A GRAPHICAL DIAGNOSTIC METHOD FOR ASSESSING THE ROTATION IN FACTOR ANALYTICAL MODELS OF ATMOSPHERIC POLLUTION. (R831078)

EPA Science Inventory

Factor analytic tools such as principal component analysis (PCA) and positive matrix factorization (PMF), suffer from rotational ambiguity in the results: different solutions (factors) provide equally good fits to the measured data. The PMF model imposes non-negativity of both...

Poster — Thur Eve — 03: Application of the non-negative matrix factorization technique to [{sup 11}C]-DTBZ dynamic PET data for the early detection of Parkinson's disease

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

Lee, Dong-Chang; Jans, Hans; McEwan, Sandy

2014-08-15

In this work, a class of non-negative matrix factorization (NMF) technique known as alternating non-negative least squares, combined with the projected gradient method, is used to analyze twenty-five [{sup 11}C]-DTBZ dynamic PET/CT brain data. For each subject, a two-factor model is assumed and two factors representing the striatum (factor 1) and the non-striatum (factor 2) tissues are extracted using the proposed NMF technique and commercially available factor analysis software “Pixies”. The extracted factor 1 and 2 curves represent the binding site of the radiotracer and describe the uptake and clearance of the radiotracer by soft tissues in the brain, respectively.more » The proposed NMF technique uses prior information about the dynamic data to obtain sample time-activity curves representing the striatum and the non-striatum tissues. These curves are then used for “warm” starting the optimization. Factor solutions from the two methods are compared graphically and quantitatively. In healthy subjects, radiotracer uptake by factors 1 and 2 are approximately 35–40% and 60–65%, respectively. The solutions are also used to develop a factor-based metric for the detection of early, untreated Parkinson's disease. The metric stratifies healthy subjects from suspected Parkinson's patients (based on the graphical method). The analysis shows that both techniques produce comparable results with similar computational time. The “semi-automatic” approach used by the NMF technique allows clinicians to manually set a starting condition for “warm” starting the optimization in order to facilitate control and efficient interaction with the data.« less

Attributed community mining using joint general non-negative matrix factorization with graph Laplacian

NASA Astrophysics Data System (ADS)

Chen, Zigang; Li, Lixiang; Peng, Haipeng; Liu, Yuhong; Yang, Yixian

2018-04-01

Community mining for complex social networks with link and attribute information plays an important role according to different application needs. In this paper, based on our proposed general non-negative matrix factorization (GNMF) algorithm without dimension matching constraints in our previous work, we propose the joint GNMF with graph Laplacian (LJGNMF) to implement community mining of complex social networks with link and attribute information according to different application needs. Theoretical derivation result shows that the proposed LJGNMF is fully compatible with previous methods of integrating traditional NMF and symmetric NMF. In addition, experimental results show that the proposed LJGNMF can meet the needs of different community minings by adjusting its parameters, and the effect is better than traditional NMF in the community vertices attributes entropy.

A Novel Sky-Subtraction Method Based on Non-negative Matrix Factorisation with Sparsity for Multi-object Fibre Spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Bo; Zhang, Long; Ye, Zhongfu

2016-12-01

A novel sky-subtraction method based on non-negative matrix factorisation with sparsity is proposed in this paper. The proposed non-negative matrix factorisation with sparsity method is redesigned for sky-subtraction considering the characteristics of the skylights. It has two constraint terms, one for sparsity and the other for homogeneity. Different from the standard sky-subtraction techniques, such as the B-spline curve fitting methods and the Principal Components Analysis approaches, sky-subtraction based on non-negative matrix factorisation with sparsity method has higher accuracy and flexibility. The non-negative matrix factorisation with sparsity method has research value for the sky-subtraction on multi-object fibre spectroscopic telescope surveys. To demonstrate the effectiveness and superiority of the proposed algorithm, experiments are performed on Large Sky Area Multi-Object Fiber Spectroscopic Telescope data, as the mechanisms of the multi-object fibre spectroscopic telescopes are similar.

Semi-Supervised Projective Non-Negative Matrix Factorization for Cancer Classification.

PubMed

Zhang, Xiang; Guan, Naiyang; Jia, Zhilong; Qiu, Xiaogang; Luo, Zhigang

2015-01-01

Advances in DNA microarray technologies have made gene expression profiles a significant candidate in identifying different types of cancers. Traditional learning-based cancer identification methods utilize labeled samples to train a classifier, but they are inconvenient for practical application because labels are quite expensive in the clinical cancer research community. This paper proposes a semi-supervised projective non-negative matrix factorization method (Semi-PNMF) to learn an effective classifier from both labeled and unlabeled samples, thus boosting subsequent cancer classification performance. In particular, Semi-PNMF jointly learns a non-negative subspace from concatenated labeled and unlabeled samples and indicates classes by the positions of the maximum entries of their coefficients. Because Semi-PNMF incorporates statistical information from the large volume of unlabeled samples in the learned subspace, it can learn more representative subspaces and boost classification performance. We developed a multiplicative update rule (MUR) to optimize Semi-PNMF and proved its convergence. The experimental results of cancer classification for two multiclass cancer gene expression profile datasets show that Semi-PNMF outperforms the representative methods.

Exploring syndrome differentiation using non-negative matrix factorization and cluster analysis in patients with atopic dermatitis.

PubMed

Yun, Younghee; Jung, Wonmo; Kim, Hyunho; Jang, Bo-Hyoung; Kim, Min-Hee; Noh, Jiseong; Ko, Seong-Gyu; Choi, Inhwa

2017-08-01

Syndrome differentiation (SD) results in a diagnostic conclusion based on a cluster of concurrent symptoms and signs, including pulse form and tongue color. In Korea, there is a strong interest in the standardization of Traditional Medicine (TM). In order to standardize TM treatment, standardization of SD should be given priority. The aim of this study was to explore the SD, or symptom clusters, of patients with atopic dermatitis (AD) using non-negative factorization methods and k-means clustering analysis. We screened 80 patients and enrolled 73 eligible patients. One TM dermatologist evaluated the symptoms/signs using an existing clinical dataset from patients with AD. This dataset was designed to collect 15 dermatologic and 18 systemic symptoms/signs associated with AD. Non-negative matrix factorization was used to decompose the original data into a matrix with three features and a weight matrix. The point of intersection of the three coordinates from each patient was placed in three-dimensional space. With five clusters, the silhouette score reached 0.484, and this was the best silhouette score obtained from two to nine clusters. Patients were clustered according to the varying severity of concurrent symptoms/signs. Through the distribution of the null hypothesis generated by 10,000 permutation tests, we found significant cluster-specific symptoms/signs from the confidence intervals in the upper and lower 2.5% of the distribution. Patients in each cluster showed differences in symptoms/signs and severity. In a clinical situation, SD and treatment are based on the practitioners' observations and clinical experience. SD, identified through informatics, can contribute to development of standardized, objective, and consistent SD for each disease. Copyright © 2017. Published by Elsevier Ltd.

The successive projection algorithm as an initialization method for brain tumor segmentation using non-negative matrix factorization.

PubMed

Sauwen, Nicolas; Acou, Marjan; Bharath, Halandur N; Sima, Diana M; Veraart, Jelle; Maes, Frederik; Himmelreich, Uwe; Achten, Eric; Van Huffel, Sabine

2017-01-01

Non-negative matrix factorization (NMF) has become a widely used tool for additive parts-based analysis in a wide range of applications. As NMF is a non-convex problem, the quality of the solution will depend on the initialization of the factor matrices. In this study, the successive projection algorithm (SPA) is proposed as an initialization method for NMF. SPA builds on convex geometry and allocates endmembers based on successive orthogonal subspace projections of the input data. SPA is a fast and reproducible method, and it aligns well with the assumptions made in near-separable NMF analyses. SPA was applied to multi-parametric magnetic resonance imaging (MRI) datasets for brain tumor segmentation using different NMF algorithms. Comparison with common initialization methods shows that SPA achieves similar segmentation quality and it is competitive in terms of convergence rate. Whereas SPA was previously applied as a direct endmember extraction tool, we have shown improved segmentation results when using SPA as an initialization method, as it allows further enhancement of the sources during the NMF iterative procedure.

Non-negative Matrix Factorization and Co-clustering: A Promising Tool for Multi-tasks Bearing Fault Diagnosis

NASA Astrophysics Data System (ADS)

Shen, Fei; Chen, Chao; Yan, Ruqiang

2017-05-01

Classical bearing fault diagnosis methods, being designed according to one specific task, always pay attention to the effectiveness of extracted features and the final diagnostic performance. However, most of these approaches suffer from inefficiency when multiple tasks exist, especially in a real-time diagnostic scenario. A fault diagnosis method based on Non-negative Matrix Factorization (NMF) and Co-clustering strategy is proposed to overcome this limitation. Firstly, some high-dimensional matrixes are constructed using the Short-Time Fourier Transform (STFT) features, where the dimension of each matrix equals to the number of target tasks. Then, the NMF algorithm is carried out to obtain different components in each dimension direction through optimized matching, such as Euclidean distance and divergence distance. Finally, a Co-clustering technique based on information entropy is utilized to realize classification of each component. To verity the effectiveness of the proposed approach, a series of bearing data sets were analysed in this research. The tests indicated that although the diagnostic performance of single task is comparable to traditional clustering methods such as K-mean algorithm and Guassian Mixture Model, the accuracy and computational efficiency in multi-tasks fault diagnosis are improved.

A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing

PubMed Central

Wang, Guoli; Ebrahimi, Nader

2014-01-01

Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data. PMID:25821345

A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing.

PubMed

Devarajan, Karthik; Wang, Guoli; Ebrahimi, Nader

2015-04-01

Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H , such that V ∼ W H . It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H . In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data.

Robust extraction of basis functions for simultaneous and proportional myoelectric control via sparse non-negative matrix factorization

NASA Astrophysics Data System (ADS)

Lin, Chuang; Wang, Binghui; Jiang, Ning; Farina, Dario

2018-04-01

Objective. This paper proposes a novel simultaneous and proportional multiple degree of freedom (DOF) myoelectric control method for active prostheses. Approach. The approach is based on non-negative matrix factorization (NMF) of surface EMG signals with the inclusion of sparseness constraints. By applying a sparseness constraint to the control signal matrix, it is possible to extract the basis information from arbitrary movements (quasi-unsupervised approach) for multiple DOFs concurrently. Main Results. In online testing based on target hitting, able-bodied subjects reached a greater throughput (TP) when using sparse NMF (SNMF) than with classic NMF or with linear regression (LR). Accordingly, the completion time (CT) was shorter for SNMF than NMF or LR. The same observations were made in two patients with unilateral limb deficiencies. Significance. The addition of sparseness constraints to NMF allows for a quasi-unsupervised approach to myoelectric control with superior results with respect to previous methods for the simultaneous and proportional control of multi-DOF. The proposed factorization algorithm allows robust simultaneous and proportional control, is superior to previous supervised algorithms, and, because of minimal supervision, paves the way to online adaptation in myoelectric control.

Characterizing muscular activities using non-negative matrix factorization from EMG channels for driver swings in golf.

PubMed

Ozaki, Yasunori; Aoki, Ryosuke; Kimura, Toshitaka; Takashima, Youichi; Yamada, Tomohiro

2016-08-01

The goal of this study is to propose a data driven approach method to characterize muscular activities of complex actions in sports such as golf from a lot of EMG channels. Two problems occur in a many channel measurement. The first problem is that it takes a lot of time to check the many channel data because of combinatorial explosion. The second problem is that it is difficult to understand muscle activities related with complex actions. To solve these problems, we propose an analysis method of multi EMG channels using Non-negative Matrix Factorization and adopt the method to driver swings in golf. We measured 26 EMG channels about 4 professional coaches of golf. The results show that the proposed method detected 9 muscle synergies and the activation of each synergy were mostly fitted by sigmoid curve (R2=0.85).

Comparative study of original recover and recover KL in separable non-negative matrix factorization for topic detection in Twitter

NASA Astrophysics Data System (ADS)

Prabandari, R. D.; Murfi, H.

2017-07-01

An increasing amount of information on social media such as Twitter requires an efficient way to find the topics so that the information can be well managed. One of an automated method for topic detection is separable non-negative matrix factorization (SNMF). SNMF assumes that each topic has at least one word that does not appear on other topics. This method uses the direct approach and gives polynomial-time complexity, while the previous methods are iterative approaches and have NP-hard complexity. There are three steps of SNMF algorithm, i.e. constructing word co-occurrences, finding anchor words, and recovering topics. In this paper, we examine two topic recover methods, namely original recover that is using algebraic manipulation and recover KL that using probability approach with Kullback-Leibler divergence. Our simulations show that recover KL provides better accuracies in term of topic recall than original recover.

Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization

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

Chennubhotla, Chakra; Castro, Jason

2013-01-01

In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain un- clear. Here, we use non-negative matrix factorization (NMF) - a dimensionality reduction technique - to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable for the analysis of such lexical and perceptual data, and lead to a high-dimensional account of odor space. We further provide evidence that odor di- mensions apply categorically. That is, odor space is not occupied homogenously, but rather in a discrete and intrinsically clustered manner.more » We discuss the potential implications of these results for the neural coding of odors, as well as for developing classifiers on larger datasets that may be useful for predicting perceptual qualities from chemical structures.« less

A Novel Semi-Supervised Methodology for Extracting Tumor Type-Specific MRS Sources in Human Brain Data

PubMed Central

Ortega-Martorell, Sandra; Ruiz, Héctor; Vellido, Alfredo; Olier, Iván; Romero, Enrique; Julià-Sapé, Margarida; Martín, José D.; Jarman, Ian H.; Arús, Carles; Lisboa, Paulo J. G.

2013-01-01

Background The clinical investigation of human brain tumors often starts with a non-invasive imaging study, providing information about the tumor extent and location, but little insight into the biochemistry of the analyzed tissue. Magnetic Resonance Spectroscopy can complement imaging by supplying a metabolic fingerprint of the tissue. This study analyzes single-voxel magnetic resonance spectra, which represent signal information in the frequency domain. Given that a single voxel may contain a heterogeneous mix of tissues, signal source identification is a relevant challenge for the problem of tumor type classification from the spectroscopic signal. Methodology/Principal Findings Non-negative matrix factorization techniques have recently shown their potential for the identification of meaningful sources from brain tissue spectroscopy data. In this study, we use a convex variant of these methods that is capable of handling negatively-valued data and generating sources that can be interpreted as tumor class prototypes. A novel approach to convex non-negative matrix factorization is proposed, in which prior knowledge about class information is utilized in model optimization. Class-specific information is integrated into this semi-supervised process by setting the metric of a latent variable space where the matrix factorization is carried out. The reported experimental study comprises 196 cases from different tumor types drawn from two international, multi-center databases. The results indicate that the proposed approach outperforms a purely unsupervised process by achieving near perfect correlation of the extracted sources with the mean spectra of the tumor types. It also improves tissue type classification. Conclusions/Significance We show that source extraction by unsupervised matrix factorization benefits from the integration of the available class information, so operating in a semi-supervised learning manner, for discriminative source identification and brain tumor labeling from single-voxel spectroscopy data. We are confident that the proposed methodology has wider applicability for biomedical signal processing. PMID:24376744

Structured and Collaborative Signal Models: Theory and Applications in Image, Video, and Audio Analysis

DTIC Science & Technology

2013-01-01

Received Paper 01/22/2013 12.00 E. Esser, M. Moller, S. Osher, G. Sapiro, and J . Xin. A convex modelfor non-negative matrix factorization and...Ernie Esser, Michael M¨ oller , Stanley Osher, Guillermo Sapiro, Jack Xin. A convex model for non-negative matrixfactorization and dimensionality...still have one patent pending (with Adobe): X. Bai, J . Wang, and G. Sapiro, Methods and apparatus for dynamic color modeling. Patents Awarded Awards

On non-negative matrix factorization algorithms for signal-dependent noise with application to electromyography data

PubMed Central

Devarajan, Karthik; Cheung, Vincent C.K.

2017-01-01

Non-negative matrix factorization (NMF) by the multiplicative updates algorithm is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into two nonnegative matrices, W and H where V ~ WH. It has been successfully applied in the analysis and interpretation of large-scale data arising in neuroscience, computational biology and natural language processing, among other areas. A distinctive feature of NMF is its nonnegativity constraints that allow only additive linear combinations of the data, thus enabling it to learn parts that have distinct physical representations in reality. In this paper, we describe an information-theoretic approach to NMF for signal-dependent noise based on the generalized inverse Gaussian model. Specifically, we propose three novel algorithms in this setting, each based on multiplicative updates and prove monotonicity of updates using the EM algorithm. In addition, we develop algorithm-specific measures to evaluate their goodness-of-fit on data. Our methods are demonstrated using experimental data from electromyography studies as well as simulated data in the extraction of muscle synergies, and compared with existing algorithms for signal-dependent noise. PMID:24684448

Discriminative non-negative matrix factorization (DNMF) and its application to the fault diagnosis of diesel engine

NASA Astrophysics Data System (ADS)

Yang, Yong-sheng; Ming, An-bo; Zhang, You-yun; Zhu, Yong-sheng

2017-10-01

Diesel engines, widely used in engineering, are very important for the running of equipments and their fault diagnosis have attracted much attention. In the past several decades, the image based fault diagnosis methods have provided efficient ways for the diesel engine fault diagnosis. By introducing the class information into the traditional non-negative matrix factorization (NMF), an improved NMF algorithm named as discriminative NMF (DNMF) was developed and a novel imaged based fault diagnosis method was proposed by the combination of the DNMF and the KNN classifier. Experiments performed on the fault diagnosis of diesel engine were used to validate the efficacy of the proposed method. It is shown that the fault conditions of diesel engine can be efficiently classified by the proposed method using the coefficient matrix obtained by DNMF. Compared with the original NMF (ONMF) and principle component analysis (PCA), the DNMF can represent the class information more efficiently because the class characters of basis matrices obtained by the DNMF are more visible than those in the basis matrices obtained by the ONMF and PCA.

Finding Imaging Patterns of Structural Covariance via Non-Negative Matrix Factorization

PubMed Central

Sotiras, Aristeidis; Resnick, Susan M.; Davatzikos, Christos

2015-01-01

In this paper, we investigate the use of Non-Negative Matrix Factorization (NNMF) for the analysis of structural neuroimaging data. The goal is to identify the brain regions that co-vary across individuals in a consistent way, hence potentially being part of underlying brain networks or otherwise influenced by underlying common mechanisms such as genetics and pathologies. NNMF offers a directly data-driven way of extracting relatively localized co-varying structural regions, thereby transcending limitations of Principal Component Analysis (PCA), Independent Component Analysis (ICA) and other related methods that tend to produce dispersed components of positive and negative loadings. In particular, leveraging upon the well known ability of NNMF to produce parts-based representations of image data, we derive decompositions that partition the brain into regions that vary in consistent ways across individuals. Importantly, these decompositions achieve dimensionality reduction via highly interpretable ways and generalize well to new data as shown via split-sample experiments. We empirically validate NNMF in two data sets: i) a Diffusion Tensor (DT) mouse brain development study, and ii) a structural Magnetic Resonance (sMR) study of human brain aging. We demonstrate the ability of NNMF to produce sparse parts-based representations of the data at various resolutions. These representations seem to follow what we know about the underlying functional organization of the brain and also capture some pathological processes. Moreover, we show that these low dimensional representations favorably compare to descriptions obtained with more commonly used matrix factorization methods like PCA and ICA. PMID:25497684

A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations.

PubMed

Xiao, Qiu; Luo, Jiawei; Liang, Cheng; Cai, Jie; Ding, Pingjian

2017-09-01

MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulations and various cellular processes. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases at a system level. However, most existing computational approaches are biased towards known miRNA-disease associations, which is inappropriate for those new diseases or miRNAs without any known association information. In this study, we propose a new method with graph regularized non-negative matrix factorization in heterogeneous omics data, called GRNMF, to discover potential associations between miRNAs and diseases, especially for new diseases and miRNAs or those diseases and miRNAs with sparse known associations. First, we integrate the disease semantic information and miRNA functional information to estimate disease similarity and miRNA similarity, respectively. Considering that there is no available interaction observed for new diseases or miRNAs, a preprocessing step is developed to construct the interaction score profiles that will assist in prediction. Next, a graph regularized non-negative matrix factorization framework is utilized to simultaneously identify potential associations for all diseases. The results indicated that our proposed method can effectively prioritize disease-associated miRNAs with higher accuracy compared with other recent approaches. Moreover, case studies also demonstrated the effectiveness of GRNMF to infer unknown miRNA-disease associations for those novel diseases and miRNAs. The code of GRNMF is freely available at https://github.com/XIAO-HN/GRNMF/. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Evaluation of non-negative matrix factorization of grey matter in age prediction.

PubMed

Varikuti, Deepthi P; Genon, Sarah; Sotiras, Aristeidis; Schwender, Holger; Hoffstaedter, Felix; Patil, Kaustubh R; Jockwitz, Christiane; Caspers, Svenja; Moebus, Susanne; Amunts, Katrin; Davatzikos, Christos; Eickhoff, Simon B

2018-06-01

The relationship between grey matter volume (GMV) patterns and age can be captured by multivariate pattern analysis, allowing prediction of individuals' age based on structural imaging. Raw data, voxel-wise GMV and non-sparse factorization (with Principal Component Analysis, PCA) show good performance but do not promote relatively localized brain components for post-hoc examinations. Here we evaluated a non-negative matrix factorization (NNMF) approach to provide a reduced, but also interpretable representation of GMV data in age prediction frameworks in healthy and clinical populations. This examination was performed using three datasets: a multi-site cohort of life-span healthy adults, a single site cohort of older adults and clinical samples from the ADNI dataset with healthy subjects, participants with Mild Cognitive Impairment and patients with Alzheimer's disease (AD) subsamples. T1-weighted images were preprocessed with VBM8 standard settings to compute GMV values after normalization, segmentation and modulation for non-linear transformations only. Non-negative matrix factorization was computed on the GM voxel-wise values for a range of granularities (50-690 components) and LASSO (Least Absolute Shrinkage and Selection Operator) regression were used for age prediction. First, we compared the performance of our data compression procedure (i.e., NNMF) to various other approaches (i.e., uncompressed VBM data, PCA-based factorization and parcellation-based compression). We then investigated the impact of the granularity on the accuracy of age prediction, as well as the transferability of the factorization and model generalization across datasets. We finally validated our framework by examining age prediction in ADNI samples. Our results showed that our framework favorably compares with other approaches. They also demonstrated that the NNMF based factorization derived from one dataset could be efficiently applied to compress VBM data of another dataset and that granularities between 300 and 500 components give an optimal representation for age prediction. In addition to the good performance in healthy subjects our framework provided relatively localized brain regions as the features contributing to the prediction, thereby offering further insights into structural changes due to brain aging. Finally, our validation in clinical populations showed that our framework is sensitive to deviance from normal structural variations in pathological aging. Copyright © 2018 Elsevier Inc. All rights reserved.

