments. This tutorial review, divided in two parts, explores the rich literature related to the introduction of organic/hydro-organic matrices in ICP-OES and ICP-MS. The present Part I, provides theoretical considerations in connection with the physico-chemical properties of organic/hydro-organic matrices, in order to better understand the induced phenomena. This focal point is divided in four chapters highlighting: (i) the impact of organic/hydro-organic matrices from aerosol generation to atomization/excitation/ionization processes; (ii) the production of carbon molecular constituents and their spatial distribution in the plasma with respect to analytes repartition; (iii) the subsequent modifications of plasma fundamental properties; and (iv) the resulting spectroscopic and non spectroscopic interferences. This first part of this tutorial review is addressed either to beginners or to more experienced scientists who are interested in the analysis of organic/hydro-organic matrices by ICP sources and would like to consider the theoretical background of effects induced by such matrices. The second part of this tutorial review will be dedicated to more practical consideration on instrumentation, such as adapted introductions devices, as well as instrumental and operating parameters optimization. The analytical strategies for elemental quantification in such matrices will also be addressed. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid screening of N-oxides of chemical warfare agents degradation products by ESI-tandem mass spectrometry.

PubMed

Sridhar, L; Karthikraj, R; Lakshmi, V V S; Raju, N Prasada; Prabhakar, S

2014-08-01

Rapid detection and identification of chemical warfare agents and related precursors/degradation products in various environmental matrices is of paramount importance for verification of standards set by the chemical weapons convention (CWC). Nitrogen mustards, N,N-dialkylaminoethyl-2-chlorides, N,N-dialkylaminoethanols, N-alkyldiethanolamines, and triethanolamine, which are listed CWC scheduled chemicals, are prone to undergo N-oxidation in environmental matrices or during decontamination process. Thus, screening of the oxidized products of these compounds is also an important task in the verification process because the presence of these products reveals alleged use of nitrogen mustards or precursors of VX compounds. The N-oxides of aminoethanols and aminoethylchlorides easily produce [M + H](+) ions under electrospray ionization conditions, and their collision-induced dissociation spectra include a specific neutral loss of 48 u (OH + CH2OH) and 66 u (OH + CH2Cl), respectively. Based on this specific fragmentation, a rapid screening method was developed for screening of the N-oxides by applying neutral loss scan technique. The method was validated and the applicability of the method was demonstrated by analyzing positive and negative samples. The method was useful in the detection of N-oxides of aminoethanols and aminoethylchlorides in environmental matrices at trace levels (LOD, up to 500 ppb), even in the presence of complex masking agents, without the use of time-consuming sample preparation methods and chromatographic steps. This method is advantageous for the off-site verification program and also for participation in official proficiency tests conducted by the Organization for the Prohibition of Chemical Weapons (OPCW), the Netherlands. The structure of N-oxides can be confirmed by the MS/MS experiments on the detected peaks. A liquid chromatography-mass spectrometry (LC-MS) method was developed for the separation of isomeric N-oxides of aminoethanols and aminoethylchlorides using a C18 Hilic column. Critical isomeric compounds can be confirmed by LC-MS/MS experiments, after detecting the N-oxides from the neutral loss scanning method.

Liquid chromatography-mass spectrometry in metabolomics research: mass analyzers in ultra high pressure liquid chromatography coupling.

PubMed

Forcisi, Sara; Moritz, Franco; Kanawati, Basem; Tziotis, Dimitrios; Lehmann, Rainer; Schmitt-Kopplin, Philippe

2013-05-31

The present review gives an introduction into the concept of metabolomics and provides an overview of the analytical tools applied in non-targeted metabolomics with a focus on liquid chromatography (LC). LC is a powerful analytical tool in the study of complex sample matrices. A further development and configuration employing Ultra-High Pressure Liquid Chromatography (UHPLC) is optimized to provide the largest known liquid chromatographic resolution and peak capacity. Reasonably UHPLC plays an important role in separation and consequent metabolite identification of complex molecular mixtures such as bio-fluids. The most sensitive detectors for these purposes are mass spectrometers. Almost any mass analyzer can be optimized to identify and quantify small pre-defined sets of targets; however, the number of analytes in metabolomics is far greater. Optimized protocols for quantification of large sets of targets may be rendered inapplicable. Results on small target set analyses on different sample matrices are easily comparable with each other. In non-targeted metabolomics there is almost no analytical method which is applicable to all different matrices due to limitations pertaining to mass analyzers and chromatographic tools. The specifications of the most important interfaces and mass analyzers are discussed. We additionally provide an exemplary application in order to demonstrate the level of complexity which remains intractable up to date. The potential of coupling a high field Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (ICR-FT/MS), the mass analyzer with the largest known mass resolving power, to UHPLC is given with an example of one human pre-treated plasma sample. This experimental example illustrates one way of overcoming the necessity of faster scanning rates in the coupling with UHPLC. The experiment enabled the extraction of thousands of features (analytical signals). A small subset of this compositional space could be mapped into a mass difference network whose topology shows specificity toward putative metabolite classes and retention time. Copyright © 2013 Elsevier B.V. All rights reserved.