Automatic annotation of histopathological images using a latent topic model based on non-negative matrix factorization

PubMed Central

Cruz-Roa, Angel; Díaz, Gloria; Romero, Eduardo; González, Fabio A.

2011-01-01

Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively. PMID:22811960

Community detection enhancement using non-negative matrix factorization with graph regularization

NASA Astrophysics Data System (ADS)

Liu, Xiao; Wei, Yi-Ming; Wang, Jian; Wang, Wen-Jun; He, Dong-Xiao; Song, Zhan-Jie

2016-06-01

Community detection is a meaningful task in the analysis of complex networks, which has received great concern in various domains. A plethora of exhaustive studies has made great effort and proposed many methods on community detection. Particularly, a kind of attractive one is the two-step method which first makes a preprocessing for the network and then identifies its communities. However, not all types of methods can achieve satisfactory results by using such preprocessing strategy, such as the non-negative matrix factorization (NMF) methods. In this paper, rather than using the above two-step method as most works did, we propose a graph regularized-based model to improve, specialized, the NMF-based methods for the detection of communities, namely NMFGR. In NMFGR, we introduce the similarity metric which contains both the global and local information of networks, to reflect the relationships between two nodes, so as to improve the accuracy of community detection. Experimental results on both artificial and real-world networks demonstrate the superior performance of NMFGR to some competing methods.

Identifying group discriminative and age regressive sub-networks from DTI-based connectivity via a unified framework of non-negative matrix factorization and graph embedding

PubMed Central

Ghanbari, Yasser; Smith, Alex R.; Schultz, Robert T.; Verma, Ragini

2014-01-01

Diffusion tensor imaging (DTI) offers rich insights into the physical characteristics of white matter (WM) fiber tracts and their development in the brain, facilitating a network representation of brain’s traffic pathways. Such a network representation of brain connectivity has provided a novel means of investigating brain changes arising from pathology, development or aging. The high dimensionality of these connectivity networks necessitates the development of methods that identify the connectivity building blocks or sub-network components that characterize the underlying variation in the population. In addition, the projection of the subject networks into the basis set provides a low dimensional representation of it, that teases apart different sources of variation in the sample, facilitating variation-specific statistical analysis. We propose a unified framework of non-negative matrix factorization and graph embedding for learning sub-network patterns of connectivity by their projective non-negative decomposition into a reconstructive basis set, as well as, additional basis sets representing variational sources in the population like age and pathology. The proposed framework is applied to a study of diffusion-based connectivity in subjects with autism that shows localized sparse sub-networks which mostly capture the changes related to pathology and developmental variations. PMID:25037933

Practical limits on muscle synergy identification by non-negative matrix factorization in systems with mechanical constraints.

PubMed

Burkholder, Thomas J; van Antwerp, Keith W

2013-02-01

Statistical decomposition, including non-negative matrix factorization (NMF), is a convenient tool for identifying patterns of structured variability within behavioral motor programs, but it is unclear how the resolved factors relate to actual neural structures. Factors can be extracted from a uniformly sampled, low-dimension command space. In practical application, the command space is limited, either to those activations that perform some task(s) successfully or to activations induced in response to specific perturbations. NMF was applied to muscle activation patterns synthesized from low dimensional, synergy-like control modules mimicking simple task performance or feedback activation from proprioceptive signals. In the task-constrained paradigm, the accuracy of control module recovery was highly dependent on the sampled volume of control space, such that sampling even 50% of control space produced a substantial degradation in factor accuracy. In the feedback paradigm, NMF was not capable of extracting more than four control modules, even in a mechanical model with seven internal degrees of freedom. Reduced access to the low-dimensional control space imposed by physical constraints may result in substantial distortion of an existing low dimensional controller, such that neither the dimensionality nor the composition of the recovered/extracted factors match the original controller.

Finding imaging patterns of structural covariance via Non-Negative Matrix Factorization.

PubMed

Sotiras, Aristeidis; Resnick, Susan M; Davatzikos, Christos

2015-03-01

In this paper, we investigate the use of Non-Negative Matrix Factorization (NNMF) for the analysis of structural neuroimaging data. The goal is to identify the brain regions that co-vary across individuals in a consistent way, hence potentially being part of underlying brain networks or otherwise influenced by underlying common mechanisms such as genetics and pathologies. NNMF offers a directly data-driven way of extracting relatively localized co-varying structural regions, thereby transcending limitations of Principal Component Analysis (PCA), Independent Component Analysis (ICA) and other related methods that tend to produce dispersed components of positive and negative loadings. In particular, leveraging upon the well known ability of NNMF to produce parts-based representations of image data, we derive decompositions that partition the brain into regions that vary in consistent ways across individuals. Importantly, these decompositions achieve dimensionality reduction via highly interpretable ways and generalize well to new data as shown via split-sample experiments. We empirically validate NNMF in two data sets: i) a Diffusion Tensor (DT) mouse brain development study, and ii) a structural Magnetic Resonance (sMR) study of human brain aging. We demonstrate the ability of NNMF to produce sparse parts-based representations of the data at various resolutions. These representations seem to follow what we know about the underlying functional organization of the brain and also capture some pathological processes. Moreover, we show that these low dimensional representations favorably compare to descriptions obtained with more commonly used matrix factorization methods like PCA and ICA. Copyright © 2014 Elsevier Inc. All rights reserved.

Contribution of non-negative matrix factorization to the classification of remote sensing images

NASA Astrophysics Data System (ADS)

Karoui, M. S.; Deville, Y.; Hosseini, S.; Ouamri, A.; Ducrot, D.

2008-10-01

Remote sensing has become an unavoidable tool for better managing our environment, generally by realizing maps of land cover using classification techniques. The classification process requires some pre-processing, especially for data size reduction. The most usual technique is Principal Component Analysis. Another approach consists in regarding each pixel of the multispectral image as a mixture of pure elements contained in the observed area. Using Blind Source Separation (BSS) methods, one can hope to unmix each pixel and to perform the recognition of the classes constituting the observed scene. Our contribution consists in using Non-negative Matrix Factorization (NMF) combined with sparse coding as a solution to BSS, in order to generate new images (which are at least partly separated images) using HRV SPOT images from Oran area, Algeria). These images are then used as inputs of a supervised classifier integrating textural information. The results of classifications of these "separated" images show a clear improvement (correct pixel classification rate improved by more than 20%) compared to classification of initial (i.e. non separated) images. These results show the contribution of NMF as an attractive pre-processing for classification of multispectral remote sensing imagery.

GC[Formula: see text]NMF: A Novel Matrix Factorization Framework for Gene-Phenotype Association Prediction.

PubMed

Zhang, Yaogong; Liu, Jiahui; Liu, Xiaohu; Hong, Yuxiang; Fan, Xin; Huang, Yalou; Wang, Yuan; Xie, Maoqiang

2018-04-24

Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene-phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene-phenotype association detection. In this paper, we propose a novel method by exploiting weighted graph constraint learned from hierarchical structures of phenotype data and group prior information among genes by inheriting advantages of Non-negative Matrix Factorization (NMF), called Weighted Graph Constraint and Group Centric Non-negative Matrix Factorization (GC[Formula: see text]NMF). Specifically, first we introduce the depth of parent-child relationships between two adjacent phenotypes in hierarchical phenotypic data as weighted graph constraint for a better phenotype understanding. Second, we utilize intra-group correlation among genes in a gene group as group constraint for gene understanding. Such information provides us with the intuition that genes in a group probably result in similar phenotypes. The model not only allows us to achieve a high-grade prediction performance, but also helps us to learn interpretable representation of genes and phenotypes simultaneously to facilitate future biological analysis. Experimental results on biological gene-phenotype association datasets of mouse and human demonstrate that GC[Formula: see text]NMF can obtain superior prediction accuracy and good understandability for biological explanation over other state-of-the-arts methods.

Peak picking NMR spectral data using non-negative matrix factorization.

PubMed

Tikole, Suhas; Jaravine, Victor; Rogov, Vladimir; Dötsch, Volker; Güntert, Peter

2014-02-11

Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap.

The Comparison Between Nmf and Ica in Pigment Mixture Identification of Ancient Chinese Paintings

NASA Astrophysics Data System (ADS)

Liu, Y.; Lyu, S.; Hou, M.; Yin, Q.

2018-04-01

Since the colour in painting cultural relics observed by our naked eyes or hyperspectral cameras is usually a mixture of several kinds of pigments, the mixed pigments analysis will be an important subject in the field of ancient painting conservation and restoration. This paper aims to find a more effective method to confirm the types of every pure pigment from mixture on the surface of paintings. Firstly, we adopted two kinds of blind source separation algorithms, which are independent component analysis and non-negative matrix factorization, to extract the pure pigment component from mixed spectrum respectively. Moreover, we matched the separated pure spectrum with the pigments spectra library built by our team to determine the pigment type. Furthermore, three kinds of data including simulation data, mixed pigments spectral data measured in laboratory, and the spectral data of an ancient painting were chosen to evaluate the performance of the different algorithms. And the accuracy was compared between the two algorithms. Finally, the experimental results show that non-negative matrix factorization method is more suitable for endmember extraction in the field of ancient painting conservation and restoration.

3D tensor-based blind multispectral image decomposition for tumor demarcation

NASA Astrophysics Data System (ADS)

Kopriva, Ivica; Peršin, Antun

2010-03-01

Blind decomposition of multi-spectral fluorescent image for tumor demarcation is formulated exploiting tensorial structure of the image. First contribution of the paper is identification of the matrix of spectral responses and 3D tensor of spatial distributions of the materials present in the image from Tucker3 or PARAFAC models of 3D image tensor. Second contribution of the paper is clustering based estimation of the number of the materials present in the image as well as matrix of their spectral profiles. 3D tensor of the spatial distributions of the materials is recovered through 3-mode multiplication of the multi-spectral image tensor and inverse of the matrix of spectral profiles. Tensor representation of the multi-spectral image preserves its local spatial structure that is lost, due to vectorization process, when matrix factorization-based decomposition methods (such as non-negative matrix factorization and independent component analysis) are used. Superior performance of the tensor-based image decomposition over matrix factorization-based decompositions is demonstrated on experimental red-green-blue (RGB) image with known ground truth as well as on RGB fluorescent images of the skin tumor (basal cell carcinoma).

Bird sound spectrogram decomposition through Non-Negative Matrix Factorization for the acoustic classification of bird species.

PubMed

Ludeña-Choez, Jimmy; Quispe-Soncco, Raisa; Gallardo-Antolín, Ascensión

2017-01-01

Feature extraction for Acoustic Bird Species Classification (ABSC) tasks has traditionally been based on parametric representations that were specifically developed for speech signals, such as Mel Frequency Cepstral Coefficients (MFCC). However, the discrimination capabilities of these features for ABSC could be enhanced by accounting for the vocal production mechanisms of birds, and, in particular, the spectro-temporal structure of bird sounds. In this paper, a new front-end for ABSC is proposed that incorporates this specific information through the non-negative decomposition of bird sound spectrograms. It consists of the following two different stages: short-time feature extraction and temporal feature integration. In the first stage, which aims at providing a better spectral representation of bird sounds on a frame-by-frame basis, two methods are evaluated. In the first method, cepstral-like features (NMF_CC) are extracted by using a filter bank that is automatically learned by means of the application of Non-Negative Matrix Factorization (NMF) on bird audio spectrograms. In the second method, the features are directly derived from the activation coefficients of the spectrogram decomposition as performed through NMF (H_CC). The second stage summarizes the most relevant information contained in the short-time features by computing several statistical measures over long segments. The experiments show that the use of NMF_CC and H_CC in conjunction with temporal integration significantly improves the performance of a Support Vector Machine (SVM)-based ABSC system with respect to conventional MFCC.

Bird sound spectrogram decomposition through Non-Negative Matrix Factorization for the acoustic classification of bird species

PubMed Central

Quispe-Soncco, Raisa

2017-01-01

Feature extraction for Acoustic Bird Species Classification (ABSC) tasks has traditionally been based on parametric representations that were specifically developed for speech signals, such as Mel Frequency Cepstral Coefficients (MFCC). However, the discrimination capabilities of these features for ABSC could be enhanced by accounting for the vocal production mechanisms of birds, and, in particular, the spectro-temporal structure of bird sounds. In this paper, a new front-end for ABSC is proposed that incorporates this specific information through the non-negative decomposition of bird sound spectrograms. It consists of the following two different stages: short-time feature extraction and temporal feature integration. In the first stage, which aims at providing a better spectral representation of bird sounds on a frame-by-frame basis, two methods are evaluated. In the first method, cepstral-like features (NMF_CC) are extracted by using a filter bank that is automatically learned by means of the application of Non-Negative Matrix Factorization (NMF) on bird audio spectrograms. In the second method, the features are directly derived from the activation coefficients of the spectrogram decomposition as performed through NMF (H_CC). The second stage summarizes the most relevant information contained in the short-time features by computing several statistical measures over long segments. The experiments show that the use of NMF_CC and H_CC in conjunction with temporal integration significantly improves the performance of a Support Vector Machine (SVM)-based ABSC system with respect to conventional MFCC. PMID:28628630

Deep learning and non-negative matrix factorization in recognition of mammograms

NASA Astrophysics Data System (ADS)

Swiderski, Bartosz; Kurek, Jaroslaw; Osowski, Stanislaw; Kruk, Michal; Barhoumi, Walid

2017-02-01

This paper presents novel approach to the recognition of mammograms. The analyzed mammograms represent the normal and breast cancer (benign and malignant) cases. The solution applies the deep learning technique in image recognition. To obtain increased accuracy of classification the nonnegative matrix factorization and statistical self-similarity of images are applied. The images reconstructed by using these two approaches enrich the data base and thanks to this improve of quality measures of mammogram recognition (increase of accuracy, sensitivity and specificity). The results of numerical experiments performed on large DDSM data base containing more than 10000 mammograms have confirmed good accuracy of class recognition, exceeding the best results reported in the actual publications for this data base.

Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

PubMed

Ray, Sumanta; Maulik, Ujjwal

2016-12-20

Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

Peak picking NMR spectral data using non-negative matrix factorization

PubMed Central

2014-01-01

Background Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. Results To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Conclusions Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap. PMID:24511909

Matrix- and plasma-derived peptides promote tissue-specific injury responses and wound healing in diabetic swine.

PubMed

Sheets, Anthony R; Massey, Conner J; Cronk, Stephen M; Iafrati, Mark D; Herman, Ira M

2016-07-02

Non-healing wounds are a major global health concern and account for the majority of non-traumatic limb amputations worldwide. However, compared to standard care practices, few advanced therapeutics effectively resolve these injuries stemming from cardiovascular disease, aging, and diabetes-related vasculopathies. While matrix turnover is disrupted in these injuries, debriding enzymes may promote healing by releasing matrix fragments that induce cell migration, proliferation, and morphogenesis, and plasma products may also stimulate these processes. Thus, we created matrix- and plasma-derived peptides, Comb1 and UN3, which induce cellular injury responses in vitro, and accelerate healing in rodent models of non-healing wounds. However, the effects of these peptides in non-healing wounds in diabetes are not known. Here, we interrogated whether these peptides stimulate healing in a diabetic porcine model highly reminiscent of human healing impairments in type 1 and type 2-diabetes. After 3-6 weeks of streptozotocin-induced diabetes, full-thickness wounds were surgically created on the backs of adult female Yorkshire swine under general anesthesia. Comb1 and UN3 peptides or sterile saline (negative control) were administered to wounds daily for 3-7 days. Following sacrifice, wound tissues were harvested, and quantitative histological and immunohistochemical analyses were performed for wound closure, angiogenesis and granulation tissue deposition, along with quantitative molecular analyses of factors critical for angiogenesis, epithelialization, and dermal matrix remodeling. Comb1 and UN3 significantly increase re-epithelialization and angiogenesis in diabetic porcine wounds, compared to saline-treated controls. Additionally, fluorescein-conjugated Comb1 labels keratinocytes, fibroblasts, and vascular endothelial cells in porcine wounds, and Far western blotting reveals these cell populations express multiple fluorescein-Comb1-interacting proteins in vitro. Further, peptide treatment increases mRNA expression of several pro-angiogenic, epithelializing, and matrix-remodeling factors, importantly including balanced inductions in matrix metalloproteinase-2, -9, and tissue inhibitor of metalloproteinases-1, lending further insight into their mechanisms. Comb1 and UN3 stimulate wound resolution in diabetic Yorkshire swine through upregulation of multiple reparative growth factors and cytokines, especially matrix metalloproteinases and inhibitors that may aid in reversing the proteolytic imbalance characteristic of chronically inflamed non-healing wounds. Together, these peptides should have great therapeutic potential for all patients in need of healing, regardless of injury etiology.

Removing non-stationary noise in spectrum sensing using matrix factorization

NASA Astrophysics Data System (ADS)

van Bloem, Jan-Willem; Schiphorst, Roel; Slump, Cornelis H.

2013-12-01

Spectrum sensing is key to many applications like dynamic spectrum access (DSA) systems or telecom regulators who need to measure utilization of frequency bands. The International Telecommunication Union (ITU) recommends a 10 dB threshold above the noise to decide whether a channel is occupied or not. However, radio frequency (RF) receiver front-ends are non-ideal. This means that the obtained data is distorted with noise and imperfections from the analog front-end. As part of the front-end the automatic gain control (AGC) circuitry mainly affects the sensing performance as strong adjacent signals lift the noise level. To enhance the performance of spectrum sensing significantly we focus in this article on techniques to remove the noise caused by the AGC from the sensing data. In order to do this we have applied matrix factorization techniques, i.e., SVD (singular value decomposition) and NMF (non-negative matrix factorization), which enables signal space analysis. In addition, we use live measurement results to verify the performance and to remove the effects of the AGC from the sensing data using above mentioned techniques, i.e., applied on block-wise available spectrum data. In this article it is shown that the occupancy in the industrial, scientific and medical (ISM) band, obtained by using energy detection (ITU recommended threshold), can be an overestimation of spectrum usage by 60%.

Regular approximate factorization of a class of matrix-function with an unstable set of partial indices

PubMed Central

Rogosin, S.

2018-01-01

From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII, 3–72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions. PMID:29434502

Regular approximate factorization of a class of matrix-function with an unstable set of partial indices.

PubMed

Mishuris, G; Rogosin, S

2018-01-01

From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII , 3-72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions.

Informed Source Separation of Atmospheric and Surface Signal Contributions in Shortwave Hyperspectral Imagery using Non-negative Matrix Factorization

NASA Astrophysics Data System (ADS)

Wright, L.; Coddington, O.; Pilewskie, P.

2015-12-01

Current challenges in Earth remote sensing require improved instrument spectral resolution, spectral coverage, and radiometric accuracy. Hyperspectral instruments, deployed on both aircraft and spacecraft, are a growing class of Earth observing sensors designed to meet these challenges. They collect large amounts of spectral data, allowing thorough characterization of both atmospheric and surface properties. The higher accuracy and increased spectral and spatial resolutions of new imagers require new numerical approaches for processing imagery and separating surface and atmospheric signals. One potential approach is source separation, which allows us to determine the underlying physical causes of observed changes. Improved signal separation will allow hyperspectral instruments to better address key science questions relevant to climate change, including land-use changes, trends in clouds and atmospheric water vapor, and aerosol characteristics. In this work, we investigate a Non-negative Matrix Factorization (NMF) method for the separation of atmospheric and land surface signal sources. NMF offers marked benefits over other commonly employed techniques, including non-negativity, which avoids physically impossible results, and adaptability, which allows the method to be tailored to hyperspectral source separation. We adapt our NMF algorithm to distinguish between contributions from different physically distinct sources by introducing constraints on spectral and spatial variability and by using library spectra to inform separation. We evaluate our NMF algorithm with simulated hyperspectral images as well as hyperspectral imagery from several instruments including, the NASA Airborne Visible/Infrared Imaging Spectrometer (AVIRIS), NASA Hyperspectral Imager for the Coastal Ocean (HICO) and National Ecological Observatory Network (NEON) Imaging Spectrometer.