Child–Pugh Versus MELD Score for the Assessment of Prognosis in Liver Cirrhosis

PubMed Central

Peng, Ying; Qi, Xingshun; Guo, Xiaozhong

2016-01-01

Abstract Child–Pugh and MELD scores have been widely used for the assessment of prognosis in liver cirrhosis. A systematic review and meta-analysis aimed to compare the discriminative ability of Child–Pugh versus MELD score to assess the prognosis of cirrhotic patients. PubMed and EMBASE databases were searched. The statistical results were summarized from every individual study. The summary areas under receiver operating characteristic curves, sensitivities, specificities, positive and negative likelihood ratios, and diagnostic odds ratios were also calculated. Of the 1095 papers initially identified, 119 were eligible for the systematic review. Study population was heterogeneous among studies. They included 269 comparisons, of which 44 favored MELD score, 16 favored Child–Pugh score, 99 did not find any significant difference between them, and 110 did not report the statistical significance. Forty-two papers were further included in the meta-analysis. In patients with acute-on-chronic liver failure, Child–Pugh score had a higher sensitivity and a lower specificity than MELD score. In patients admitted to ICU, MELD score had a smaller negative likelihood ratio and a higher sensitivity than Child–Pugh score. In patients undergoing surgery, Child–Pugh score had a higher specificity than MELD score. In other subgroup analyses, Child–Pugh and MELD scores had statistically similar discriminative abilities or could not be compared due to the presence of significant diagnostic threshold effects. Although Child–Pugh and MELD scores had similar prognostic values in most of cases, their benefits might be heterogeneous in some specific conditions. The indications for Child–Pugh and MELD scores should be further identified. PMID:26937922

Estimating soil matric potential in Owens Valley, California

USGS Publications Warehouse

Sorenson, Stephen K.; Miller, Reuben F.; Welch, Michael R.; Groeneveld, David P.; Branson, Farrel A.

1989-01-01

Much of the floor of Owens Valley, California, is covered with alkaline scrub and alkaline meadow plant communities, whose existence is dependent partly on precipitation and partly on water infiltrated into the rooting zone from the shallow water table. The extent to which these plant communities are capable of adapting to and surviving fluctuations in the water table depends on physiological adaptations of the plants and on the water content, matric potential characteristics of the soils. Two methods were used to estimate soil matric potential in test sites in Owens Valley. The first, the filter-paper method, uses water content of filter papers equilibrated to water content of soil samples taken with a hand auger. The previously published calibration relations used to estimate soil matric potential from the water content of the filter papers were modified on the basis of current laboratory data. The other method of estimating soil matric potential was a modeling approach based on data from this and previous investigations. These data indicate that the base-10 logarithm of soil matric potential is a linear function of gravimetric soil water content for a particular soil. The slope and intercepts of this function vary with the texture and saturation capacity of the soil. Estimates of soil water characteristic curves were made at two sites by averaging the gravimetric soil water content and soil matric potential values from multiple samples at 0.1-m depth intervals derived by using the hand auger and filter-paper method and entering these values in the soil water model. The characteristic curves then were used to estimate soil matric potential from estimates of volumetric soil water content derived from neutron-probe readings. Evaluation of the modeling technique at two study sites indicated that estimates of soil matric potential within 0.5 pF units of the soil matric potential value derived by using the filter-paper method could be obtained 90 to 95 percent of the time in soils where water content was less than field capacity. The greatest errors occurred at depths where there was a distinct transition between soils of different textures.