Enforced Sparse Non-Negative Matrix Factorization

DTIC Science & Technology

2016-01-23

documents to find interesting pieces of information. With limited resources, analysts often employ automated text - mining tools that highlight common...represented as an undirected bipartite graph. It has become a common method for generating topic models of text data because it is known to produce good results...model and the convergence rate of the underlying algorithm. I. Introduction A common analyst challenge is searching through large quantities of text

Recurrent triple-negative breast cancer (TNBC) tissues contain a higher amount of phosphatidylcholine (32:1) than non-recurrent TNBC tissues

PubMed Central

Masaki, Noritaka; Takei, Shiro; Horikawa, Makoto; Matsushita, Shoko; Sugiyama, Eiji; Ogura, Hiroyuki; Shiiya, Norihiko; Setou, Mitsutoshi

2017-01-01

Triple-negative breast cancer (TNBC) is one of the breast cancer subtype that displays a high risk of early recurrence and short overall survival. Improvement of the prognosis of patients with TNBC requires identifying a predictive factor of recurrence, which would make it possible to provide beneficial personalized treatment. However, no clinically reliable predictive factor is currently known. In this study, we investigated the predictive factor of recurrence in TNBC using matrix-assisted laser desorption/ionization-imaging mass spectrometry for lipid profiling of breast cancer specimens obtained from three and six patients with recurrent and non-recurrent TNBC, respectively. The signal for phosphatidylcholine (PC) (32:1) at m/z 732.5 was significantly higher in the recurrence group compared to the non-recurrence group (P = 0.024). PC (32:1) was more abundant in the cancer epithelial area than it was in the surrounding stroma, suggesting that abnormal lipid metabolism was associated with malignant transformation. Our results indicate PC (32:1) as a candidate predictive factor of TNBC recurrence. A future prospective study investigating whether personalized therapy based on PC (32:1) intensity improves the prognosis of patients with TNBC is recommended. PMID:28832678

Identifying constituent spectra sources in multispectral images to quantify and locate cervical neoplasia

NASA Astrophysics Data System (ADS)

Baker, Kevin C.; Bambot, Shabbir

2011-02-01

Optical spectroscopy has been shown to be an effective method for detecting neoplasia. Guided Therapeutics has developed LightTouch, a non invasive device that uses a combination of reflectance and fluorescence spectroscopy for identifying early cancer of the human cervix. The combination of the multispectral information from the two spectroscopic modalities has been shown to be an effective method to screen for cervical cancer. There has however been a relative paucity of work in identifying the individual spectral components that contribute to the measured fluorescence and reflectance spectra. This work aims to identify the constituent source spectra and their concentrations. We used non-negative matrix factorization (NNMF) numerical methods to decompose the mixed multispectral data into the constituent spectra and their corresponding concentrations. NNMF is an iterative approach that factorizes the measured data into non-negative factors. The factors are chosen to minimize the root-mean-squared residual error. NNMF has shown promise for feature extraction and identification in the fields of text mining and spectral data analysis. Since both the constituent source spectra and their corresponding concentrations are assumed to be non-negative by nature NNMF is a reasonable approach to deconvolve the measured multispectral data. Supervised learning methods were then used to determine which of the constituent spectra sources best predict the amount of neoplasia. The constituent spectra sources found to best predict neoplasia were then compared with spectra of known biological chromophores.

Non-negative Matrix Factorization for Self-calibration of Photometric Redshift Scatter in Weak-lensing Surveys

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

Zhang, Le; Yu, Yu; Zhang, Pengjie, E-mail: lezhang@sjtu.edu.cn

Photo- z error is one of the major sources of systematics degrading the accuracy of weak-lensing cosmological inferences. Zhang et al. proposed a self-calibration method combining galaxy–galaxy correlations and galaxy–shear correlations between different photo- z bins. Fisher matrix analysis shows that it can determine the rate of photo- z outliers at a level of 0.01%–1% merely using photometric data and do not rely on any prior knowledge. In this paper, we develop a new algorithm to implement this method by solving a constrained nonlinear optimization problem arising in the self-calibration process. Based on the techniques of fixed-point iteration and non-negativemore » matrix factorization, the proposed algorithm can efficiently and robustly reconstruct the scattering probabilities between the true- z and photo- z bins. The algorithm has been tested extensively by applying it to mock data from simulated stage IV weak-lensing projects. We find that the algorithm provides a successful recovery of the scatter rates at the level of 0.01%–1%, and the true mean redshifts of photo- z bins at the level of 0.001, which may satisfy the requirements in future lensing surveys.« less

Financial Distress Prediction Using Discrete-time Hazard Model and Rating Transition Matrix Approach

NASA Astrophysics Data System (ADS)

Tsai, Bi-Huei; Chang, Chih-Huei

2009-08-01

Previous studies used constant cut-off indicator to distinguish distressed firms from non-distressed ones in the one-stage prediction models. However, distressed cut-off indicator must shift according to economic prosperity, rather than remains fixed all the time. This study focuses on Taiwanese listed firms and develops financial distress prediction models based upon the two-stage method. First, this study employs the firm-specific financial ratio and market factors to measure the probability of financial distress based on the discrete-time hazard models. Second, this paper further focuses on macroeconomic factors and applies rating transition matrix approach to determine the distressed cut-off indicator. The prediction models are developed by using the training sample from 1987 to 2004, and their levels of accuracy are compared with the test sample from 2005 to 2007. As for the one-stage prediction model, the model in incorporation with macroeconomic factors does not perform better than that without macroeconomic factors. This suggests that the accuracy is not improved for one-stage models which pool the firm-specific and macroeconomic factors together. In regards to the two stage models, the negative credit cycle index implies the worse economic status during the test period, so the distressed cut-off point is adjusted to increase based on such negative credit cycle index. After the two-stage models employ such adjusted cut-off point to discriminate the distressed firms from non-distressed ones, their error of misclassification becomes lower than that of one-stage ones. The two-stage models presented in this paper have incremental usefulness in predicting financial distress.

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

PubMed

Jia, Zhilong; Zhang, Xiang; Guan, Naiyang; Bo, Xiaochen; Barnes, Michael R; Luo, Zhigang

2015-01-01

RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. This paper proposes an accurate and sensitive gene ranking method that implements discriminant non-negative matrix factorization (DNMF) for RNA-seq data. To the best of our knowledge, this is the first work to explore the utility of DNMF for gene ranking. When incorporating Fisher's discriminant criteria and setting the reduced dimension as two, DNMF learns two factors to approximate the original gene expression data, abstracting the up-regulated or down-regulated metagene by using the sample label information. The first factor denotes all the genes' weights of two metagenes as the additive combination of all genes, while the second learned factor represents the expression values of two metagenes. In the gene ranking stage, all the genes are ranked as a descending sequence according to the differential values of the metagene weights. Leveraging the nature of NMF and Fisher's criterion, DNMF can robustly boost the gene ranking performance. The Area Under the Curve analysis of differential expression analysis on two benchmarking tests of four RNA-seq data sets with similar phenotypes showed that our proposed DNMF-based gene ranking method outperforms other widely used methods. Moreover, the Gene Set Enrichment Analysis also showed DNMF outweighs others. DNMF is also computationally efficient, substantially outperforming all other benchmarked methods. Consequently, we suggest DNMF is an effective method for the analysis of differential gene expression and gene ranking for RNA-seq data.

Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text

PubMed Central

Xin, Yu; Hochberg, Ephraim; Joshi, Rohit; Uzuner, Ozlem; Szolovits, Peter

2015-01-01

Objective Extracting medical knowledge from electronic medical records requires automated approaches to combat scalability limitations and selection biases. However, existing machine learning approaches are often regarded by clinicians as black boxes. Moreover, training data for these automated approaches at often sparsely annotated at best. The authors target unsupervised learning for modeling clinical narrative text, aiming at improving both accuracy and interpretability. Methods The authors introduce a novel framework named subgraph augmented non-negative tensor factorization (SANTF). In addition to relying on atomic features (e.g., words in clinical narrative text), SANTF automatically mines higher-order features (e.g., relations of lymphoid cells expressing antigens) from clinical narrative text by converting sentences into a graph representation and identifying important subgraphs. The authors compose a tensor using patients, higher-order features, and atomic features as its respective modes. We then apply non-negative tensor factorization to cluster patients, and simultaneously identify latent groups of higher-order features that link to patient clusters, as in clinical guidelines where a panel of immunophenotypic features and laboratory results are used to specify diagnostic criteria. Results and Conclusion SANTF demonstrated over 10% improvement in averaged F-measure on patient clustering compared to widely used non-negative matrix factorization (NMF) and k-means clustering methods. Multiple baselines were established by modeling patient data using patient-by-features matrices with different feature configurations and then performing NMF or k-means to cluster patients. Feature analysis identified latent groups of higher-order features that lead to medical insights. We also found that the latent groups of atomic features help to better correlate the latent groups of higher-order features. PMID:25862765

Separating Atmospheric and Surface Contributions in Hyperspectral Imager for the Coastal Ocean (HICO) Scenes using Informed Non-Negative Matrix Factorization

NASA Astrophysics Data System (ADS)

Wright, L.; Coddington, O.; Pilewskie, P.

2016-12-01

Hyperspectral instruments are a growing class of Earth observing sensors designed to improve remote sensing capabilities beyond discrete multi-band sensors by providing tens to hundreds of continuous spectral channels. Improved spectral resolution, range and radiometric accuracy allow the collection of large amounts of spectral data, facilitating thorough characterization of both atmospheric and surface properties. These new instruments require novel approaches for processing imagery and separating surface and atmospheric signals. One approach is numerical source separation, which allows the determination of the underlying physical causes of observed signals. Improved source separation will enable hyperspectral imagery to better address key science questions relevant to climate change, including land-use changes, trends in clouds and atmospheric water vapor, and aerosol characteristics. We developed an Informed Non-negative Matrix Factorization (INMF) method for separating atmospheric and surface sources. INMF offers marked benefits over other commonly employed techniques including non-negativity, which avoids physically impossible results; and adaptability, which tailors the method to hyperspectral source separation. The INMF algorithm is adapted to separate contributions from physically distinct sources using constraints on spectral and spatial variability, and library spectra to improve the initial guess. We also explore methods to produce an initial guess of the spatial separation patterns. Using this INMF algorithm we decompose hyperspectral imagery from the NASA Hyperspectral Imager for the Coastal Ocean (HICO) with a focus on separating surface and atmospheric signal contributions. HICO's coastal ocean focus provides a dataset with a wide range of atmospheric conditions, including high and low aerosol optical thickness and cloud cover, with only minor contributions from the ocean surfaces in order to isolate the contributions of the multiple atmospheric sources.

Validation of Spectral Unmixing Results from Informed Non-Negative Matrix Factorization (INMF) of Hyperspectral Imagery

NASA Astrophysics Data System (ADS)

Wright, L.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral instruments are a growing class of Earth observing sensors designed to improve remote sensing capabilities beyond discrete multi-band sensors by providing tens to hundreds of continuous spectral channels. Improved spectral resolution, range and radiometric accuracy allow the collection of large amounts of spectral data, facilitating thorough characterization of both atmospheric and surface properties. We describe the development of an Informed Non-Negative Matrix Factorization (INMF) spectral unmixing method to exploit this spectral information and separate atmospheric and surface signals based on their physical sources. INMF offers marked benefits over other commonly employed techniques including non-negativity, which avoids physically impossible results; and adaptability, which tailors the method to hyperspectral source separation. The INMF algorithm is adapted to separate contributions from physically distinct sources using constraints on spectral and spatial variability, and library spectra to improve the initial guess. Using this INMF algorithm we decompose hyperspectral imagery from the NASA Hyperspectral Imager for the Coastal Ocean (HICO), with a focus on separating surface and atmospheric signal contributions. HICO's coastal ocean focus provides a dataset with a wide range of atmospheric and surface conditions. These include atmospheres with varying aerosol optical thicknesses and cloud cover. HICO images also provide a range of surface conditions including deep ocean regions, with only minor contributions from the ocean surfaces; and more complex shallow coastal regions with contributions from the seafloor or suspended sediments. We provide extensive comparison of INMF decomposition results against independent measurements of physical properties. These include comparison against traditional model-based retrievals of water-leaving, aerosol, and molecular scattering radiances and other satellite products, such as aerosol optical thickness from the Moderate Resolution Imaging Spectroradiometer (MODIS).

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

Development of a Real Time Sparse Non-Negative Matrix Factorization Module for Cochlear Implants by Using xPC Target

PubMed Central

Hu, Hongmei; Krasoulis, Agamemnon; Lutman, Mark; Bleeck, Stefan

2013-01-01

Cochlear implants (CIS) require efficient speech processing to maximize information transmission to the brain, especially in noise. A novel CI processing strategy was proposed in our previous studies, in which sparsity-constrained non-negative matrix factorization (NMF) was applied to the envelope matrix in order to improve the CI performance in noisy environments. It showed that the algorithm needs to be adaptive, rather than fixed, in order to adjust to acoustical conditions and individual characteristics. Here, we explore the benefit of a system that allows the user to adjust the signal processing in real time according to their individual listening needs and their individual hearing capabilities. In this system, which is based on MATLAB®, SIMULINK® and the xPC Target™ environment, the input/outupt (I/O) boards are interfaced between the SIMULINK blocks and the CI stimulation system, such that the output can be controlled successfully in the manner of a hardware-in-the-loop (HIL) simulation, hence offering a convenient way to implement a real time signal processing module that does not require any low level language. The sparsity constrained parameter of the algorithm was adapted online subjectively during an experiment with normal-hearing subjects and noise vocoded speech simulation. Results show that subjects chose different parameter values according to their own intelligibility preferences, indicating that adaptive real time algorithms are beneficial to fully explore subjective preferences. We conclude that the adaptive real time systems are beneficial for the experimental design, and such systems allow one to conduct psychophysical experiments with high ecological validity. PMID:24129021

Development of a real time sparse non-negative matrix factorization module for cochlear implants by using xPC target.

PubMed

Hu, Hongmei; Krasoulis, Agamemnon; Lutman, Mark; Bleeck, Stefan

2013-10-14

Cochlear implants (CIs) require efficient speech processing to maximize information transmission to the brain, especially in noise. A novel CI processing strategy was proposed in our previous studies, in which sparsity-constrained non-negative matrix factorization (NMF) was applied to the envelope matrix in order to improve the CI performance in noisy environments. It showed that the algorithm needs to be adaptive, rather than fixed, in order to adjust to acoustical conditions and individual characteristics. Here, we explore the benefit of a system that allows the user to adjust the signal processing in real time according to their individual listening needs and their individual hearing capabilities. In this system, which is based on MATLAB®, SIMULINK® and the xPC Target™ environment, the input/outupt (I/O) boards are interfaced between the SIMULINK blocks and the CI stimulation system, such that the output can be controlled successfully in the manner of a hardware-in-the-loop (HIL) simulation, hence offering a convenient way to implement a real time signal processing module that does not require any low level language. The sparsity constrained parameter of the algorithm was adapted online subjectively during an experiment with normal-hearing subjects and noise vocoded speech simulation. Results show that subjects chose different parameter values according to their own intelligibility preferences, indicating that adaptive real time algorithms are beneficial to fully explore subjective preferences. We conclude that the adaptive real time systems are beneficial for the experimental design, and such systems allow one to conduct psychophysical experiments with high ecological validity.

Decoding the encoding of functional brain networks: An fMRI classification comparison of non-negative matrix factorization (NMF), independent component analysis (ICA), and sparse coding algorithms.

PubMed

Xie, Jianwen; Douglas, Pamela K; Wu, Ying Nian; Brody, Arthur L; Anderson, Ariana E

2017-04-15

Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet other mathematical constraints provide alternate biologically-plausible frameworks for generating brain networks. Non-negative matrix factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms (L1 Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks within scan for different constraints are used as basis functions to encode observed functional activity. These encodings are then decoded using machine learning, by using the time series weights to predict within scan whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. The sparse coding algorithm of L1 Regularized Learning outperformed 4 variations of ICA (p<0.001) for predicting the task being performed within each scan using artifact-cleaned components. The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy compared to the ICA and sparse coding algorithms. Holding constant the effect of the extraction algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p<0.001). Lower classification accuracy occurred when the extracted spatial maps contained more CSF regions (p<0.001). The success of sparse coding algorithms suggests that algorithms which enforce sparsity, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA. Negative BOLD signal may capture task-related activations. Copyright © 2017 Elsevier B.V. All rights reserved.

Tuning of Muscle Synergies During Walking Along Rectilinear and Curvilinear Trajectories in Humans.

PubMed

Chia Bejarano, Noelia; Pedrocchi, Alessandra; Nardone, Antonio; Schieppati, Marco; Baccinelli, Walter; Monticone, Marco; Ferrigno, Giancarlo; Ferrante, Simona

2017-05-01

The aim of this study was to develop a methodology based on muscle synergies to investigate whether rectilinear and curvilinear walking shared the same neuro-motor organization, and how this organization was fine-tuned by the walking condition. Thirteen healthy subjects walked on rectilinear and curvilinear paths. Electromyographic data from thirteen back and lower-limb muscles were acquired, together with kinematic data using inertial sensors. Four macroscopically invariant muscle synergies, extracted through non-negative matrix factorization, proved a shared modular organization across conditions. The fine-tuning of muscle synergies was studied through non-negative matrix reconstruction, applied by fixing muscle weights or activation profiles to those of the rectilinear condition. The activation profiles tended to be recruited for a longer period and with a larger amplitude during curvilinear walking. The muscles of the posterior side of the lower limb were those mainly influenced by the fine-tuning, with the muscles inside the rotation path being more active than the outer muscles. This study shows that rectilinear and curvilinear walking share a unique motor command. However, a fine-tuning in muscle synergies is introduced during curvilinear conditions, adapting the kinematic strategy to the new biomechanical needs.

BJUT at TREC 2015 Microblog Track: Real-Time Filtering Using Non-negative Matrix Factorization

DTIC Science & Technology

2015-11-20

information to extend the query, al- leviates the problem of concept drift in query expansion. In User profiles Twitter Google Bing accurate ambiguity...index as the query expansion document set; second- ly,put the interest file in twitter search energy to get back the relevant twetts, the interest in...for clustering is demonstrated in Figure 2. We will be the result of the search energy Twitter as the original expression of interest, the initial

Scale-Free Nonparametric Factor Analysis: A User-Friendly Introduction with Concrete Heuristic Examples.

ERIC Educational Resources Information Center

Mittag, Kathleen Cage

Most researchers using factor analysis extract factors from a matrix of Pearson product-moment correlation coefficients. A method is presented for extracting factors in a non-parametric way, by extracting factors from a matrix of Spearman rho (rank correlation) coefficients. It is possible to factor analyze a matrix of association such that…

Global attractivity of non-autonomous Lotka-Volterra competition system without instantaneous negative feedback

NASA Astrophysics Data System (ADS)

Tang, X. H.; Zou, Xingfu

We consider a non-autonomous Lotka-Volterra competition system with distributed delays but without instantaneous negative feedbacks (i.e., pure delay systems). We establish some 3/2-type and M-matrix-type criteria for global attractivity of the positive equilibrium of the system, which generalise and improve the existing ones.

Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform.

PubMed

Kannan, R; Ievlev, A V; Laanait, N; Ziatdinov, M A; Vasudevan, R K; Jesse, S; Kalinin, S V

2018-01-01

Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.

Estimation of tissue optical parameters with hyperspectral imaging and spectral unmixing

NASA Astrophysics Data System (ADS)

Lu, Guolan; Qin, Xulei; Wang, Dongsheng; Chen, Zhuo G.; Fei, Baowei

2015-03-01

Early detection of oral cancer and its curable precursors can improve patient survival and quality of life. Hyperspectral imaging (HSI) holds the potential for noninvasive early detection of oral cancer. The quantification of tissue chromophores by spectral unmixing of hyperspectral images could provide insights for evaluating cancer progression. In this study, non-negative matrix factorization has been applied for decomposing hyperspectral images into physiologically meaningful chromophore concentration maps. The approach has been validated by computer-simulated hyperspectral images and in vivo tumor hyperspectral images from a head and neck cancer animal model.

Limited-memory fast gradient descent method for graph regularized nonnegative matrix factorization.

PubMed

Guan, Naiyang; Wei, Lei; Luo, Zhigang; Tao, Dacheng

2013-01-01

Graph regularized nonnegative matrix factorization (GNMF) decomposes a nonnegative data matrix X[Symbol:see text]R(m x n) to the product of two lower-rank nonnegative factor matrices, i.e.,W[Symbol:see text]R(m x r) and H[Symbol:see text]R(r x n) (r < min {m,n}) and aims to preserve the local geometric structure of the dataset by minimizing squared Euclidean distance or Kullback-Leibler (KL) divergence between X and WH. The multiplicative update rule (MUR) is usually applied to optimize GNMF, but it suffers from the drawback of slow-convergence because it intrinsically advances one step along the rescaled negative gradient direction with a non-optimal step size. Recently, a multiple step-sizes fast gradient descent (MFGD) method has been proposed for optimizing NMF which accelerates MUR by searching the optimal step-size along the rescaled negative gradient direction with Newton's method. However, the computational cost of MFGD is high because 1) the high-dimensional Hessian matrix is dense and costs too much memory; and 2) the Hessian inverse operator and its multiplication with gradient cost too much time. To overcome these deficiencies of MFGD, we propose an efficient limited-memory FGD (L-FGD) method for optimizing GNMF. In particular, we apply the limited-memory BFGS (L-BFGS) method to directly approximate the multiplication of the inverse Hessian and the gradient for searching the optimal step size in MFGD. The preliminary results on real-world datasets show that L-FGD is more efficient than both MFGD and MUR. To evaluate the effectiveness of L-FGD, we validate its clustering performance for optimizing KL-divergence based GNMF on two popular face image datasets including ORL and PIE and two text corpora including Reuters and TDT2. The experimental results confirm the effectiveness of L-FGD by comparing it with the representative GNMF solvers.

Using Separable Nonnegative Matrix Factorization Techniques for the Analysis of Time-Resolved Raman Spectra

NASA Astrophysics Data System (ADS)

Luce, R.; Hildebrandt, P.; Kuhlmann, U.; Liesen, J.

2016-09-01

The key challenge of time-resolved Raman spectroscopy is the identification of the constituent species and the analysis of the kinetics of the underlying reaction network. In this work we present an integral approach that allows for determining both the component spectra and the rate constants simultaneously from a series of vibrational spectra. It is based on an algorithm for non-negative matrix factorization which is applied to the experimental data set following a few pre-processing steps. As a prerequisite for physically unambiguous solutions, each component spectrum must include one vibrational band that does not significantly interfere with vibrational bands of other species. The approach is applied to synthetic "experimental" spectra derived from model systems comprising a set of species with component spectra differing with respect to their degree of spectral interferences and signal-to-noise ratios. In each case, the species involved are connected via monomolecular reaction pathways. The potential and limitations of the approach for recovering the respective rate constants and component spectra are discussed.

Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix.

PubMed

Jovanović, Marko; Peter-Katalinić, Jasna

2016-02-01

Oligosaccharides represent complex class of analytes for mass spectrometric analysis due to the high variety of structural isomers concerning glycosidic linkages and possible branching. A systematic study of the negative ion mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of various neutral oligosaccharides under selection of an appropriate matrix, like 2,5-dihydroxyacetophenone (2,5-DHAP) is reported here, without commonly used anion dopant strategies. Nevertheless, we were able to generate relevant in-source decay (ISD) cross-ring fragment ions, typically obtained in the negative ion mode. Data observed indicate that the intrinsic property of the terminal non-reduced aldose is crucial for this behavior. A systematic study of the post source decay (PSD) of molecular, pseudomolecular and ISD cross-ring cleavage precursor ions is reported here. A direct comparison of the positive and negative ion mode MALDI MS1 and PSD behavior of neutral oligosaccharides could also be performed under the use of the same matrix preparation, because 2,5-DHAP is fully compatible with positive ion mode acquisition. We found that PSD spectra of deprotonated neutral oligosaccharides obtained in the negative ion mode are richer, because they contained both glycosidic and cross-ring fragment ions. However, we also found that cross-ring fragment ions are readily produced in the positive ion mode when potassiated precursor ions were selected. In addition, we show evidence that non-anionic dopants and specific instrumental parameters can also significantly influence the ISD fragmentation. Taken together, our results should increase our understanding of oligosaccharide behavior in the negative ion mode as well as increase our knowledge regarding many aspects of in-source MALDI chemistry. Copyright © 2016 John Wiley & Sons, Ltd.

Blind decomposition of Herschel-HIFI spectral maps of the NGC 7023 nebula

NASA Astrophysics Data System (ADS)

Berné, O.; Joblin, C.; Deville, Y.; Pilleri, P.; Pety, J.; Teyssier, D.; Gerin, M.; Fuente, A.

2012-12-01

Large spatial-spectral surveys are more and more common in astronomy. This calls for the need of new methods to analyze such mega- to giga-pixel data-cubes. In this paper we present a method to decompose such observations into a limited and comprehensive set of components. The original data can then be interpreted in terms of linear combinations of these components. The method uses non-negative matrix factorization (NMF) to extract latent spectral end-members in the data. The number of needed end-members is estimated based on the level of noise in the data. A Monte-Carlo scheme is adopted to estimate the optimal end-members, and their standard deviations. Finally, the maps of linear coefficients are reconstructed using non-negative least squares. We apply this method to a set of hyperspectral data of the NGC 7023 nebula, obtained recently with the HIFI instrument onboard the Herschel space observatory, and provide a first interpretation of the results in terms of 3-dimensional dynamical structure of the region.

Comment on ``The problem of deficiency indices for discrete Schrödinger operators on locally finite graphs'' [J. Math. Phys. 52, 063512 (2011)

NASA Astrophysics Data System (ADS)

Golénia, Sylvain; Schumacher, Christoph

2013-06-01

In this comment we answer negatively to our conjecture concerning the deficiency indices. More precisely, given any non-negative integer n, there is locally finite graph on which the adjacency matrix has deficiency indices (n, n).

THz spectral data analysis and components unmixing based on non-negative matrix factorization methods

NASA Astrophysics Data System (ADS)

Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

2017-04-01

In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification.

THz spectral data analysis and components unmixing based on non-negative matrix factorization methods.

PubMed

Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

2017-04-15

In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification. Copyright © 2017 Elsevier B.V. All rights reserved.

PM2.5 source apportionment in a French urban coastal site under steelworks emission influences using constrained non-negative matrix factorization receptor model.

PubMed

Kfoury, Adib; Ledoux, Frédéric; Roche, Cloé; Delmaire, Gilles; Roussel, Gilles; Courcot, Dominique

2016-02-01

The constrained weighted-non-negative matrix factorization (CW-NMF) hybrid receptor model was applied to study the influence of steelmaking activities on PM2.5 (particulate matter with equivalent aerodynamic diameter less than 2.5 μm) composition in Dunkerque, Northern France. Semi-diurnal PM2.5 samples were collected using a high volume sampler in winter 2010 and spring 2011 and were analyzed for trace metals, water-soluble ions, and total carbon using inductively coupled plasma--atomic emission spectrometry (ICP-AES), ICP--mass spectrometry (ICP-MS), ionic chromatography and micro elemental carbon analyzer. The elemental composition shows that NO3(-), SO4(2-), NH4(+) and total carbon are the main PM2.5 constituents. Trace metals data were interpreted using concentration roses and both influences of integrated steelworks and electric steel plant were evidenced. The distinction between the two sources is made possible by the use Zn/Fe and Zn/Mn diagnostic ratios. Moreover Rb/Cr, Pb/Cr and Cu/Cd combination ratio are proposed to distinguish the ISW-sintering stack from the ISW-fugitive emissions. The a priori knowledge on the influencing source was introduced in the CW-NMF to guide the calculation. Eleven source profiles with various contributions were identified: 8 are characteristics of coastal urban background site profiles and 3 are related to the steelmaking activities. Between them, secondary nitrates, secondary sulfates and combustion profiles give the highest contributions and account for 93% of the PM2.5 concentration. The steelwork facilities contribute in about 2% of the total PM2.5 concentration and appear to be the main source of Cr, Cu, Fe, Mn, Zn. Copyright © 2015. Published by Elsevier B.V.

Uncertainty of relative sensitivity factors in glow discharge mass spectrometry

NASA Astrophysics Data System (ADS)

Meija, Juris; Methven, Brad; Sturgeon, Ralph E.

2017-10-01

The concept of the relative sensitivity factors required for the correction of the measured ion beam ratios in pin-cell glow discharge mass spectrometry is examined in detail. We propose a data-driven model for predicting the relative response factors, which relies on a non-linear least squares adjustment and analyte/matrix interchangeability phenomena. The model provides a self-consistent set of response factors for any analyte/matrix combination of any element that appears as either an analyte or matrix in at least one known response factor.

Quantitative assessment in thermal image segmentation for artistic objects

NASA Astrophysics Data System (ADS)

Yousefi, Bardia; Sfarra, Stefano; Maldague, Xavier P. V.

2017-07-01

The application of the thermal and infrared technology in different areas of research is considerably increasing. These applications involve Non-destructive Testing (NDT), Medical analysis (Computer Aid Diagnosis/Detection- CAD), Arts and Archaeology among many others. In the arts and archaeology field, infrared technology provides significant contributions in term of finding defects of possible impaired regions. This has been done through a wide range of different thermographic experiments and infrared methods. The proposed approach here focuses on application of some known factor analysis methods such as standard Non-Negative Matrix Factorization (NMF) optimized by gradient-descent-based multiplicative rules (SNMF1) and standard NMF optimized by Non-negative least squares (NNLS) active-set algorithm (SNMF2) and eigen decomposition approaches such as Principal Component Thermography (PCT), Candid Covariance-Free Incremental Principal Component Thermography (CCIPCT) to obtain the thermal features. On one hand, these methods are usually applied as preprocessing before clustering for the purpose of segmentation of possible defects. On the other hand, a wavelet based data fusion combines the data of each method with PCT to increase the accuracy of the algorithm. The quantitative assessment of these approaches indicates considerable segmentation along with the reasonable computational complexity. It shows the promising performance and demonstrated a confirmation for the outlined properties. In particular, a polychromatic wooden statue and a fresco were analyzed using the above mentioned methods and interesting results were obtained.

Integration of Breast Cancer Secretomes with Clinical Data Elucidates Potential Serum Markers for Disease Detection, Diagnosis, and Prognosis.

PubMed

Ziegler, Yvonne S; Moresco, James J; Yates, John R; Nardulli, Ann M

2016-01-01

Cancer cells secrete factors that influence adjacent cell behavior and can lead to enhanced proliferation and metastasis. To better understand the role of these factors in oncogenesis and disease progression, estrogen and progesterone receptor positive MCF-7 cells, triple negative breast cancer MDA-MB-231, DT22, and DT28 cells, and MCF-10A non-transformed mammary epithelial cells were grown in 3D cultures. A special emphasis was placed on triple negative breast cancer since these tumors are highly aggressive and no targeted treatments are currently available. The breast cancer cells secreted factors of variable potency that stimulated proliferation of the relatively quiescent MCF-10A cells. The conditioned medium from each cell line was subjected to mass spectrometry analysis and a variety of secreted proteins were identified including glycolytic enzymes, proteases, protease inhibitors, extracellular matrix proteins, and insulin-like growth factor binding proteins. An investigation of the secretome from each cell line yielded clues about strategies used for breast cancer proliferation and metastasis. Some of the proteins we identified may be useful in the development of a serum-based test for breast cancer detection, diagnosis, prognosis, and monitoring.

Fluorescence spectroscopy using excitation and emission matrix for quantification of tissue native fluorophores and cancer diagnosis

NASA Astrophysics Data System (ADS)

Wu, Binlin; Gayen, S. K.; Xu, M.

2014-03-01

Native fluorescence spectrum of normal and cancerous human prostate tissues is studied to distinguish between normal and cancerous tissues, and cancerous tissues at different cancer grade. The tissue samples were obtained from Cooperative Human Tissue Network (CHTN) and National Disease Research Interchange(NDRI). An excitation and emission matrix (EEM) was generated for each tissue sample by acquiring native fluorescence spectrum of the sample using multiple excitation wavelengths. The non-negative matrix factorization algorithm was used to generate fluorescence EEMs that correspond to the fluorophores in biological tissues, including tryptophan, collagen, elastin, nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD) and the background paraffin. We hypothesize that, as a consequence of metabolic changes associated with the development of cancer, the concentrations of NADH and FAD are different in normal and cancerous tissues, and also different for different cancer grades. We used the ratio of the abundances of FAD and NADH to distinguish between normal and cancerous tissues, and the tissue cancer grade. The FAD-to-NADH ratio was found to be the highest for normal tissue and decreased as the cancer grade increased.

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.

PubMed

Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas; Leclerc, Marion; Laroche, Béatrice

2016-12-01

Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs) accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF) problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other metabolic processes in the gut or in other ecosystems.

Discovering SIFIs in Interbank Communities

PubMed Central

Pecora, Nicolò; Rovira Kaltwasser, Pablo; Spelta, Alessandro

2016-01-01

This paper proposes a new methodology based on non-negative matrix factorization to detect communities and to identify central nodes in a network as well as within communities. The method is specifically designed for directed weighted networks and, consequently, it has been applied to the interbank network derived from the e-MID interbank market. In an interbank network indeed links are directed, representing flows of funds between lenders and borrowers. Besides distinguishing between Systemically Important Borrowers and Lenders, the technique complements the detection of systemically important banks, revealing the community structure of the network, that proxies the most plausible areas of contagion of institutions’ distress. PMID:28002445

Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone-related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor.

PubMed

Kong, Li; Zhao, Yun-Peng; Tian, Qing-Yun; Feng, Jian-Quan; Kobayashi, Tatsuya; Merregaert, Joseph; Liu, Chuan-Ju

2016-08-01

Chondrogenesis and endochondral ossification are precisely controlled by cellular interactions with surrounding matrix proteins and growth factors that mediate cellular signaling pathways. Here, we report that extracellular matrix protein 1 (ECM1) is a previously unrecognized regulator of chondrogenesis. ECM1 is induced in the course of chondrogenesis and its expression in chondrocytes strictly depends on parathyroid hormone-related peptide (PTHrP) signaling pathway. Overexpression of ECM1 suppresses, whereas suppression of ECM1 enhances, chondrocyte differentiation and hypertrophy in vitro and ex vivo In addition, target transgene of ECM1 in chondrocytes or osteoblasts in mice leads to striking defects in cartilage development and endochondral bone formation. Of importance, ECM1 seems to be critical for PTHrP action in chondrogenesis, as blockage of ECM1 nearly abolishes PTHrP regulation of chondrocyte hypertrophy, and overexpression of ECM1 rescues disorganized growth plates of PTHrP-null mice. Furthermore, ECM1 and progranulin chondrogenic growth factor constitute an interaction network and act in concert in the regulation of chondrogenesis.-Kong, L., Zhao, Y.-P., Tian, Q.-Y., Feng, J.-Q., Kobayashi, T., Merregaert, J., Liu, C.-J. Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone-related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor. © FASEB.

Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone–related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor

PubMed Central

Kong, Li; Zhao, Yun-Peng; Tian, Qing-Yun; Feng, Jian-Quan; Kobayashi, Tatsuya; Merregaert, Joseph; Liu, Chuan-Ju

2016-01-01

Chondrogenesis and endochondral ossification are precisely controlled by cellular interactions with surrounding matrix proteins and growth factors that mediate cellular signaling pathways. Here, we report that extracellular matrix protein 1 (ECM1) is a previously unrecognized regulator of chondrogenesis. ECM1 is induced in the course of chondrogenesis and its expression in chondrocytes strictly depends on parathyroid hormone–related peptide (PTHrP) signaling pathway. Overexpression of ECM1 suppresses, whereas suppression of ECM1 enhances, chondrocyte differentiation and hypertrophy in vitro and ex vivo. In addition, target transgene of ECM1 in chondrocytes or osteoblasts in mice leads to striking defects in cartilage development and endochondral bone formation. Of importance, ECM1 seems to be critical for PTHrP action in chondrogenesis, as blockage of ECM1 nearly abolishes PTHrP regulation of chondrocyte hypertrophy, and overexpression of ECM1 rescues disorganized growth plates of PTHrP-null mice. Furthermore, ECM1 and progranulin chondrogenic growth factor constitute an interaction network and act in concert in the regulation of chondrogenesis.—Kong, L., Zhao, Y.-P., Tian, Q.-Y., Feng, J.-Q., Kobayashi, T., Merregaert, J., Liu, C.-J. Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone–related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor. PMID:27075243

Matrix Metalloproteinases in Non-Neoplastic Disorders

PubMed Central

Tokito, Akinori; Jougasaki, Michihisa

2016-01-01

The matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases belonging to the metzincin superfamily. There are at least 23 members of MMPs ever reported in human, and they and their substrates are widely expressed in many tissues. Recent growing evidence has established that MMP not only can degrade a variety of components of extracellular matrix, but also can cleave and activate various non-matrix proteins, including cytokines, chemokines and growth factors, contributing to both physiological and pathological processes. In normal conditions, MMP expression and activity are tightly regulated via interactions between their activators and inhibitors. Imbalance among these factors, however, results in dysregulated MMP activity, which causes tissue destruction and functional alteration or local inflammation, leading to the development of diverse diseases, such as cardiovascular disease, arthritis, neurodegenerative disease, as well as cancer. This article focuses on the accumulated evidence supporting a wide range of roles of MMPs in various non-neoplastic diseases and provides an outlook on the therapeutic potential of inhibiting MMP action. PMID:27455234

Detection of extracellular matrix modification in cancer models with inverse spectroscopic optical coherence tomography

NASA Astrophysics Data System (ADS)

Spicer, Graham L. C.; Azarin, Samira M.; Yi, Ji; Young, Scott T.; Ellis, Ronald; Bauer, Greta M.; Shea, Lonnie D.; Backman, Vadim

2016-10-01

In cancer biology, there has been a recent effort to understand tumor formation in the context of the tissue microenvironment. In particular, recent progress has explored the mechanisms behind how changes in the cell-extracellular matrix ensemble influence progression of the disease. The extensive use of in vitro tissue culture models in simulant matrix has proven effective at studying such interactions, but modalities for non-invasively quantifying aspects of these systems are scant. We present the novel application of an imaging technique, Inverse Spectroscopic Optical Coherence Tomography, for the non-destructive measurement of in vitro biological samples during matrix remodeling. Our findings indicate that the nanoscale-sensitive mass density correlation shape factor D of cancer cells increases in response to a more crosslinked matrix. We present a facile technique for the non-invasive, quantitative study of the micro- and nano-scale structure of the extracellular matrix and its host cells.

A musculoskeletal model of human locomotion driven by a low dimensional set of impulsive excitation primitives

PubMed Central

Sartori, Massimo; Gizzi, Leonardo; Lloyd, David G.; Farina, Dario

2013-01-01

Human locomotion has been described as being generated by an impulsive (burst-like) excitation of groups of musculotendon units, with timing dependent on the biomechanical goal of the task. Despite this view being supported by many experimental observations on specific locomotion tasks, it is still unknown if the same impulsive controller (i.e., a low-dimensional set of time-delayed excitastion primitives) can be used as input drive for large musculoskeletal models across different human locomotion tasks. For this purpose, we extracted, with non-negative matrix factorization, five non-negative factors from a large sample of muscle electromyograms in two healthy subjects during four motor tasks. These included walking, running, sidestepping, and crossover cutting maneuvers. The extracted non-negative factors were then averaged and parameterized to obtain task-generic Gaussian-shaped impulsive excitation curves or primitives. These were used to drive a subject-specific musculoskeletal model of the human lower extremity. Results showed that the same set of five impulsive excitation primitives could be used to predict the dynamics of 34 musculotendon units and the resulting hip, knee and ankle joint moments (i.e., NRMSE = 0.18 ± 0.08, and R2 = 0.73 ± 0.22 across all tasks and subjects) without substantial loss of accuracy with respect to using experimental electromyograms (i.e., NRMSE = 0.16 ± 0.07, and R2 = 0.78 ± 0.18 across all tasks and subjects). Results support the hypothesis that biomechanically different motor tasks might share similar neuromuscular control strategies. This might have implications in neurorehabilitation technologies such as human-machine interfaces for the torque-driven, proportional control of powered prostheses and orthoses. In this, device control commands (i.e., predicted joint torque) could be derived without direct experimental data but relying on simple parameterized Gaussian-shaped curves, thus decreasing the input drive complexity and the number of needed sensors. PMID:23805099

A musculoskeletal model of human locomotion driven by a low dimensional set of impulsive excitation primitives.

PubMed

Sartori, Massimo; Gizzi, Leonardo; Lloyd, David G; Farina, Dario

2013-01-01

Human locomotion has been described as being generated by an impulsive (burst-like) excitation of groups of musculotendon units, with timing dependent on the biomechanical goal of the task. Despite this view being supported by many experimental observations on specific locomotion tasks, it is still unknown if the same impulsive controller (i.e., a low-dimensional set of time-delayed excitastion primitives) can be used as input drive for large musculoskeletal models across different human locomotion tasks. For this purpose, we extracted, with non-negative matrix factorization, five non-negative factors from a large sample of muscle electromyograms in two healthy subjects during four motor tasks. These included walking, running, sidestepping, and crossover cutting maneuvers. The extracted non-negative factors were then averaged and parameterized to obtain task-generic Gaussian-shaped impulsive excitation curves or primitives. These were used to drive a subject-specific musculoskeletal model of the human lower extremity. Results showed that the same set of five impulsive excitation primitives could be used to predict the dynamics of 34 musculotendon units and the resulting hip, knee and ankle joint moments (i.e., NRMSE = 0.18 ± 0.08, and R (2) = 0.73 ± 0.22 across all tasks and subjects) without substantial loss of accuracy with respect to using experimental electromyograms (i.e., NRMSE = 0.16 ± 0.07, and R (2) = 0.78 ± 0.18 across all tasks and subjects). Results support the hypothesis that biomechanically different motor tasks might share similar neuromuscular control strategies. This might have implications in neurorehabilitation technologies such as human-machine interfaces for the torque-driven, proportional control of powered prostheses and orthoses. In this, device control commands (i.e., predicted joint torque) could be derived without direct experimental data but relying on simple parameterized Gaussian-shaped curves, thus decreasing the input drive complexity and the number of needed sensors.

Population clustering based on copy number variations detected from next generation sequencing data.

PubMed

Duan, Junbo; Zhang, Ji-Gang; Wan, Mingxi; Deng, Hong-Wen; Wang, Yu-Ping

2014-08-01

Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering.

A neighboring structure reconstructed matching algorithm based on LARK features

NASA Astrophysics Data System (ADS)

Xue, Taobei; Han, Jing; Zhang, Yi; Bai, Lianfa

2015-11-01

Aimed at the low contrast ratio and high noise of infrared images, and the randomness and ambient occlusion of its objects, this paper presents a neighboring structure reconstructed matching (NSRM) algorithm based on LARK features. The neighboring structure relationships of local window are considered based on a non-negative linear reconstruction method to build a neighboring structure relationship matrix. Then the LARK feature matrix and the NSRM matrix are processed separately to get two different similarity images. By fusing and analyzing the two similarity images, those infrared objects are detected and marked by the non-maximum suppression. The NSRM approach is extended to detect infrared objects with incompact structure. High performance is demonstrated on infrared body set, indicating a lower false detecting rate than conventional methods in complex natural scenes.

Non-Abelian integrable hierarchies: matrix biorthogonal polynomials and perturbations

NASA Astrophysics Data System (ADS)

Ariznabarreta, Gerardo; García-Ardila, Juan C.; Mañas, Manuel; Marcellán, Francisco

2018-05-01

In this paper, Geronimus–Uvarov perturbations for matrix orthogonal polynomials on the real line are studied and then applied to the analysis of non-Abelian integrable hierarchies. The orthogonality is understood in full generality, i.e. in terms of a nondegenerate continuous sesquilinear form, determined by a quasidefinite matrix of bivariate generalized functions with a well-defined support. We derive Christoffel-type formulas that give the perturbed matrix biorthogonal polynomials and their norms in terms of the original ones. The keystone for this finding is the Gauss–Borel factorization of the Gram matrix. Geronimus–Uvarov transformations are considered in the context of the 2D non-Abelian Toda lattice and noncommutative KP hierarchies. The interplay between transformations and integrable flows is discussed. Miwa shifts, τ-ratio matrix functions and Sato formulas are given. Bilinear identities, involving Geronimus–Uvarov transformations, first for the Baker functions, then secondly for the biorthogonal polynomials and its second kind functions, and finally for the τ-ratio matrix functions, are found.