Spatial Distribution and Relationship of T1ρ and T2 Relaxation Times in Knee Cartilage With Osteoarthritis

PubMed Central

Li, Xiaojuan; Pai, Alex; Blumenkrantz, Gabrielle; Carballido-Gamio, Julio; Link, Thomas; Ma, Benjamin; Ries, Michael; Majumdar, Sharmila

2009-01-01

T1ρ and T2 relaxation time constants have been proposed to probe biochemical changes in osteoarthritic cartilage. This study aimed to evaluate the spatial correlation and distribution of T1ρ and T2 values in osteoarthritic cartilage. Ten patients with osteoarthritis (OA) and 10 controls were studied at 3T. The spatial correlation of T1ρ and T2 values was investigated using Z-scores. The spatial variation of T1ρ and T2 values in patellar cartilage was studied in different cartilage layers. The distribution of these relaxation time constants was measured using texture analysis parameters based on gray-level co-occurrence matrices (GLCM). The mean Z-scores for T1ρ and T2 values were significantly higher in OA patients vs. controls (P < 0.05). Regional correlation coefficients of T1ρ and T2 Z-scores showed a large range in both controls and OA patients (0.2– 0.7). OA patients had significantly greater GLCM contrast and entropy of T1ρ values than controls (P < 0.05). In summary, T1ρ and T2 values are not only increased but are also more heterogeneous in osteoarthritic cartilage. T1ρ and T2 values show different spatial distributions and may provide complementary information regarding cartilage degeneration in OA. PMID:19319904

Condition Number Estimation of Preconditioned Matrices

PubMed Central

Kushida, Noriyuki

2015-01-01

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager’s method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei’s matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei’s matrix, and matrices generated with the finite element method. PMID:25816331

Graphene oxide-stimulated myogenic differentiation of C2C12 cells on PLGA/RGD peptide nanofiber matrices

NASA Astrophysics Data System (ADS)

Shin, Y. C.; Lee, J. H.; Kim, M. J.; Hong, S. W.; Oh, J.-W.; Kim, C.-S.; Kim, B.; Hyun, J. K.; Kim, Y.-J.; Han, D.-W.

2015-07-01

During the last decade, much attention has been paid to graphene-based nanomaterials because they are considered as potential candidates for biomedical applications such as scaffolds for tissue engineering and substrates for the differentiation of stem cells. Until now, electrospun matrices composed of various biodegradable copolymers have been extensively developed for tissue engineering and regeneration; however, their use in combination with graphene oxide (GO) is novel and challenging. In this study, nanofiber matrices composed of poly(lactic-co-glycolic acid, PLGA) and M13 phage with RGD peptide displayed on its surface (RGD peptide-M13 phage) were prepared as extracellular matrix (ECM)-mimicking substrates. RGD peptide is a tripeptide (Arg-Gly-Asp) found on ECM proteins that promotes various cellular behaviors. The physicochemical properties of PLGA and RGD peptide-M13 phage (PLGA/RGD peptide) nanofiber matrices were characterized by atomic force microscopy, Fourier-transform infrared spectroscopy and thermogravimetric analysis. In addition, the growth of C2C12 mouse myoblasts on the PLGA/RGD peptide matrices was examined by measuring the metabolic activity. Moreover, the differentiation of C2C12 mouse myoblasts on the matrices when treated with GO was evaluated. The cellular behaviors, including growth and differentiation of C2C12 mouse myoblasts, were substantially enhanced on the PLGA/RGD peptide nanofiber matrices when treated with GO. Overall, these findings suggest that the PLGA/RGD peptide nanofiber matrices can be used in combination with GO as a novel strategy for skeletal tissue regeneration.

Examining the validity of self-reports on scales measuring students' strategic processing.

PubMed

Samuelstuen, Marit S; Bråten, Ivar

2007-06-01

Self-report inventories trying to measure strategic processing at a global level have been much used in both basic and applied research. However, the validity of global strategy scores is open to question because such inventories assess strategy perceptions outside the context of specific task performance. The primary aim was to examine the criterion-related and construct validity of the global strategy data obtained with the Cross-Curricular Competencies (CCC) scale. Additionally, we wanted to compare the validity of these data with the validity of data obtained with a task-specific self-report inventory focusing on the same types of strategies. The sample included 269 10th-grade students from 12 different junior high schools. Global strategy use as assessed with the CCC was compared with task-specific strategy use reported in three different reading situations. Moreover, relationships between scores on the CCC and scores on measures of text comprehension were examined and compared with relationships between scores on the task-specific strategy measure and the same comprehension measures. The comparison between the CCC strategy scores and the task-specific strategy scores suggested only modest criterion-related validity for the data obtained with the global strategy inventory. The CCC strategy scores were also not related to the text comprehension measures, indicating poor construct validity. In contrast, the task-specific strategy scores were positively related to the comprehension measures, indicating good construct validity. Attempts to measure strategic processing at a global level seem to have limited validity and utility.

Comprehensive Investigation of White Matter Tracts in Professional Chess Players and Relation to Expertise: Region of Interest and DMRI Connectometry.

PubMed

Mayeli, Mahsa; Rahmani, Farzaneh; Aarabi, Mohammad Hadi

2018-01-01

Purpose: Expertise is the product of training. Few studies have used functional connectivity or conventional diffusometric methods to identify neural underpinnings of chess expertise. Diffusometric variables of white matter might reflect these adaptive changes, along with changes in structural connectivity, which is a sensitive measure of microstructural changes. Method: Diffusometric variables of 29 professional chess players and 29 age-sex matched controls were extracted for white matter regions based on John Hopkin's Mori white matter atlas and partially correlated against professional training time and level of chess proficiency. Diffusion MRI connectometry was implemented to identify changes in structural connectivity in professional players compared to novices. Result: Compared to novices, higher planar anisotropy (CP) was observed in inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus (SLF) and cingulate gyrus, in professional chess players, which correlated with higher RPM score in this group. Higher fractional anisotropy (FA) was observed in ILF, uncinate fasciculus (UF) and hippocampus and correlated with better scores in Raven's progressive matrices (RPM) score and longer duration of chess training in professional players. Consistently, radial diffusivity in bilateral IFOF, bilateral ILF and bilateral SLF was inversely correlated with level of training in professional players. DMRI connectometry analysis identified increased connectivity in bilateral UF, bilateral IFOF, bilateral cingulum, and corpus callosum in chess player's compared to controls. Conclusion: Structural connectivity of major associational subcortical white matter fibers are increased in professional chess players. FA and CP of ILF, SLF and UF directly correlates with duration of professional training and RPM score, in professional chess players.

Comprehensive Investigation of White Matter Tracts in Professional Chess Players and Relation to Expertise: Region of Interest and DMRI Connectometry

PubMed Central

Mayeli, Mahsa; Rahmani, Farzaneh; Aarabi, Mohammad Hadi

2018-01-01

Purpose: Expertise is the product of training. Few studies have used functional connectivity or conventional diffusometric methods to identify neural underpinnings of chess expertise. Diffusometric variables of white matter might reflect these adaptive changes, along with changes in structural connectivity, which is a sensitive measure of microstructural changes. Method: Diffusometric variables of 29 professional chess players and 29 age-sex matched controls were extracted for white matter regions based on John Hopkin's Mori white matter atlas and partially correlated against professional training time and level of chess proficiency. Diffusion MRI connectometry was implemented to identify changes in structural connectivity in professional players compared to novices. Result: Compared to novices, higher planar anisotropy (CP) was observed in inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus (SLF) and cingulate gyrus, in professional chess players, which correlated with higher RPM score in this group. Higher fractional anisotropy (FA) was observed in ILF, uncinate fasciculus (UF) and hippocampus and correlated with better scores in Raven's progressive matrices (RPM) score and longer duration of chess training in professional players. Consistently, radial diffusivity in bilateral IFOF, bilateral ILF and bilateral SLF was inversely correlated with level of training in professional players. DMRI connectometry analysis identified increased connectivity in bilateral UF, bilateral IFOF, bilateral cingulum, and corpus callosum in chess player's compared to controls. Conclusion: Structural connectivity of major associational subcortical white matter fibers are increased in professional chess players. FA and CP of ILF, SLF and UF directly correlates with duration of professional training and RPM score, in professional chess players. PMID:29773973

A study on different forms of intelligence in Indian school-going children

PubMed Central

Singh, Yashpal; Makharia, Archita; Sharma, Abhilasha; Agrawal, Kruti; Varma, Gowtham; Yadav, Tarun