HPC-NMF: A High-Performance Parallel Algorithm for Nonnegative Matrix Factorization

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

Kannan, Ramakrishnan; Sukumar, Sreenivas R.; Ballard, Grey M.

NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient distributed algorithms to solve the problem for big data sets. We propose a high-performance distributed-memory parallel algorithm that computes the factorization by iteratively solving alternating non-negative least squares (NLS) subproblems formore » $$\\WW$$ and $$\\HH$$. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). As opposed to previous implementation, our algorithm is also flexible: It performs well for both dense and sparse matrices, and allows the user to choose any one of the multiple algorithms for solving the updates to low rank factors $$\\WW$$ and $$\\HH$$ within the alternating iterations.« less

Dimension Reduction With Extreme Learning Machine.

PubMed

Kasun, Liyanaarachchi Lekamalage Chamara; Yang, Yan; Huang, Guang-Bin; Zhang, Zhengyou

2016-08-01

Data may often contain noise or irrelevant information, which negatively affect the generalization capability of machine learning algorithms. The objective of dimension reduction algorithms, such as principal component analysis (PCA), non-negative matrix factorization (NMF), random projection (RP), and auto-encoder (AE), is to reduce the noise or irrelevant information of the data. The features of PCA (eigenvectors) and linear AE are not able to represent data as parts (e.g. nose in a face image). On the other hand, NMF and non-linear AE are maimed by slow learning speed and RP only represents a subspace of original data. This paper introduces a dimension reduction framework which to some extend represents data as parts, has fast learning speed, and learns the between-class scatter subspace. To this end, this paper investigates a linear and non-linear dimension reduction framework referred to as extreme learning machine AE (ELM-AE) and sparse ELM-AE (SELM-AE). In contrast to tied weight AE, the hidden neurons in ELM-AE and SELM-AE need not be tuned, and their parameters (e.g, input weights in additive neurons) are initialized using orthogonal and sparse random weights, respectively. Experimental results on USPS handwritten digit recognition data set, CIFAR-10 object recognition, and NORB object recognition data set show the efficacy of linear and non-linear ELM-AE and SELM-AE in terms of discriminative capability, sparsity, training time, and normalized mean square error.

Semi-automated brain tumor segmentation on multi-parametric MRI using regularized non-negative matrix factorization.

PubMed

Sauwen, Nicolas; Acou, Marjan; Sima, Diana M; Veraart, Jelle; Maes, Frederik; Himmelreich, Uwe; Achten, Eric; Huffel, Sabine Van

2017-05-04

Segmentation of gliomas in multi-parametric (MP-)MR images is challenging due to their heterogeneous nature in terms of size, appearance and location. Manual tumor segmentation is a time-consuming task and clinical practice would benefit from (semi-) automated segmentation of the different tumor compartments. We present a semi-automated framework for brain tumor segmentation based on non-negative matrix factorization (NMF) that does not require prior training of the method. L1-regularization is incorporated into the NMF objective function to promote spatial consistency and sparseness of the tissue abundance maps. The pathological sources are initialized through user-defined voxel selection. Knowledge about the spatial location of the selected voxels is combined with tissue adjacency constraints in a post-processing step to enhance segmentation quality. The method is applied to an MP-MRI dataset of 21 high-grade glioma patients, including conventional, perfusion-weighted and diffusion-weighted MRI. To assess the effect of using MP-MRI data and the L1-regularization term, analyses are also run using only conventional MRI and without L1-regularization. Robustness against user input variability is verified by considering the statistical distribution of the segmentation results when repeatedly analyzing each patient's dataset with a different set of random seeding points. Using L1-regularized semi-automated NMF segmentation, mean Dice-scores of 65%, 74 and 80% are found for active tumor, the tumor core and the whole tumor region. Mean Hausdorff distances of 6.1 mm, 7.4 mm and 8.2 mm are found for active tumor, the tumor core and the whole tumor region. Lower Dice-scores and higher Hausdorff distances are found without L1-regularization and when only considering conventional MRI data. Based on the mean Dice-scores and Hausdorff distances, segmentation results are competitive with state-of-the-art in literature. Robust results were found for most patients, although careful voxel selection is mandatory to avoid sub-optimal segmentation.

Constructing the tree-level Yang-Mills S-matrix using complex factorization

NASA Astrophysics Data System (ADS)

Schuster, Philip C.; Toro, Natalia

2009-06-01

A remarkable connection between BCFW recursion relations and constraints on the S-matrix was made by Benincasa and Cachazo in 0705.4305, who noted that mutual consistency of different BCFW constructions of four-particle amplitudes generates non-trivial (but familiar) constraints on three-particle coupling constants — these include gauge invariance, the equivalence principle, and the lack of non-trivial couplings for spins > 2. These constraints can also be derived with weaker assumptions, by demanding the existence of four-point amplitudes that factorize properly in all unitarity limits with complex momenta. From this starting point, we show that the BCFW prescription can be interpreted as an algorithm for fully constructing a tree-level S-matrix, and that complex factorization of general BCFW amplitudes follows from the factorization of four-particle amplitudes. The allowed set of BCFW deformations is identified, formulated entirely as a statement on the three-particle sector, and using only complex factorization as a guide. Consequently, our analysis based on the physical consistency of the S-matrix is entirely independent of field theory. We analyze the case of pure Yang-Mills, and outline a proof for gravity. For Yang-Mills, we also show that the well-known scaling behavior of BCFW-deformed amplitudes at large z is a simple consequence of factorization. For gravity, factorization in certain channels requires asymptotic behavior ~ 1/z2.

Study on the Algorithm of Judgment Matrix in Analytic Hierarchy Process

NASA Astrophysics Data System (ADS)

Lu, Zhiyong; Qin, Futong; Jin, Yican

2017-10-01

A new algorithm is proposed for the non-consistent judgment matrix in AHP. A primary judgment matrix is generated firstly through pre-ordering the targeted factor set, and a compared matrix is built through the top integral function. Then a relative error matrix is created by comparing the compared matrix with the primary judgment matrix which is regulated under the control of the relative error matrix and the dissimilar degree of the matrix step by step. Lastly, the targeted judgment matrix is generated to satisfy the requirement of consistence and the least dissimilar degree. The feasibility and validity of the proposed method are verified by simulation results.

[Hair growth effect of minoxidil].

PubMed

Otomo, Susumu

2002-03-01

The length and size of hair are depend on the anagen term in its hair cycle. It has been reported that the some cell growth factors, such as VEGF, FGF-5S, IGF-1 and KGF, induce the proliferation of cells in the matrix, dermal papilla and dermal papillary vascular system and increase the amount of extra cellular matrix in dermal papilla and then maintain follicles in the anagen phase. On the other hand, negative factors, like FGF-5, thrombospondin, or still unknown ones, terminate the anagen phase. If the negative factors become dominant against cell proliferation factors according to fulfilling some time set by the biological clock for hair follicles, TGF beta induced in the matrix tissues evokes apoptosis of matrix cells and shifts the follicles from anagen to catagen. Androgenetic alopecia is caused by miniaturizing of hair follicles located in the frontal or crown part of scalp and are hereditarily more sensitive to androgen. In their hair cycles, the androgen shortens the anagen phase of follicles and shifts them to the catagen phase earlier than usual. The mode of action of hair growth effect of minoxidil is not completely elucidated, but the most plausible explanation proposed here is that minoxidil works as a sulfonylurea receptor (SUR) activator and prolongs the anagen phase of hair follicles in the following manner: minoxidil (1) induces cell growth factors such as VEGF, HGF, IGF-1 and potentiates HGF and IGF-1 actions by the activation of uncoupled SUR on the plasma membrane of dermal papilla cells, (2) inhibits of TGF beta induced apoptosis of hair matrix cells by opening the Kir 6.0 channel pore coupled with SUR on the mitochondrial inner membrane, and (3) dilates hair follicle arteries and increases blood flow in dermal papilla by opening the Kir 6.0 channel pore coupled with SUR on the plasma membrane of vascular smooth muscle cells.

Single element of the matrix source of negative hydrogen ions: Measurements of the extracted currents combined with diagnostics

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

Yordanov, D., E-mail: yordanov@phys.uni-sofia.bg; Lishev, St.; Shivarova, A.

2016-02-15

Combining measurements of the extracted currents with probe and laser-photodetachment diagnostics, the study is an extension of recent tests of factors and gas-discharge conditions stimulating the extraction of volume produced negative ions. The experiment is in a single element of a rf source with the design of a matrix of small-radius inductively driven discharges. The results are for the electron and negative-ion densities, for the plasma potential and for the electronegativity in the vicinity of the plasma electrode as well as for the currents of the extracted negative ions and electrons. The plasma-electrode bias and the rf power have beenmore » varied. Necessity of a high bias to the plasma electrode and stable linear increase of the extracted currents with the rf power are the main conclusions.« less

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry.

PubMed

Patty, C H Lucas; Luo, David A; Snik, Frans; Ariese, Freek; Buma, Wybren Jan; Ten Kate, Inge Loes; van Spanning, Rob J M; Sparks, William B; Germer, Thomas A; Garab, Győző; Kudenov, Michael W

2018-06-01

Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650 nm to 710 nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

PubMed

Fertig, Elana J; Stein-O'Brien, Genevieve; Jaffe, Andrew; Colantuoni, Carlo

2014-01-01

Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confounds expression changes resulting from simultaneous, non-orthogonal biological processes. Previously, we have shown that Markov chain Monte Carlo nonnegative matrix factorization algorithms are particularly adept at distinguishing such concurrent patterns. One such matrix factorization is implemented in the software package CoGAPS. We describe the application of this software and several technical considerations for identification of age-related patterns in a public, prefrontal cortex gene expression dataset.

Calabi-Yau structures on categories of matrix factorizations

NASA Astrophysics Data System (ADS)

Shklyarov, Dmytro

2017-09-01

Using tools of complex geometry, we construct explicit proper Calabi-Yau structures, that is, non-degenerate cyclic cocycles on differential graded categories of matrix factorizations of regular functions with isolated critical points. The formulas involve the Kapustin-Li trace and its higher corrections. From the physics perspective, our result yields explicit 'off-shell' models for categories of topological D-branes in B-twisted Landau-Ginzburg models.

Estimating Depolarization with the Jones Matrix Quality Factor

NASA Astrophysics Data System (ADS)

Hilfiker, James N.; Hale, Jeffrey S.; Herzinger, Craig M.; Tiwald, Tom; Hong, Nina; Schöche, Stefan; Arwin, Hans

2017-11-01

Mueller matrix (MM) measurements offer the ability to quantify the depolarization capability of a sample. Depolarization can be estimated using terms such as the depolarization index or the average degree of polarization. However, these calculations require measurement of the complete MM. We propose an alternate depolarization metric, termed the Jones matrix quality factor, QJM, which does not require the complete MM. This metric provides a measure of how close, in a least-squares sense, a Jones matrix can be found to the measured Mueller matrix. We demonstrate and compare the use of QJM to other traditional calculations of depolarization for both isotropic and anisotropic depolarizing samples; including non-uniform coatings, anisotropic crystal substrates, and beetle cuticles that exhibit both depolarization and circular diattenuation.

Analysis of spectrally resolved autofluorescence images by support vector machines

NASA Astrophysics Data System (ADS)

Mateasik, A.; Chorvat, D.; Chorvatova, A.

2013-02-01

Spectral analysis of the autofluorescence images of isolated cardiac cells was performed to evaluate and to classify the metabolic state of the cells in respect to the responses to metabolic modulators. The classification was done using machine learning approach based on support vector machine with the set of the automatically calculated features from recorded spectral profile of spectral autofluorescence images. This classification method was compared with the classical approach where the individual spectral components contributing to cell autofluorescence were estimated by spectral analysis, namely by blind source separation using non-negative matrix factorization. Comparison of both methods showed that machine learning can effectively classify the spectrally resolved autofluorescence images without the need of detailed knowledge about the sources of autofluorescence and their spectral properties.

Expression of receptors for putative anabolic growth factors in human intervertebral disc: implications for repair and regeneration of the disc.

PubMed

Le Maitre, Christine L; Richardson, Stephen M A; Baird, Pauline; Freemont, Anthony J; Hoyland, Judith A

2005-12-01

Low back pain (LBP) is a common, debilitating and economically important disorder. Current evidence implicates loss of intervertebral disc (IVD) matrix consequent upon 'degeneration' as a major cause of LBP. Degeneration of the IVD involves increases in degradative enzymes and decreases in the extracellular matrix (ECM) component in a process that is controlled by a range of cytokines and growth factors. Studies have suggested using anabolic growth factors to regenerate the normal matrix of the IVD, hence restoring disc height and reversing degenerative disc disease. However, for such therapies to be successful it is vital that the target cells (i.e. the disc cells) express the appropriate receptors. This immunohistochemical study has for the first time investigated the expression and localization of four potentially beneficial growth factor receptors (i.e. TGFbetaRII, BMPRII, FGFR3 and IGFRI) in non-degenerate and degenerate human IVDs. Receptor expression was quantified across regions of the normal and degenerate disc and showed that cells of the nucleus pulposus (NP) and inner annulus fibrosus (IAF) expressed significantly higher levels of the four growth factor receptors investigated. There were no significant differences between the four growth factor expression in non-degenerate and degenerate biopsies. However, expression of TGFbetaRII, FGFR3 and IGFRI, but not BMP RII, were observed in the ingrowing blood vessels that characterize part of the disease aetiology. In conclusion, this study has demonstrated the expression of the four growth factor receptors at similar levels in the chondrocyte-like cells of the NP and IAF in both non-degenerate and degenerate discs, implicating a role in normal disc homeostasis and suggesting that the application of these growth factors to the degenerate human IVD would stimulate matrix production. However, the expression of some of the growth factor receptors on ingrowing blood vessels might be problematic in a therapeutic approach. Copyright 2005 Pathological Society of Great Britain and Ireland.

Non-Rigid Structure Estimation in Trajectory Space from Monocular Vision

PubMed Central

Wang, Yaming; Tong, Lingling; Jiang, Mingfeng; Zheng, Junbao

2015-01-01

In this paper, the problem of non-rigid structure estimation in trajectory space from monocular vision is investigated. Similar to the Point Trajectory Approach (PTA), based on characteristic points’ trajectories described by a predefined Discrete Cosine Transform (DCT) basis, the structure matrix was also calculated by using a factorization method. To further optimize the non-rigid structure estimation from monocular vision, the rank minimization problem about structure matrix is proposed to implement the non-rigid structure estimation by introducing the basic low-rank condition. Moreover, the Accelerated Proximal Gradient (APG) algorithm is proposed to solve the rank minimization problem, and the initial structure matrix calculated by the PTA method is optimized. The APG algorithm can converge to efficient solutions quickly and lessen the reconstruction error obviously. The reconstruction results of real image sequences indicate that the proposed approach runs reliably, and effectively improves the accuracy of non-rigid structure estimation from monocular vision. PMID:26473863

A fast fully constrained geometric unmixing of hyperspectral images

NASA Astrophysics Data System (ADS)

Zhou, Xin; Li, Xiao-run; Cui, Jian-tao; Zhao, Liao-ying; Zheng, Jun-peng

2014-11-01

A great challenge in hyperspectral image analysis is decomposing a mixed pixel into a collection of endmembers and their corresponding abundance fractions. This paper presents an improved implementation of Barycentric Coordinate approach to unmix hyperspectral images, integrating with the Most-Negative Remove Projection method to meet the abundance sum-to-one constraint (ASC) and abundance non-negativity constraint (ANC). The original barycentric coordinate approach interprets the endmember unmixing problem as a simplex volume ratio problem, which is solved by calculate the determinants of two augmented matrix. One consists of all the members and the other consist of the to-be-unmixed pixel and all the endmembers except for the one corresponding to the specific abundance that is to be estimated. In this paper, we first modified the algorithm of Barycentric Coordinate approach by bringing in the Matrix Determinant Lemma to simplify the unmixing process, which makes the calculation only contains linear matrix and vector operations. So, the matrix determinant calculation of every pixel, as the original algorithm did, is avoided. By the end of this step, the estimated abundance meet the ASC constraint. Then, the Most-Negative Remove Projection method is used to make the abundance fractions meet the full constraints. This algorithm is demonstrated both on synthetic and real images. The resulting algorithm yields the abundance maps that are similar to those obtained by FCLS, while the runtime is outperformed as its computational simplicity.

Discriminative Transfer Subspace Learning via Low-Rank and Sparse Representation.

PubMed

Xu, Yong; Fang, Xiaozhao; Wu, Jian; Li, Xuelong; Zhang, David

2016-02-01

In this paper, we address the problem of unsupervised domain transfer learning in which no labels are available in the target domain. We use a transformation matrix to transfer both the source and target data to a common subspace, where each target sample can be represented by a combination of source samples such that the samples from different domains can be well interlaced. In this way, the discrepancy of the source and target domains is reduced. By imposing joint low-rank and sparse constraints on the reconstruction coefficient matrix, the global and local structures of data can be preserved. To enlarge the margins between different classes as much as possible and provide more freedom to diminish the discrepancy, a flexible linear classifier (projection) is obtained by learning a non-negative label relaxation matrix that allows the strict binary label matrix to relax into a slack variable matrix. Our method can avoid a potentially negative transfer by using a sparse matrix to model the noise and, thus, is more robust to different types of noise. We formulate our problem as a constrained low-rankness and sparsity minimization problem and solve it by the inexact augmented Lagrange multiplier method. Extensive experiments on various visual domain adaptation tasks show the superiority of the proposed method over the state-of-the art methods. The MATLAB code of our method will be publicly available at http://www.yongxu.org/lunwen.html.

Effects of Non-Collagenous Proteins, TGF-β1, and PDGF-BB on Viability and Proliferation of Dental Pulp Stem Cells

PubMed Central

Tabatabaei, Fahimeh Sadat

2016-01-01

ABSTRACT Objectives The dentin matrix servers as a reservoir of growth factors, sequestered during dentinogenesis. The aim of this study was to assess the viability and proliferation of dental pulp stem cells in the presence of dentin matrix-derived non-collagenous proteins and two growth factors; platelet-derived growth factor BB and transforming growth factor beta 1. Material and Methods The dental pulp cells were isolated and cultured. The dentin proteins were extracted and purified. The MTT assay was performed for assessment of cell viability and proliferation in the presence of different concentrations of dentin proteins and growth factors during 24 - 72 h post-treatment. Results The cells treated with 250 ng/mL dentin proteins had the best viability and proliferation ability in comparison with other concentrations (P < 0.05). The MTT assay demonstrated that cells cultured with 5 ng/mL platelet-derived growth factor BB had the highest viability at each time point as compared to other groups (P < 0.05). However, in presence of platelet-derived growth factor BB alone and in combination with transforming growth factor beta 1 and dentin proteins (10 ng/mL), significant higher viability was seen at all time points (P < 0.05). The least viability and proliferation at each growth factor concentration was seen in cells treated with combination of transforming growth factor beta 1 and dentin proteins at 72 h (P < 0.05). Conclusions The results indicated that the triple combination of growth factors and matrix-derived non-collagenous proteins (especially at 10 ng/mL concentration) has mitogenic effect on dental pulp stem cells. PMID:27099698

Correct definition of color singlet P-wave non-perturbative matrix element of heavy quarkonium production

NASA Astrophysics Data System (ADS)

Nayak, Gouranga C.

2017-09-01

Recently we have proved factorization of infrared divergences in NRQCD S-wave heavy quarkonium production at high energy colliders at all orders in coupling constant. One of the problem which still exists in the higher order pQCD calculation of color singlet P-wave heavy quarkonium production/anihillation is the appearance of noncanceling infrared divergences due to real soft gluons exchange, although no such infrared divergences are present in the color singlet S-wave heavy quarkonium. In this paper we find that since the non-perturbative matrix element of the color singlet P-wave heavy quarkonium production contains derivative operators, the gauge links are necessary to make it gauge invariant and be consistent with the factorization of such non-canceling infrared divergences at all orders in coupling constant.

Two-faced property of a market factor in asset pricing and diversification effect

NASA Astrophysics Data System (ADS)

Eom, Cheoljun

2017-04-01

This study empirically investigates the test hypothesis that a market factor acting as a representative common factor in the pricing models has a negative influence on constructing a well-diversified portfolio from the Markowitz mean-variance optimization function (MVOF). We use the comparative correlation matrix (C-CM) method to control a single eigenvalue among all eigenvalues included in the sample correlation matrix (S-CM), through the random matrix theory (RMT). In particular, this study observes the effect of the largest eigenvalue that has the property of the market factor. According to the results, the largest eigenvalue has the highest explanatory power on the stock return changes. The C-CM without the largest eigenvalue in the S-CM constructs a more diversified portfolio capable of improving the practical applicability of the MVOF. Moreover, the more diversified portfolio constructed from this C-CM has better out-of-sample performance in the future period. These results support the test hypothesis for the two-faced property of the market factor, defined by the largest eigenvalue.

Quantification of a Non-conventional Protein Secretion: The Low-Molecular-Weight FGF-2 Example.

PubMed

Arcondéguy, Tania; Touriol, Christian; Lacazette, Eric

2016-01-01

Quantification of secreted factors is most often measured with enzyme-linked immunosorbent assay (ELISA), Western Blot, or more recently with antibody arrays. However, some of these, like low-molecular-weight fibroblast growth factor-2 (LMW FGF-2; the 18 kDa form), exemplify a set of secreted but almost non-diffusible molecular actors. It has been proposed that phosphorylated FGF-2 is secreted via a non-vesicular mechanism and that heparan sulfate proteoglycans function as extracellular reservoir but also as actors for its secretion. Heparan sulfate is a linear sulfated polysaccharide present on proteoglycans found in the extracellular matrix or anchored in the plasma membrane (syndecan). Moreover the LMW FGF-2 secretion appears to be activated upon FGF-1 treatment. In order to estimate quantification of such factor export across the plasma membrane, technical approaches are presented (evaluation of LMW FGF-2: (1) secretion, (2) extracellular matrix reservoir, and (3) secretion modulation by surrounding factors) and the importance of such procedures in the comprehension of the biology of these growth factors is underlined.

Evaluating the MSCEIT V2.0 via CFA: comment on Mayer et al. (2003).

PubMed

Gignac, Gilles E

2005-06-01

This investigation uncovered several substantial errors in the confirmatory factor analysis results reported by J. D. Mayer, P. Salovey, D. R. Caruso, and G. Sitarenios (see record 2003-02341-015). Specifically, the values associated with the close-fit indices (normed fit index, Tucker-Lewis Index, and root-mean-square error of approximation) are inaccurate. A reanalysis of the Mayer et al. subscale intercorrelation matrix provided accurate values of the close-fit indices, which resulted in different evaluations of the models tested by J. D. Mayer et al. Contrary to J. D. Mayer et al., the 1-factor model and the 2-factor model did not provide good fit. Although the 4-factor model was still considered good fitting, the non-constrained 4-factor model yielded a non-positive definite matrix, which was interpreted to be due to the fact that two of the branch-level factors (Perceiving and Facilitating) were collinear, suggesting that a model with 4 factors was implausible.

Dealing with non-unique and non-monotonic response in particle sizing instruments

NASA Astrophysics Data System (ADS)

Rosenberg, Phil

2017-04-01

A number of instruments used as de-facto standards for measuring particle size distributions are actually incapable of uniquely determining the size of an individual particle. This is due to non-unique or non-monotonic response functions. Optical particle counters have non monotonic response due to oscillations in the Mie response curves, especially for large aerosol and small cloud droplets. Scanning mobility particle sizers respond identically to two particles where the ratio of particle size to particle charge is approximately the same. Images of two differently sized cloud or precipitation particles taken by an optical array probe can have similar dimensions or shadowed area depending upon where they are in the imaging plane. A number of methods exist to deal with these issues, including assuming that positive and negative errors cancel, smoothing response curves, integrating regions in measurement space before conversion to size space and matrix inversion. Matrix inversion (also called kernel inversion) has the advantage that it determines the size distribution which best matches the observations, given specific information about the instrument (a matrix which specifies the probability that a particle of a given size will be measured in a given instrument size bin). In this way it maximises use of the information in the measurements. However this technique can be confused by poor counting statistics which can cause erroneous results and negative concentrations. Also an effective method for propagating uncertainties is yet to be published or routinely implemented. Her we present a new alternative which overcomes these issues. We use Bayesian methods to determine the probability that a given size distribution is correct given a set of instrument data and then we use Markov Chain Monte Carlo methods to sample this many dimensional probability distribution function to determine the expectation and (co)variances - hence providing a best guess and an uncertainty for the size distribution which includes contributions from the non-unique response curve, counting statistics and can propagate calibration uncertainties.

Joint Dictionary Learning-Based Non-Negative Matrix Factorization for Voice Conversion to Improve Speech Intelligibility After Oral Surgery.

PubMed

Fu, Szu-Wei; Li, Pei-Chun; Lai, Ying-Hui; Yang, Cheng-Chien; Hsieh, Li-Chun; Tsao, Yu

2017-11-01

Objective: This paper focuses on machine learning based voice conversion (VC) techniques for improving the speech intelligibility of surgical patients who have had parts of their articulators removed. Because of the removal of parts of the articulator, a patient's speech may be distorted and difficult to understand. To overcome this problem, VC methods can be applied to convert the distorted speech such that it is clear and more intelligible. To design an effective VC method, two key points must be considered: 1) the amount of training data may be limited (because speaking for a long time is usually difficult for postoperative patients); 2) rapid conversion is desirable (for better communication). Methods: We propose a novel joint dictionary learning based non-negative matrix factorization (JD-NMF) algorithm. Compared to conventional VC techniques, JD-NMF can perform VC efficiently and effectively with only a small amount of training data. Results: The experimental results demonstrate that the proposed JD-NMF method not only achieves notably higher short-time objective intelligibility (STOI) scores (a standardized objective intelligibility evaluation metric) than those obtained using the original unconverted speech but is also significantly more efficient and effective than a conventional exemplar-based NMF VC method. Conclusion: The proposed JD-NMF method may outperform the state-of-the-art exemplar-based NMF VC method in terms of STOI scores under the desired scenario. Significance: We confirmed the advantages of the proposed joint training criterion for the NMF-based VC. Moreover, we verified that the proposed JD-NMF can effectively improve the speech intelligibility scores of oral surgery patients. Objective: This paper focuses on machine learning based voice conversion (VC) techniques for improving the speech intelligibility of surgical patients who have had parts of their articulators removed. Because of the removal of parts of the articulator, a patient's speech may be distorted and difficult to understand. To overcome this problem, VC methods can be applied to convert the distorted speech such that it is clear and more intelligible. To design an effective VC method, two key points must be considered: 1) the amount of training data may be limited (because speaking for a long time is usually difficult for postoperative patients); 2) rapid conversion is desirable (for better communication). Methods: We propose a novel joint dictionary learning based non-negative matrix factorization (JD-NMF) algorithm. Compared to conventional VC techniques, JD-NMF can perform VC efficiently and effectively with only a small amount of training data. Results: The experimental results demonstrate that the proposed JD-NMF method not only achieves notably higher short-time objective intelligibility (STOI) scores (a standardized objective intelligibility evaluation metric) than those obtained using the original unconverted speech but is also significantly more efficient and effective than a conventional exemplar-based NMF VC method. Conclusion: The proposed JD-NMF method may outperform the state-of-the-art exemplar-based NMF VC method in terms of STOI scores under the desired scenario. Significance: We confirmed the advantages of the proposed joint training criterion for the NMF-based VC. Moreover, we verified that the proposed JD-NMF can effectively improve the speech intelligibility scores of oral surgery patients.

Differential stimulation of neurotrophin release by the biocompatible nano-material (carbon nanotube) in primary cultured neurons.

PubMed

Kim, Yun Gi; Kim, Jong Wan; Pyeon, Hee Jang; Hyun, Jung Keun; Hwang, Ji-Young; Choi, Seong-Jun; Lee, Ja-Yeon; Deák, Ferenc; Kim, Hae-Won; Lee, Young Il

2014-01-01

In order to develop novel, effective therapies for central nervous system regeneration, it is essential to better understand the role of neurotrophic factors and to design, accordingly, better artificial scaffolds to support both neurite outgrowth and synapse formation. Both nerve growth factor and brain-derived neurotrophic factor are major factors in neural survival, development, synaptogenesis, and synaptic connectivity of primary cultured neurons. As a prime candidate coating material for such neural cultures, carbon nanotubes offer unique structural, mechanical, and electrical properties. In this study, carbon nanotubes coated glass-coverslips were used as the matrix of a primary neural culture system used to investigate the effects of carbon nanotubes on neurite outgrowth and nerve growth factor/brain-derived neurotrophic factor release and expression. For these purposes, we performed comparative analyses of primary cultured neurons on carbon nanotubes coated, non-coated, and Matrigel-coated coverslips. The morphological findings showed definite carbon nanotubes effects on the neurite outgrowths and synaptogenic figures in both cortical and hippocampal neurons when compared with the non-coated negative control. Although the carbon nanotubes did not change neurotrophin expression levels, it stimulated brain-derived neurotrophic factor release into the media from both types of neurons. Accordingly, we suggest a different mechanism of action between carbon nanotubes and Matrigel in relation to the specific neurotrophic factors. Since carbon nanotubes supply long-term extracellular molecular cues for the survival and neurite outgrowths of cultured neurons, the results from this study will contribute to an understanding of carbon nanotubes biological effects and provide new insight into their role in the secretion of neurotrophic factors.

Improving performances of suboptimal greedy iterative biclustering heuristics via localization.

PubMed

Erten, Cesim; Sözdinler, Melih

2010-10-15

Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. Even the simplest versions of the problem are computationally hard. Most of the proposed solutions therefore employ greedy iterative heuristics that locally optimize a suitably assigned scoring function. We provide a fast and simple pre-processing algorithm called localization that reorders the rows and columns of the input data matrix in such a way as to group correlated entries in small local neighborhoods within the matrix. The proposed localization algorithm takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. In order to evaluate the effectivenesss of the localization pre-processing algorithm, we focus on three representative greedy iterative heuristic methods. We show how the localization pre-processing can be incorporated into each representative algorithm to improve biclustering performance. Furthermore, we propose a simple biclustering algorithm, Random Extraction After Localization (REAL) that randomly extracts submatrices from the localization pre-processed data matrix, eliminates those with low similarity scores, and provides the rest as correlated structures representing biclusters. We compare the proposed localization pre-processing with another pre-processing alternative, non-negative matrix factorization. We show that our fast and simple localization procedure provides similar or even better results than the computationally heavy matrix factorization pre-processing with regards to H-value tests. We next demonstrate that the performances of the three representative greedy iterative heuristic methods improve with localization pre-processing when biological correlations in the form of functional enrichment and PPI verification constitute the main performance criteria. The fact that the random extraction method based on localization REAL performs better than the representative greedy heuristic methods under same criteria also confirms the effectiveness of the suggested pre-processing method. Supplementary material including code implementations in LEDA C++ library, experimental data, and the results are available at http://code.google.com/p/biclustering/ cesim@khas.edu.tr; melihsozdinler@boun.edu.tr Supplementary data are available at Bioinformatics online.

Fourier transform inequalities for phylogenetic trees.

PubMed

Matsen, Frederick A

2009-01-01

Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

Simulating the effect of non-linear mode coupling in cosmological parameter estimation

NASA Astrophysics Data System (ADS)

Kiessling, A.; Taylor, A. N.; Heavens, A. F.

2011-09-01

Fisher Information Matrix methods are commonly used in cosmology to estimate the accuracy that cosmological parameters can be measured with a given experiment and to optimize the design of experiments. However, the standard approach usually assumes both data and parameter estimates are Gaussian-distributed. Further, for survey forecasts and optimization it is usually assumed that the power-spectrum covariance matrix is diagonal in Fourier space. However, in the low-redshift Universe, non-linear mode coupling will tend to correlate small-scale power, moving information from lower to higher order moments of the field. This movement of information will change the predictions of cosmological parameter accuracy. In this paper we quantify this loss of information by comparing naïve Gaussian Fisher matrix forecasts with a maximum likelihood parameter estimation analysis of a suite of mock weak lensing catalogues derived from N-body simulations, based on the SUNGLASS pipeline, for a 2D and tomographic shear analysis of a Euclid-like survey. In both cases, we find that the 68 per cent confidence area of the Ωm-σ8 plane increases by a factor of 5. However, the marginal errors increase by just 20-40 per cent. We propose a new method to model the effects of non-linear shear-power mode coupling in the Fisher matrix by approximating the shear-power distribution as a multivariate Gaussian with a covariance matrix derived from the mock weak lensing survey. We find that this approximation can reproduce the 68 per cent confidence regions of the full maximum likelihood analysis in the Ωm-σ8 plane to high accuracy for both 2D and tomographic weak lensing surveys. Finally, we perform a multiparameter analysis of Ωm, σ8, h, ns, w0 and wa to compare the Gaussian and non-linear mode-coupled Fisher matrix contours. The 6D volume of the 1σ error contours for the non-linear Fisher analysis is a factor of 3 larger than for the Gaussian case, and the shape of the 68 per cent confidence volume is modified. We propose that future Fisher matrix estimates of cosmological parameter accuracies should include mode-coupling effects.

Biomechanical cell regulatory networks as complex adaptive systems in relation to cancer.

PubMed

Feller, Liviu; Khammissa, Razia Abdool Gafaar; Lemmer, Johan

2017-01-01

Physiological structure and function of cells are maintained by ongoing complex dynamic adaptive processes in the intracellular molecular pathways controlling the overall profile of gene expression, and by genes in cellular gene regulatory circuits. Cytogenetic mutations and non-genetic factors such as chronic inflammation or repetitive trauma, intrinsic mechanical stresses within extracellular matrix may induce redirection of gene regulatory circuits with abnormal reactivation of embryonic developmental programmes which can now drive cell transformation and cancer initiation, and later cancer progression and metastasis. Some of the non-genetic factors that may also favour cancerization are dysregulation in epithelial-mesenchymal interactions, in cell-to-cell communication, in extracellular matrix turnover, in extracellular matrix-to-cell interactions and in mechanotransduction pathways. Persistent increase in extracellular matrix stiffness, for whatever reason, has been shown to play an important role in cell transformation, and later in cancer cell invasion. In this article we review certain cell regulatory networks driving carcinogenesis, focussing on the role of mechanical stresses modulating structure and function of cells and their extracellular matrices.

Model-free data analysis for source separation based on Non-Negative Matrix Factorization and k-means clustering (NMFk)

NASA Astrophysics Data System (ADS)

Vesselinov, V. V.; Alexandrov, B.

2014-12-01

The identification of the physical sources causing spatial and temporal fluctuations of state variables such as river stage levels and aquifer hydraulic heads is challenging. The fluctuations can be caused by variations in natural and anthropogenic sources such as precipitation events, infiltration, groundwater pumping, barometric pressures, etc. The source identification and separation can be crucial for conceptualization of the hydrological conditions and characterization of system properties. If the original signals that cause the observed state-variable transients can be successfully "unmixed", decoupled physics models may then be applied to analyze the propagation of each signal independently. We propose a new model-free inverse analysis of transient data based on Non-negative Matrix Factorization (NMF) method for Blind Source Separation (BSS) coupled with k-means clustering algorithm, which we call NMFk. NMFk is capable of identifying a set of unique sources from a set of experimentally measured mixed signals, without any information about the sources, their transients, and the physical mechanisms and properties controlling the signal propagation through the system. A classical BSS conundrum is the so-called "cocktail-party" problem where several microphones are recording the sounds in a ballroom (music, conversations, noise, etc.). Each of the microphones is recording a mixture of the sounds. The goal of BSS is to "unmix'" and reconstruct the original sounds from the microphone records. Similarly to the "cocktail-party" problem, our model-freee analysis only requires information about state-variable transients at a number of observation points, m, where m > r, and r is the number of unknown unique sources causing the observed fluctuations. We apply the analysis on a dataset from the Los Alamos National Laboratory (LANL) site. We identify and estimate the impact and sources are barometric pressure and water-supply pumping effects. We also estimate the location of the water-supply pumping wells based on the available data. The possible applications of the NMFk algorithm are not limited to hydrology problems; NMFk can be applied to any problem where temporal system behavior is observed at multiple locations and an unknown number of physical sources are causing these fluctuations.

An ignition key for atomic-scale engines

NASA Astrophysics Data System (ADS)

Dundas, Daniel; Cunningham, Brian; Buchanan, Claire; Terasawa, Asako; Paxton, Anthony T.; Todorov, Tchavdar N.

2012-10-01

A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.

Factorization of differential expansion for non-rectangular representations

NASA Astrophysics Data System (ADS)

Morozov, A.

2018-04-01

Factorization of the differential expansion (DE) coefficients for colored HOMFLY-PT polynomials of antiparallel double braids, originally discovered for rectangular representations R, in the case of rectangular representations R, is extended to the first non-rectangular representations R = [2, 1] and R = [3, 1]. This increases chances that such factorization will take place for generic R, thus fixing the shape of the DE. We illustrate the power of the method by conjecturing the DE-induced expression for double-braid polynomials for all R = [r, 1]. In variance with the rectangular case, the knowledge for double braids is not fully sufficient to deduce the exclusive Racah matrix S¯ — the entries in the sectors with nontrivial multiplicities sum up and remain unseparated. Still, a considerable piece of the matrix is extracted directly and its other elements can be found by solving the unitarity constraints.

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

PubMed Central

Jaeger, Sébastien; Thieffry, Denis

2017-01-01

Abstract Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. PMID:28591841

Co-clustering phenome–genome for phenotype classification and disease gene discovery

PubMed Central

Hwang, TaeHyun; Atluri, Gowtham; Xie, MaoQiang; Dey, Sanjoy; Hong, Changjin; Kumar, Vipin; Kuang, Rui

2012-01-01

Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped >2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways. PMID:22735708

A Structural Finite Element Model for Lamellar Unit of Aortic Media Indicates Heterogeneous Stress Field After Collagen Recruitment

PubMed Central

Thunes, James R.; Pal, Siladitya; Fortunato, Ronald N.; Phillippi, Julie A.; Gleason, Thomas G.; Vorp, David A.; Maiti, Spandan

2016-01-01

Incorporation of collagen structural information into the study of biomechanical behavior of ascending thoracic aortic (ATA) wall tissue should provide better insight into the pathophysiology of ATA. Structurally motivated constitutive models that include fiber dispersion and recruitment can successfully capture overall mechanical response of the arterial wall tissue. However, these models cannot examine local microarchitectural features of the collagen network, such as the effect of fiber disruptions and interaction between fibrous and non-fibrous components, which may influence emergent biomechanical properties of the tissue. Motivated by this need, we developed a finite element based three-dimensional structural model of the lamellar units of the ATA media that directly incorporates the collagen fiber microarchitecture. The fiber architecture was computer generated utilizing network features, namely fiber orientation distribution, intersection density and areal concentration, obtained from image analysis of multiphoton microscopy images taken from human aneurysmal ascending thoracic aortic media specimens with bicuspid aortic valve (BAV) phenotype. Our model reproduces the typical J-shaped constitutive response of the aortic wall tissue. We found that the stress state in the non-fibrous matrix was homogeneous until the collagen fibers were recruited, but became highly heterogeneous after that event. The degree of heterogeneity was dependent upon local network architecture with high stresses observed near disrupted fibers. The magnitude of non-fibrous matrix stress at higher stretch levels was negatively correlated with local fiber density. The localized stress concentrations, elucidated by this model, may be a factor in the degenerative changes in aneurysmal ATA tissue. PMID:27113538

Evidence of the presence of nucleic acids and β-glucan in the matrix of non-typeable Haemophilus influenzae in vitro biofilms

PubMed Central

Domenech, Mirian; Pedrero-Vega, Elena; Prieto, Alicia; García, Ernesto

2016-01-01

Non-typeable Haemophilus influenzae (NTHi) is a Gram-negative bacterium that frequently colonizes the human nasopharynx; it is a common cause of chronic and recurrent otitis media in children and of exacerbations of chronic obstructive pulmonary disease. To date, no exopolysaccharide clearly contributing to NTHi biofilms has been identified. Consequently, there is some debate as to whether NTHi forms biofilms during colonization and infection. The present work shows that NTHi can form biofilms in vitro, producing an extracellular matrix composed of proteins, nucleic acids, and a β-glucan. Extracellular DNA, visualized by immunostaining and using fluorochromes, is an important component of this matrix and appears to be essential in biofilm maintenance. Extracellular RNA appears to be required only in the first steps of biofilm formation. Evidence of a matrix polysaccharide was obtained by staining with Calcofluor white M2R and by disaggregating biofilms with cellulase. Using strain 54997, residues of Glcp(1→4) in the NTHi biofilm were confirmed by gas-liquid chromatography-mass spectrometry. Evidence that N-acetyl-L-cysteine shows notable killing activity towards in vitro NTHi biofilm-forming bacteria is also provided. PMID:27805043

Evidence of the presence of nucleic acids and β-glucan in the matrix of non-typeable Haemophilus influenzae in vitro biofilms.

PubMed

Domenech, Mirian; Pedrero-Vega, Elena; Prieto, Alicia; García, Ernesto

2016-11-02

Non-typeable Haemophilus influenzae (NTHi) is a Gram-negative bacterium that frequently colonizes the human nasopharynx; it is a common cause of chronic and recurrent otitis media in children and of exacerbations of chronic obstructive pulmonary disease. To date, no exopolysaccharide clearly contributing to NTHi biofilms has been identified. Consequently, there is some debate as to whether NTHi forms biofilms during colonization and infection. The present work shows that NTHi can form biofilms in vitro, producing an extracellular matrix composed of proteins, nucleic acids, and a β-glucan. Extracellular DNA, visualized by immunostaining and using fluorochromes, is an important component of this matrix and appears to be essential in biofilm maintenance. Extracellular RNA appears to be required only in the first steps of biofilm formation. Evidence of a matrix polysaccharide was obtained by staining with Calcofluor white M2R and by disaggregating biofilms with cellulase. Using strain 54997, residues of Glcp(1→4) in the NTHi biofilm were confirmed by gas-liquid chromatography-mass spectrometry. Evidence that N-acetyl-L-cysteine shows notable killing activity towards in vitro NTHi biofilm-forming bacteria is also provided.