2017-01-01

Introduction: Most definitions of intelligence focus on capabilities that are relevant to scholastic performances. However, there are seven forms of intelligences. There is a lack of data on multiple intelligences in Indian children. Hence, this study was conducted to assess different forms of intelligences in students and compared these diverse intelligences with intelligence quotient (IQ) scores. Materials and Methods: In this cross-sectional observational study, we recruited 1065 school children between the age of 12 and 16 years from two government and 13 private schools in five towns, six cities, and two villages across India. All the children were administered multiple intelligences questionnaire by Armstrong, consisting of thirty true/false types of questions to assess the intelligences of a child in seven domains including linguistic skills, logical/mathematical abilities, musical skills, spatial intelligence, bodily-kinesthetic skills, intrapersonal intelligence, and interpersonal intelligence. IQ scores were assessed by Ravens Standard Progressive Matrices. Results: We found that different students possessed different forms of intelligences and most students had more than one forms of intelligence. Of seven forms of intelligence, only three forms of intelligence such as logical/mathematical, musical, and spatial were positively correlated with the IQ score. Conclusions: Even in the children with low IQ, many students had other forms of intelligences. The IQ scores correlated with only logical/mathematical, spatial, and musical intelligence. Hence, tapping the intelligences of students can help enhance their learning process. Our curriculum should have an amalgamation of teaching for all kinds of intelligences for maximum productivity. PMID:29456325

Spatial and Visual Reasoning: Do These Abilities Improve in First-Year Veterinary Medical Students Exposed to an Integrated Curriculum?

PubMed

Gutierrez, J Claudio; Chigerwe, Munashe; Ilkiw, Jan E; Youngblood, Patricia; Holladay, Steven D; Srivastava, Sakti

Spatial visualization ability refers to the human cognitive ability to form, retrieve, and manipulate mental models of spatial nature. Visual reasoning ability has been linked to spatial ability. There is currently limited information about how entry-level spatial and visual reasoning abilities may predict veterinary anatomy performance or may be enhanced with progression through the veterinary anatomy content in an integrated curriculum. The present study made use of two tests that measure spatial ability and one test that measures visual reasoning ability in veterinary students: Guay's Visualization of Views Test, adapted version (GVVT), the Mental Rotations Test (MRT), and Raven's Advanced Progressive Matrices Test, short form (RavenT). The tests were given to the entering class of veterinary students during their orientation week and at week 32 in the veterinary medical curriculum. Mean score on the MRT significantly increased from 15.2 to 20.1, and on the RavenT significantly increased from 7.5 to 8.8. When females only were evaluated, results were similar to the total class outcome; however, all three tests showed significant increases in mean scores. A positive correlation between the pre- and post-test scores was found for all three tests. The present results should be considered preliminary at best for associating anatomic learning in an integrated curriculum with spatial and visual reasoning abilities. Other components of the curriculum, for instance histology or physiology, could also influence the improved spatial visualization and visual reasoning test scores at week 32.

Introduction to the QIAT Self-Evaluation Matrices

ERIC Educational Resources Information Center

Zabala, Joy Smiley; Carl, Diana F.

2004-01-01

The QIAT Self-Evaluation Matrices (QILT, 2001) were developed in response to formative evaluation data indicating a need for a model that could assist in the application of the Quality Indicators for Assistive Technology Services in Schools (Zabala, et al, 2000). The QIAT Matrices are based on the idea that change does not happen immediately, but…

Evaluation of an Approximate Method for Synthesizing Covariance Matrices for Use in Meta-Analytic SEM

ERIC Educational Resources Information Center

Beretvas, S. Natasha; Furlow, Carolyn F.

2006-01-01

Meta-analytic structural equation modeling (MA-SEM) is increasingly being used to assess model-fit for variables' interrelations synthesized across studies. MA-SEM researchers have analyzed synthesized correlation matrices using structural equation modeling (SEM) estimation that is designed for covariance matrices. This can produce incorrect…

An Alternative Method to Gauss-Jordan Elimination: Minimizing Fraction Arithmetic

ERIC Educational Resources Information Center

Smith, Luke; Powell, Joan

2011-01-01

When solving systems of equations by using matrices, many teachers present a Gauss-Jordan elimination approach to row reducing matrices that can involve painfully tedious operations with fractions (which I will call the traditional method). In this essay, I present an alternative method to row reduce matrices that does not introduce additional…

The Approximation of Two-Mode Proximity Matrices by Sums of Order-Constrained Matrices.

ERIC Educational Resources Information Center

Hubert, Lawrence; Arabie, Phipps

1995-01-01

A least-squares strategy is proposed for representing a two-mode proximity matrix as an approximate sum of a small number of matrices that satisfy certain simple order constraints on their entries. The primary class of constraints considered defines Q-forms for particular conditions in a two-mode matrix. (SLD)