Beyond the Matrix: The Many Non-ECM Ligands for Integrins

PubMed Central

LaFoya, Bryce; Munroe, Jordan A.; Miyamoto, Alison; Detweiler, Michael A.; Crow, Jacob J.; Gazdik, Tana

2018-01-01

The traditional view of integrins portrays these highly conserved cell surface receptors as mediators of cellular attachment to the extracellular matrix (ECM), and to a lesser degree, as coordinators of leukocyte adhesion to the endothelium. These canonical activities are indispensable; however, there is also a wide variety of integrin functions mediated by non-ECM ligands that transcend the traditional roles of integrins. Some of these unorthodox roles involve cell-cell interactions and are engaged to support immune functions such as leukocyte transmigration, recognition of opsonization factors, and stimulation of neutrophil extracellular traps. Other cell-cell interactions mediated by integrins include hematopoietic stem cell and tumor cell homing to target tissues. Integrins also serve as cell-surface receptors for various growth factors, hormones, and small molecules. Interestingly, integrins have also been exploited by a wide variety of organisms including viruses and bacteria to support infectious activities such as cellular adhesion and/or cellular internalization. Additionally, the disruption of integrin function through the use of soluble integrin ligands is a common strategy adopted by several parasites in order to inhibit blood clotting during hematophagy, or by venomous snakes to kill prey. In this review, we strive to go beyond the matrix and summarize non-ECM ligands that interact with integrins in order to highlight these non-traditional functions of integrins. PMID:29393909

Speech enhancement on smartphone voice recording

NASA Astrophysics Data System (ADS)

Tris Atmaja, Bagus; Nur Farid, Mifta; Arifianto, Dhany

2016-11-01

Speech enhancement is challenging task in audio signal processing to enhance the quality of targeted speech signal while suppress other noises. In the beginning, the speech enhancement algorithm growth rapidly from spectral subtraction, Wiener filtering, spectral amplitude MMSE estimator to Non-negative Matrix Factorization (NMF). Smartphone as revolutionary device now is being used in all aspect of life including journalism; personally and professionally. Although many smartphones have two microphones (main and rear) the only main microphone is widely used for voice recording. This is why the NMF algorithm widely used for this purpose of speech enhancement. This paper evaluate speech enhancement on smartphone voice recording by using some algorithms mentioned previously. We also extend the NMF algorithm to Kulback-Leibler NMF with supervised separation. The last algorithm shows improved result compared to others by spectrogram and PESQ score evaluation.

Correlated Noise: How it Breaks NMF, and What to Do About It.

PubMed

Plis, Sergey M; Potluru, Vamsi K; Lane, Terran; Calhoun, Vince D

2011-01-12

Non-negative matrix factorization (NMF) is a problem of decomposing multivariate data into a set of features and their corresponding activations. When applied to experimental data, NMF has to cope with noise, which is often highly correlated. We show that correlated noise can break the Donoho and Stodden separability conditions of a dataset and a regular NMF algorithm will fail to decompose it, even when given freedom to be able to represent the noise as a separate feature. To cope with this issue, we present an algorithm for NMF with a generalized least squares objective function (glsNMF) and derive multiplicative updates for the method together with proving their convergence. The new algorithm successfully recovers the true representation from the noisy data. Robust performance can make glsNMF a valuable tool for analyzing empirical data.

Correlated Noise: How it Breaks NMF, and What to Do About It

PubMed Central

Plis, Sergey M.; Potluru, Vamsi K.; Lane, Terran; Calhoun, Vince D.

2010-01-01

Non-negative matrix factorization (NMF) is a problem of decomposing multivariate data into a set of features and their corresponding activations. When applied to experimental data, NMF has to cope with noise, which is often highly correlated. We show that correlated noise can break the Donoho and Stodden separability conditions of a dataset and a regular NMF algorithm will fail to decompose it, even when given freedom to be able to represent the noise as a separate feature. To cope with this issue, we present an algorithm for NMF with a generalized least squares objective function (glsNMF) and derive multiplicative updates for the method together with proving their convergence. The new algorithm successfully recovers the true representation from the noisy data. Robust performance can make glsNMF a valuable tool for analyzing empirical data. PMID:23750288

Non-invasive dual fluorescence in vivo imaging for detection of macrophage infiltration and matrix metalloproteinase (MMP) activity in inflammatory arthritic joints

PubMed Central

Cho, Hongsik; Bhatti, Fazal-Ur-Rehman; Yoon, Tae Won; Hasty, Karen A.; Stuart, John M.; Yi, Ae-Kyung

2016-01-01

Detection and intervention at an early stage is a critical factor to impede arthritis progress. Here we present a non-invasive method to detect inflammatory changes in joints of arthritic mice. Inflammation was monitored by dual fluorescence optical imaging for near-infrared fluorescent (750F) matrix-metalloproteinase activatable agent and allophycocyanin-conjugated anti-mouse CD11b. Increased intensity of allophycocyanin (indication of macrophage accumulation) and 750F (indication of matrix-metalloproteinase activity) showed a biological relationship with the arthritis severity score and the histopathology score of arthritic joints. Our results demonstrate that this method can be used to detect early stages of arthritis with minimum intervention in small animal models. PMID:27231625

The synergic role of sociotechnical and personal characteristics on work injuries in mines.

PubMed

Paul, P S; Maiti, J

2008-05-01

Occupational injuries in mines are attributed to many factors. In this study, an attempt was made to identify the various factors related to work injuries in mines and to estimate their effects on work injuries to mine workers. An accident path model was developed to estimate the pattern and strength of relationships amongst the personal and sociotechnical variables in accident/injury occurrences. The input data for the model were the correlation matrix of 18 variables, which were collected from the case study mines. The case study results showed that there are sequential interactions amongst the sociotechnical and personal factors leading to accidents/injuries in mines. Amongst the latent endogenous constructs, job dissatisfaction and safe work behaviour show a significant positive and negative direct relationship with work injury, respectively. However, the construct safety environment has a significant negative indirect relationship with work injury. The safety environment is negatively affected by work hazards and positively affected by social support. The safety environment also shows a significant negative relationship with job stress and job dissatisfaction. However, negative personality has no significant direct or indirect effect on work injury, but it has a significant negative relationship with safe work behaviour. The endogenous construct negative personality is positively influenced by job stress and negatively influenced by social support.

Optical properties of nanowire metamaterials with gain

NASA Astrophysics Data System (ADS)

Lima, Joaquim; Adam, Jost; Rego, Davi; Esquerre, Vitaly; Bordo, Vladimir

2016-11-01

The transmittance, reflectance and absorption of a nanowire metamaterial with optical gain are numerically simulated and investigated. It is assumed that the metamaterial is represented by aligned silver nanowires embedded into a semiconductor matrix, made of either silicon or gallium phosphide. The gain in the matrix is modeled by adding a negative imaginary part to the dielectric function of the semiconductor. It is found that the optical coefficients of the metamaterial depend on the gain magnitude in a non-trivial way: they can both increase and decrease with gain depending on the lattice constant of the metamaterial. This peculiar behavior is explained by the field redistribution between the lossy metal nanowires and the amplifying matrix material. These findings are significant for a proper design of nanowire metamaterials with low optical losses for diverse applications.

Open Quantum Random Walks on the Half-Line: The Karlin-McGregor Formula, Path Counting and Foster's Theorem

NASA Astrophysics Data System (ADS)

Jacq, Thomas S.; Lardizabal, Carlos F.

2017-11-01

In this work we consider open quantum random walks on the non-negative integers. By considering orthogonal matrix polynomials we are able to describe transition probability expressions for classes of walks via a matrix version of the Karlin-McGregor formula. We focus on absorbing boundary conditions and, for simpler classes of examples, we consider path counting and the corresponding combinatorial tools. A non-commutative version of the gambler's ruin is studied by obtaining the probability of reaching a certain fortune and the mean time to reach a fortune or ruin in terms of generating functions. In the case of the Hadamard coin, a counting technique for boundary restricted paths in a lattice is also presented. We discuss an open quantum version of Foster's Theorem for the expected return time together with applications.

Matrix metalloproteinases: their functional role in lung cancer.

PubMed

Merchant, Neha; Nagaraju, Ganji Purnachandra; Rajitha, Balney; Lammata, Saipriya; Jella, Kishore Kumar; Buchwald, Zachary S; Lakka, Sajani S; Ali, Arif N

2017-08-01

Lung malignancy is the foremost cause of cancer-related deaths globally and is frequently related to long-term tobacco smoking. Recent studies reveal that the expression of matrix metalloproteinases (MMPs) is extremely high in lung tumors compared with non-malignant lung tissue. MMPs are zinc-dependent proteases and are involved in the degradation of extracellular matrix (ECM). Several investigations have shown that MMPs manipulate the activity of non-ECM molecules, including cytokines, growth factors and receptors that control the tumor microenvironment. In this review, we have summarized and critically reviewed the published works on the role of MMPs in non-small-cell lung cancer. We have also explored the structure of MMPs, their various types and roles in lung cancer metastasis including invasion, migration and angiogenesis. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF).

PubMed

Wang, Xiaodong; Han, Jun; Hardie, Darryl B; Yang, Juncong; Pan, Jingxi; Borchers, Christoph H

2017-07-01

In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2017 Elsevier B.V. All rights reserved.

Linearized T-Matrix and Mie Scattering Computations

NASA Technical Reports Server (NTRS)

Spurr, R.; Wang, J.; Zeng, J.; Mishchenko, M. I.

2011-01-01

We present a new linearization of T-Matrix and Mie computations for light scattering by non-spherical and spherical particles, respectively. In addition to the usual extinction and scattering cross-sections and the scattering matrix outputs, the linearized models will generate analytical derivatives of these optical properties with respect to the real and imaginary parts of the particle refractive index, and (for non-spherical scatterers) with respect to the ''shape'' parameter (the spheroid aspect ratio, cylinder diameter/height ratio, Chebyshev particle deformation factor). These derivatives are based on the essential linearity of Maxwell's theory. Analytical derivatives are also available for polydisperse particle size distribution parameters such as the mode radius. The T-matrix formulation is based on the NASA Goddard Institute for Space Studies FORTRAN 77 code developed in the 1990s. The linearized scattering codes presented here are in FORTRAN 90 and will be made publicly available.

Relativistic, model-independent, multichannel 2 → 2 transition amplitudes in a finite volume

DOE PAGES

Briceno, Raul A.; Hansen, Maxwell T.

2016-07-13

We derive formalism for determining 2 + J → 2 infinite-volume transition amplitudes from finite-volume matrix elements. Specifically, we present a relativistic, model-independent relation between finite-volume matrix elements of external currents and the physically observable infinite-volume matrix elements involving two-particle asymptotic states. The result presented holds for states composed of two scalar bosons. These can be identical or non-identical and, in the latter case, can be either degenerate or non-degenerate. We further accommodate any number of strongly-coupled two-scalar channels. This formalism will, for example, allow future lattice QCD calculations of themore » $$\\rho$$-meson form factor, in which the unstable nature of the $$\\rho$$ is rigorously accommodated. In conclusion, we also discuss how this work will impact future extractions of nuclear parity and hadronic long-range matrix elements from lattice QCD.« less

Non-Intrusive Load Monitoring of HVAC Components using Signal Unmixing

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

Rahimpour, Alireza; Qi, Hairong; Fugate, David L

Heating, Ventilating and Air Conditioning units (HVAC) are a major electrical energy consumer in buildings. Monitoring of the operation and energy consumption of HVAC would increase the awareness of building owners and maintenance service providers of the condition and quality of performance of these units, enabling conditioned-based maintenance which would help achieving higher energy efficiency. In this paper, a novel non-intrusive load monitoring method based on group constrained non-negative matrix factorization is proposed for monitoring the different components of HVAC unit by only measuring the whole building aggregated power signal. At the first level of this hierarchical approach, power consumptionmore » of the building is decomposed to energy consumption of the HVAC unit and all the other electrical devices operating in the building such as lighting and plug loads. Then, the estimated power signal of the HVAC is used for estimating the power consumption profile of the HVAC major electrical loads such as compressors, condenser fans and indoor blower. Experiments conducted on real data collected from a building testbed maintained at the Oak Ridge National Laboratory (ORNL) demonstrate high accuracy on the disaggregation task.« less

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

PubMed

Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2017-07-27

Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Magnetic separation of coal fly ash from Bulgarian power plants.

PubMed

Shoumkova, Annie S

2011-10-01

Fly ash from three coal-burning power plants in Bulgaria: 'Maritza 3', 'Republika' and 'Rousse East' were subjected to wet low-intensity magnetic separation. The tests were performed at different combinations of magnetic field intensity, flow velocity and diameter of matrix elements. It was found that all parameters investigated affected the separation efficiency, but their influence was interlinked and was determined by the properties of the material and the combination of other conditions. Among the fly ash characteristics, the most important parameters, determining the magnetic separation applicability, were mineralogical composition and distribution of minerals in particles. The main factors limiting the process were the presence of paramagnetic Fe-containing mineral and amorphous matter, and the existence of poly-mineral particles and aggregates of magnetic and non-magnetic particles. It was demonstrated that the negative effect of both factors could be considerably limited by the selection of a proper set of separation conditions. The dependences between concentration of ferromagnetic iron in the ash, their magnetic properties and magnetic fraction yields were studied. It was experimentally proved that, for a certain set of separation conditions, the yields of magnetic fractions were directly proportional to the saturation magnetization of the ferromagnetic components of the ash. The main properties of typical magnetic and non-magnetic fractions were studied.

Involvement and Regulation of Heparanase in Prostate Cancer Progression

DTIC Science & Technology

2007-02-01

1995). On the other hand, some promoters are negatively regulated by wt p53. These include MMP-1 (Sun et al., 1999), alpha - fetoprotein (Lee et al...necrosis factor alpha is formed from the extracellular matrix by the enzyme heparanase. Proc Natl Acad Sci U S A. 1995;92: 5037-5041. 29. Zcharia E

12 CFR 217.34 - OTC derivative contracts.

Code of Federal Regulations, 2014 CFR

2014-01-01

... net present value of the amount of unpaid premiums. Table 1 to § 217.34—Conversion Factor Matrix for... single OTC derivative contract is the greater of the mark-to-fair value of the OTC derivative contract or... with a negative mark-to-fair value, is calculated by multiplying the notional principal amount of the...

Dependence of matrix effect on ionization polarity during LC-ESI-MS analysis of derivatized amino acids in some natural samples.

PubMed

Oldekop, Maarja-Liisa; Rebane, Riin; Herodes, Koit

2017-10-01

Matrix effect, the influence of co-eluting components on the ionization efficiency of the analyte, affects the trueness and precision of the LC-ESI-MS analysis. Derivatization can reduce or eliminate matrix effect, for example, diethyl ethoxymethylenemalonate (DEEMM) derivatives have shown less matrix effect compared to other derivatives. Moreover, the use of negative ion mode can further reduce matrix effect. In order to investigate the combination of derivatization and different ionization modes, an LC-ESI-MS/MS method using alternating positive/negative ion mode was developed and validated. The analyses in positive and negative ion modes had comparable limit of quantitation values. The influence of ESI polarity on matrix effect was investigated during the analysis of 22 DEEMM-derivatized amino acids in herbal extracts and honeys. Sample dilution approach was used for the evaluation of the presence of matrix effect. Altogether, 4 honeys and 11 herbal extracts were analyzed, and the concentrations of 22 amino acids in the samples are presented. In the positive ion mode, matrix effect was observed for several amino acid derivatives and the matrix effect was stronger in honey samples compared to the herbal extracts. The negative ion mode was free from matrix effect, with only few exceptions in honeys (average relative standard deviation over all analytes and matrices was 8%; SD = 7%). The matrix effect was eliminated in the positive ion mode by sample dilution and agreement between concentrations from the two ion modes was achieved for most amino acids. In conclusion, it was shown that the combination of derivatization and negative ion mode can be a powerful tool for minimizing matrix effect in more complicated applications.

MCA-NMF: Multimodal Concept Acquisition with Non-Negative Matrix Factorization

PubMed Central

Mangin, Olivier; Filliat, David; ten Bosch, Louis; Oudeyer, Pierre-Yves

2015-01-01

In this paper we introduce MCA-NMF, a computational model of the acquisition of multimodal concepts by an agent grounded in its environment. More precisely our model finds patterns in multimodal sensor input that characterize associations across modalities (speech utterances, images and motion). We propose this computational model as an answer to the question of how some class of concepts can be learnt. In addition, the model provides a way of defining such a class of plausibly learnable concepts. We detail why the multimodal nature of perception is essential to reduce the ambiguity of learnt concepts as well as to communicate about them through speech. We then present a set of experiments that demonstrate the learning of such concepts from real non-symbolic data consisting of speech sounds, images, and motions. Finally we consider structure in perceptual signals and demonstrate that a detailed knowledge of this structure, named compositional understanding can emerge from, instead of being a prerequisite of, global understanding. An open-source implementation of the MCA-NMF learner as well as scripts and associated experimental data to reproduce the experiments are publicly available. PMID:26489021

A novel rhamno-mannan exopolysaccharide isolated from biofilms of Burkholderia multivorans C1576.

PubMed

Dolfi, Stefania; Sveronis, Aris; Silipo, Alba; Rizzo, Roberto; Cescutti, Paola

2015-06-26

Burkholderia multivorans C1576 is a Gram negative opportunistic pathogen causing serious lung infection in cystic fibrosis patients. Considering that bacteria naturally form biofilms, and exopolysaccharides are recognized as important factors for biofilm architecture set-up, B. multivorans was grown both in biofilm and in non-biofilm mode on two different media in order to compare the exopolysaccharides biosynthesized in these different experimental conditions. The exopolysaccharides produced were purified and their structure was determined resorting mainly to NMR spectroscopy, ESI mass spectrometry and gas chromatography coupled to mass spectrometry. The experimental data showed that both in biofilm and non-biofilm mode B. multivorans C1576 produced a novel exopolysaccharide having the following structure: [Formula: see text]. About 50% of the 2-linked rhamnose residues are substituted on C-3 with a methyl ether group. The high percentage of deoxysugar Rha units, coupled with OMe substitutions, suggest a possible role for polymer domains with marked hydrophobic characteristics able to create exopolysaccharide junction zones favouring the stability of the biofilm matrix. Copyright © 2015 Elsevier Ltd. All rights reserved.

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

BCYCLIC: A parallel block tridiagonal matrix cyclic solver

NASA Astrophysics Data System (ADS)

Hirshman, S. P.; Perumalla, K. S.; Lynch, V. E.; Sanchez, R.

2010-09-01

A block tridiagonal matrix is factored with minimal fill-in using a cyclic reduction algorithm that is easily parallelized. Storage of the factored blocks allows the application of the inverse to multiple right-hand sides which may not be known at factorization time. Scalability with the number of block rows is achieved with cyclic reduction, while scalability with the block size is achieved using multithreaded routines (OpenMP, GotoBLAS) for block matrix manipulation. This dual scalability is a noteworthy feature of this new solver, as well as its ability to efficiently handle arbitrary (non-powers-of-2) block row and processor numbers. Comparison with a state-of-the art parallel sparse solver is presented. It is expected that this new solver will allow many physical applications to optimally use the parallel resources on current supercomputers. Example usage of the solver in magneto-hydrodynamic (MHD), three-dimensional equilibrium solvers for high-temperature fusion plasmas is cited.

Online blind source separation using incremental nonnegative matrix factorization with volume constraint.

PubMed

Zhou, Guoxu; Yang, Zuyuan; Xie, Shengli; Yang, Jun-Mei

2011-04-01

Online blind source separation (BSS) is proposed to overcome the high computational cost problem, which limits the practical applications of traditional batch BSS algorithms. However, the existing online BSS methods are mainly used to separate independent or uncorrelated sources. Recently, nonnegative matrix factorization (NMF) shows great potential to separate the correlative sources, where some constraints are often imposed to overcome the non-uniqueness of the factorization. In this paper, an incremental NMF with volume constraint is derived and utilized for solving online BSS. The volume constraint to the mixing matrix enhances the identifiability of the sources, while the incremental learning mode reduces the computational cost. The proposed method takes advantage of the natural gradient based multiplication updating rule, and it performs especially well in the recovery of dependent sources. Simulations in BSS for dual-energy X-ray images, online encrypted speech signals, and high correlative face images show the validity of the proposed method.

[Advances in the research of molecular mechanism of negative pressure wound therapy in improving wound healing].

PubMed

Liu, Y; Hu, D H

2017-11-20

Recently, negative pressure wound therapy (NPWT) is a rising technology to improve wound healing. In clinical application, it benefits fast debridement and wound close, limits infection, and promotes wound healing. It is an effective therapy for all kinds of acute or chronic wound. Currently, researches demonstrate that NPWT promotes angiogenesis, granulation tissue growth, and extracellular matrix remodeling through regulating the signaling of anti-inflammatory cytokines, mechanicalreceptor and chemoreceptor, which is related to several growth factors and inflammatory factors. Here we focus on the recent advances in the mechanism of NPWT in promoting wound healing, looking forward to providing a review of NPWT and related researches.

Distinct sets of locomotor modules control the speed and modes of human locomotion

PubMed Central

Yokoyama, Hikaru; Ogawa, Tetsuya; Kawashima, Noritaka; Shinya, Masahiro; Nakazawa, Kimitaka

2016-01-01

Although recent vertebrate studies have revealed that different spinal networks are recruited in locomotor mode- and speed-dependent manners, it is unknown whether humans share similar neural mechanisms. Here, we tested whether speed- and mode-dependence in the recruitment of human locomotor networks exists or not by statistically extracting locomotor networks. From electromyographic activity during walking and running over a wide speed range, locomotor modules generating basic patterns of muscle activities were extracted using non-negative matrix factorization. The results showed that the number of modules changed depending on the modes and speeds. Different combinations of modules were extracted during walking and running, and at different speeds even during the same locomotor mode. These results strongly suggest that, in humans, different spinal locomotor networks are recruited while walking and running, and even in the same locomotor mode different networks are probably recruited at different speeds. PMID:27805015

Machine learning for cardiac ultrasound time series data

NASA Astrophysics Data System (ADS)

Yuan, Baichuan; Chitturi, Sathya R.; Iyer, Geoffrey; Li, Nuoyu; Xu, Xiaochuan; Zhan, Ruohan; Llerena, Rafael; Yen, Jesse T.; Bertozzi, Andrea L.

2017-03-01

We consider the problem of identifying frames in a cardiac ultrasound video associated with left ventricular chamber end-systolic (ES, contraction) and end-diastolic (ED, expansion) phases of the cardiac cycle. Our procedure involves a simple application of non-negative matrix factorization (NMF) to a series of frames of a video from a single patient. Rank-2 NMF is performed to compute two end-members. The end members are shown to be close representations of the actual heart morphology at the end of each phase of the heart function. Moreover, the entire time series can be represented as a linear combination of these two end-member states thus providing a very low dimensional representation of the time dynamics of the heart. Unlike previous work, our methods do not require any electrocardiogram (ECG) information in order to select the end-diastolic frame. Results are presented for a data set of 99 patients including both healthy and diseased examples.

Electron energy-loss spectroscopy of single nanocrystals: mapping of tin allotropes.

PubMed

Roesgaard, Søren; Ramasse, Quentin; Chevallier, Jacques; Fyhn, Mogens; Julsgaard, Brian

2018-05-25

Using monochromated electron energy-loss spectroscopy (EELS), we are able to map different allotropes in Sn-nanocrystals embedded in Si. It is demonstrated that α-Sn and β-Sn, as well as an interface related plasmon, can be distinguished in embedded Sn-nanostructures. The EELS data is interpreted by standard non-negative matrix factorization followed by a manual Lorentzian decomposition. The decomposition allows for a more physical understanding of the EELS mapping without reducing the level of information. Extending the analysis from a reference system to smaller nanocrystals demonstrates that allotrope determination in nanoscale systems down below 5 nm is possible. Such local information proves the use of monochromated EELS mapping as a powerful technique to study nanoscale systems. This possibility enables investigation of small nanostructures that cannot be investigated through other means, allowing for a better understanding and thus leading to realizations that can result in nanomaterials with improved properties.

Retrieving the Quantitative Chemical Information at Nanoscale from Scanning Electron Microscope Energy Dispersive X-ray Measurements by Machine Learning

NASA Astrophysics Data System (ADS)

Jany, B. R.; Janas, A.; Krok, F.

2017-11-01

The quantitative composition of metal alloy nanowires on InSb(001) semiconductor surface and gold nanostructures on germanium surface is determined by blind source separation (BSS) machine learning (ML) method using non negative matrix factorization (NMF) from energy dispersive X-ray spectroscopy (EDX) spectrum image maps measured in a scanning electron microscope (SEM). The BSS method blindly decomposes the collected EDX spectrum image into three source components, which correspond directly to the X-ray signals coming from the supported metal nanostructures, bulk semiconductor signal and carbon background. The recovered quantitative composition is validated by detailed Monte Carlo simulations and is confirmed by separate cross-sectional TEM EDX measurements of the nanostructures. This shows that SEM EDX measurements together with machine learning blind source separation processing could be successfully used for the nanostructures quantitative chemical composition determination.

Electron energy-loss spectroscopy of single nanocrystals: mapping of tin allotropes

NASA Astrophysics Data System (ADS)

Roesgaard, Søren; Ramasse, Quentin; Chevallier, Jacques; Fyhn, Mogens; Julsgaard, Brian

2018-05-01

Using monochromated electron energy-loss spectroscopy (EELS), we are able to map different allotropes in Sn-nanocrystals embedded in Si. It is demonstrated that α-Sn and β-Sn, as well as an interface related plasmon, can be distinguished in embedded Sn-nanostructures. The EELS data is interpreted by standard non-negative matrix factorization followed by a manual Lorentzian decomposition. The decomposition allows for a more physical understanding of the EELS mapping without reducing the level of information. Extending the analysis from a reference system to smaller nanocrystals demonstrates that allotrope determination in nanoscale systems down below 5 nm is possible. Such local information proves the use of monochromated EELS mapping as a powerful technique to study nanoscale systems. This possibility enables investigation of small nanostructures that cannot be investigated through other means, allowing for a better understanding and thus leading to realizations that can result in nanomaterials with improved properties.

COMPADRE: an R and web resource for pathway activity analysis by component decompositions.

PubMed

Ramos-Rodriguez, Roberto-Rafael; Cuevas-Diaz-Duran, Raquel; Falciani, Francesco; Tamez-Peña, Jose-Gerardo; Trevino, Victor

2012-10-15

The analysis of biological networks has become essential to study functional genomic data. Compadre is a tool to estimate pathway/gene sets activity indexes using sub-matrix decompositions for biological networks analyses. The Compadre pipeline also includes one of the direct uses of activity indexes to detect altered gene sets. For this, the gene expression sub-matrix of a gene set is decomposed into components, which are used to test differences between groups of samples. This procedure is performed with and without differentially expressed genes to decrease false calls. During this process, Compadre also performs an over-representation test. Compadre already implements four decomposition methods [principal component analysis (PCA), Isomaps, independent component analysis (ICA) and non-negative matrix factorization (NMF)], six statistical tests (t- and f-test, SAM, Kruskal-Wallis, Welch and Brown-Forsythe), several gene sets (KEGG, BioCarta, Reactome, GO and MsigDB) and can be easily expanded. Our simulation results shown in Supplementary Information suggest that Compadre detects more pathways than over-representation tools like David, Babelomics and Webgestalt and less false positives than PLAGE. The output is composed of results from decomposition and over-representation analyses providing a more complete biological picture. Examples provided in Supplementary Information show the utility, versatility and simplicity of Compadre for analyses of biological networks. Compadre is freely available at http://bioinformatica.mty.itesm.mx:8080/compadre. The R package is also available at https://sourceforge.net/p/compadre.

Inflation with a graceful exit in a random landscape

NASA Astrophysics Data System (ADS)

Pedro, F. G.; Westphal, A.

2017-03-01

We develop a stochastic description of small-field inflationary histories with a graceful exit in a random potential whose Hessian is a Gaussian random matrix as a model of the unstructured part of the string landscape. The dynamical evolution in such a random potential from a small-field inflation region towards a viable late-time de Sitter (dS) minimum maps to the dynamics of Dyson Brownian motion describing the relaxation of non-equilibrium eigenvalue spectra in random matrix theory. We analytically compute the relaxation probability in a saddle point approximation of the partition function of the eigenvalue distribution of the Wigner ensemble describing the mass matrices of the critical points. When applied to small-field inflation in the landscape, this leads to an exponentially strong bias against small-field ranges and an upper bound N ≪ 10 on the number of light fields N participating during inflation from the non-observation of negative spatial curvature.

A positive correlation between serum levels of mature brain-derived neurotrophic factor and negative symptoms in schizophrenia.

PubMed

Niitsu, Tomihisa; Ishima, Tamaki; Yoshida, Taisuke; Hashimoto, Tasuku; Matsuzawa, Daisuke; Shirayama, Yukihiko; Nakazato, Michiko; Shimizu, Eiji; Hashimoto, Kenji; Iyo, Masaomi

2014-02-28

A meta-analysis study reported serum brain-derived neurotrophic factor (BDNF) levels as a potential biomarker for schizophrenia. However, at the time, commercially available human ELISA kits were unable to distinguish between pro-BDNF (precursor BDNF) and mature BDNF, because of limited antibody specificity. Here, we used new ELISA kits, to examine serum levels of mature BDNF and matrix metalloproteinase-9 (MMP-9), which converts pro-BDNF to mature BDNF in schizophrenia. Sixty-three patients with chronic schizophrenia and 52 age- and sex-matched healthy controls were enrolled. Patients were evaluated using the Brief Psychiatry Rating Scale, the Scale for the Assessment of Negative Symptoms (SANS) and neuropsychological tests. Neither serum mature BDNF nor MMP-9 levels differed between patients and controls. In male subgroups, serum MMP-9 levels of smoking patients were higher than those of non-smoking patients, but this was not observed in male controls or the female subgroup. In patients, serum mature BDNF levels were associated with SANS total scores and the Information subtest scores of the Wechsler Adult Intelligence Scale Revised (WAIS-R), while serum MMP-9 levels were associated with smoking and category fluency scores. These findings suggest that neither mature BDNF nor MMP-9 is a suitable biomarker for schizophrenia, although further studies using large samples are needed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Robustness of muscle synergies underlying three-dimensional force generation at the hand in healthy humans

PubMed Central

Rymer, William Z.; Beer, Randall F.

2012-01-01

Previous studies using advanced matrix factorization techniques have shown that the coordination of human voluntary limb movements may be accomplished using combinations of a small number of intermuscular coordination patterns, or muscle synergies. However, the potential use of muscle synergies for isometric force generation has been evaluated mostly using correlational methods. The results of such studies suggest that fixed relationships between the activations of pairs of muscles are relatively rare. There is also emerging evidence that the nervous system uses independent strategies to control movement and force generation, which suggests that one cannot conclude a priori that isometric force generation is accomplished by combining muscle synergies, as shown in movement control. In this study, we used non-negative matrix factorization to evaluate the ability of a few muscle synergies to reconstruct the activation patterns of human arm muscles underlying the generation of three-dimensional (3-D) isometric forces at the hand. Surface electromyographic (EMG) data were recorded from eight key elbow and shoulder muscles during 3-D force target-matching protocols performed across a range of load levels and hand positions. Four synergies were sufficient to explain, on average, 95% of the variance in EMG datasets. Furthermore, we found that muscle synergy composition was conserved across biomechanical task conditions, experimental protocols, and subjects. Our findings are consistent with the view that the nervous system can generate isometric forces by assembling a combination of a small number of muscle synergies, differentially weighted according to task constraints. PMID:22279190

Gene expression based mouse brain parcellation using Markov random field regularized non-negative matrix factorization

NASA Astrophysics Data System (ADS)

Pathak, Sayan D.; Haynor, David R.; Thompson, Carol L.; Lein, Ed; Hawrylycz, Michael

2009-02-01

Understanding the geography of genetic expression in the mouse brain has opened previously unexplored avenues in neuroinformatics. The Allen Brain Atlas (www.brain-map.org) (ABA) provides genome-wide colorimetric in situ hybridization (ISH) gene expression images at high spatial resolution, all mapped to a common three-dimensional 200μm3 spatial framework defined by the Allen Reference Atlas (ARA) and is a unique data set for studying expression based structural and functional organization of the brain. The goal of this study was to facilitate an unbiased data-driven structural partitioning of the major structures in the mouse brain. We have developed an algorithm that uses nonnegative matrix factorization (NMF) to perform parts based analysis of ISH gene expression images. The standard NMF approach and its variants are limited in their ability to flexibly integrate prior knowledge, in the context of spatial data. In this paper, we introduce spatial connectivity as an additional regularization in NMF decomposition via the use of Markov Random Fields (mNMF). The mNMF algorithm alternates neighborhood updates with iterations of the standard NMF algorithm to exploit spatial correlations in the data. We present the algorithm and show the sub-divisions of hippocampus and somatosensory-cortex obtained via this approach. The results are compared with established neuroanatomic knowledge. We also highlight novel gene expression based sub divisions of the hippocampus identified by using the mNMF algorithm.

Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.

PubMed

Cai, Yun; Gu, Hong; Kenney, Toby

2017-08-31

Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems. The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new). NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable and can lead to important biological insights into the structure of the communities. In addition, NMF is a dimension-reduction method (similar to PCA) in that it reduces the extremely complex microbial data into a low-dimensional representation, allowing a number of analyses to be performed more easily-for example, searching for temporal patterns in the microbiome. When we are interested in the differences between the structures of two groups of communities, supervised NMF provides a better way to do this, while retaining all the advantages of NMF-e.g. interpretability and a simple biological intuition.

Attractive electron-electron interactions within robust local fitting approximations.

PubMed

Merlot, Patrick; Kjærgaard, Thomas; Helgaker, Trygve; Lindh, Roland; Aquilante, Francesco; Reine, Simen; Pedersen, Thomas Bondo

2013-06-30

An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all Hartree-Fock and Kohn-Sham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. Copyright © 2013 Wiley Periodicals, Inc.

Matrix metalloproteinases and epidermal wound repair.

PubMed

Martins, Vera L; Caley, Matthew; O'Toole, Edel A

2013-02-01

Epidermal wound healing is a complex and highly coordinated process where several different cell types and molecules, such as growth factors and extracellular matrix (ECM) components, play an important role. Among the many proteins that are essential for the restoration of tissue integrity is the metalloproteinase (MMP) family. MMPs can act on ECM and non-ECM components affecting degradation and modulation of the ECM, growth-factor activation and cell-cell and cell-matrix signalling. MMPs are secreted by different cell types such as keratinocytes, fibroblasts and inflammatory cells at different stages and locations during wound healing, thereby regulating this process in a very coordinated and controlled way. In this article, we review the role of MMPs and their inhibitors (TIMPs), as well as the disintegrin and metalloproteinase with the thrombospondin motifs (ADAMs) family, in epithelial wound repair.

Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

PubMed

Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

2016-01-01

Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Negative Ion Chemical Ionization Mass Spectrometry for the Analysis of 3,5,6-trichloro-2-pyridinol in Saliva of Rats Exposed to Chlorpyrifos

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

Campbell, James A.; Timchalk, Chuck; Kousba, Ahmed A.

2005-05-01

Organophosphorus (OP) insecticides (e.g. chlorpyrifos) are widely used in a variety of applications, and the potential exists for significant occupational and environmental exposures. They have been associated with more occupational poisoning cases than any other class of insecticides. One of the best approaches for accurately assessing human dosimetry and determining risk from both occupational and environmental exposure is biomonitoring. Biological matrices such as blood and urine have been routinely used for biomonitoring; however, other matrices such as saliva represent a simple and readily obtainable fluid. As a result, saliva has been suggested as an alternative biological matrix for the evaluationmore » of a broad range of biomarkers such as environmental contaminants, drugs of abuse, hormones, chemotherapeutics, heavy metals, and pesticides. Chlorpyrifos (CPF), and its major metabolite, 3,5,6-trichloro-2-pyridinol (TCP), have been quantified in urine and blood as a biomarker for exposure to OP insecticides. The purpose of this study was to develop an analytical approach for detecting and quantitating the levels of TCP in saliva obtained from rats exposed to CPF and to evaluate the potential of saliva as a non-invasive biomonitoring matrix. Adult male rats were administered CPF, and blood and saliva were humanely collected for analysis of TCP and CPF. TCP was detected and quantitated in saliva using negative ion chemical ionization mass spectrometry with selected ion monitoring. Initial results indicate that saliva may be potentially utilized as a non-invasive biomonitoring matrix to determine exposure to organophosphate insecticides.« less

Investigation of colloidal graphite as a matrix for matrix-assisted laser desorption/ionisation mass spectrometry of low molecular weight analytes.

PubMed

Warren, Alexander D; Conway, Ulric; Arthur, Christopher J; Gates, Paul J

2016-07-01

The analysis of low molecular weight compounds by matrix-assisted laser desorption/ionisation mass spectrometry is problematic due to the interference and suppression of analyte ionisation by the matrices typically employed - which are themselves low molecular weight compounds. The application of colloidal graphite is demonstrated here as an easy to use matrix that can promote the ionisation of a wide range of analytes including low molecular weight organic compounds, complex natural products and inorganic complexes. Analyte ionisation with colloidal graphite is compared with traditional organic matrices along with various other sources of graphite (e.g. graphite rods and charcoal pencils). Factors such as ease of application, spectra reproducibility, spot longevity, spot-to-spot reproducibility and spot homogeneity (through single spot imaging) are explored. For some analytes, considerable matrix suppression effects are observed resulting in spectra completely devoid of matrix ions. We also report the observation of radical molecular ions [M(-●) ] in the negative ion mode, particularly with some aromatic analytes. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

NMF-mGPU: non-negative matrix factorization on multi-GPU systems.

PubMed

Mejía-Roa, Edgardo; Tabas-Madrid, Daniel; Setoain, Javier; García, Carlos; Tirado, Francisco; Pascual-Montano, Alberto

2015-02-13

In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. In this paper, we present NMF-mGPU, an efficient and easy-to-use implementation of the NMF algorithm that takes advantage of the high computing performance delivered by Graphics-Processing Units ( GPUs ). Driven by the ever-growing demands from the video-games industry, graphics cards usually provided in PCs and laptops have evolved from simple graphics-drawing platforms into high-performance programmable systems that can be used as coprocessors for linear-algebra operations. However, these devices may have a limited amount of on-board memory, which is not considered by other NMF implementations on GPU. NMF-mGPU is based on CUDA ( Compute Unified Device Architecture ), the NVIDIA's framework for GPU computing. On devices with low memory available, large input matrices are blockwise transferred from the system's main memory to the GPU's memory, and processed accordingly. In addition, NMF-mGPU has been explicitly optimized for the different CUDA architectures. Finally, platforms with multiple GPUs can be synchronized through MPI ( Message Passing Interface ). In a four-GPU system, this implementation is about 120 times faster than a single conventional processor, and more than four times faster than a single GPU device (i.e., a super-linear speedup). Applications of GPUs in Bioinformatics are getting more and more attention due to their outstanding performance when compared to traditional processors. In addition, their relatively low price represents a highly cost-effective alternative to conventional clusters. In life sciences, this results in an excellent opportunity to facilitate the daily work of bioinformaticians that are trying to extract biological meaning out of hundreds of gigabytes of experimental information. NMF-mGPU can be used "out of the box" by researchers with little or no expertise in GPU programming in a variety of platforms, such as PCs, laptops, or high-end GPU clusters. NMF-mGPU is freely available at https://github.com/bioinfo-cnb/bionmf-gpu .

Matrix Converter Interface for a Wind Energy Conversion System: Issues and Limitations

NASA Astrophysics Data System (ADS)

Patki, Chetan; Agarwal, Vivek

2009-08-01

Variable speed grid connected wind energy systems sometimes involve AC-AC power electronic interface between the generator and the grid. Matrix converter is an attractive option for such applications. Variable speed of the wind generator demands variable voltage variable frequency at the generator terminal. Matrix converter is used in this work to generate such a supply. Also, matrix converter can be appropriately controlled to compensate the grid for non-linear, reactive loads. However, any change of power factor on the grid side reflects on the voltage magnitude on the wind generator side. It is highlighted that this may contradict the maximum power point tracking control requirements. All the results of this work are presented.

Endothelial cell-derived matrix promotes the metabolic functional maturation of hepatocyte via integrin-Src signalling.

PubMed

Guo, Xinyue; Li, Weihong; Ma, Minghui; Lu, Xin; Zhang, Haiyan

2017-11-01

The extracellular matrix (ECM) microenvironment is involved in the regulation of hepatocyte phenotype and function. Recently, the cell-derived extracellular matrix has been proposed to represent the bioactive and biocompatible materials of the native ECM. Here, we show that the endothelial cell-derived matrix (EC matrix) promotes the metabolic maturation of human adipose stem cell-derived hepatocyte-like cells (hASC-HLCs) through the activation of the transcription factor forkhead box protein A2 (FOXA2) and the nuclear receptors hepatocyte nuclear factor 4 alpha (HNF4α) and pregnane X receptor (PXR). Reducing the fibronectin content in the EC matrix or silencing the expression of α5 integrin in the hASC-HLCs inhibited the effect of the EC matrix on Src phosphorylation and hepatocyte maturation. The inhibition of Src phosphorylation using the inhibitor PP2 or silencing the expression of Src in hASC-HLCs also attenuated the up-regulation of the metabolic function of hASC-HLCs in a nuclear receptor-dependent manner. These data elucidate integrin-Src signalling linking the extrinsic EC matrix signals and metabolic functional maturation of hepatocyte. This study provides a model for studying the interaction between hepatocytes and non-parenchymal cell-derived matrix. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Ward identities and combinatorics of rainbow tensor models

NASA Astrophysics Data System (ADS)

Itoyama, H.; Mironov, A.; Morozov, A.

2017-06-01

We discuss the notion of renormalization group (RG) completion of non-Gaussian Lagrangians and its treatment within the framework of Bogoliubov-Zimmermann theory in application to the matrix and tensor models. With the example of the simplest non-trivial RGB tensor theory (Aristotelian rainbow), we introduce a few methods, which allow one to connect calculations in the tensor models to those in the matrix models. As a byproduct, we obtain some new factorization formulas and sum rules for the Gaussian correlators in the Hermitian and complex matrix theories, square and rectangular. These sum rules describe correlators as solutions to finite linear systems, which are much simpler than the bilinear Hirota equations and the infinite Virasoro recursion. Search for such relations can be a way to solving the tensor models, where an explicit integrability is still obscure.

Coping with matrix effects in headspace solid phase microextraction gas chromatography using multivariate calibration strategies.

PubMed

Ferreira, Vicente; Herrero, Paula; Zapata, Julián; Escudero, Ana

2015-08-14

SPME is extremely sensitive to experimental parameters affecting liquid-gas and gas-solid distribution coefficients. Our aims were to measure the weights of these factors and to design a multivariate strategy based on the addition of a pool of internal standards, to minimize matrix effects. Synthetic but real-like wines containing selected analytes and variable amounts of ethanol, non-volatile constituents and major volatile compounds were prepared following a factorial design. The ANOVA study revealed that even using a strong matrix dilution, matrix effects are important and additive with non-significant interaction effects and that it is the presence of major volatile constituents the most dominant factor. A single internal standard provided a robust calibration for 15 out of 47 analytes. Then, two different multivariate calibration strategies based on Partial Least Square Regression were run in order to build calibration functions based on 13 different internal standards able to cope with matrix effects. The first one is based in the calculation of Multivariate Internal Standards (MIS), linear combinations of the normalized signals of the 13 internal standards, which provide the expected area of a given unit of analyte present in each sample. The second strategy is a direct calibration relating concentration to the 13 relative areas measured in each sample for each analyte. Overall, 47 different compounds can be reliably quantified in a single fully automated method with overall uncertainties better than 15%. Copyright © 2015 Elsevier B.V. All rights reserved.

SIMS of Organic Materials—Interface Location in Argon Gas Cluster Depth Profiles Using Negative Secondary Ions

NASA Astrophysics Data System (ADS)

Havelund, R.; Seah, M. P.; Tiddia, M.; Gilmore, I. S.

2018-02-01

A procedure has been established to define the interface position in depth profiles accurately when using secondary ion mass spectrometry and the negative secondary ions. The interface position varies strongly with the extent of the matrix effect and so depends on the secondary ion measured. Intensity profiles have been measured at both fluorenylmethyloxycarbonyl-uc(l)-pentafluorophenylalanine (FMOC) to Irganox 1010 and Irganox 1010 to FMOC interfaces for many secondary ions. These profiles show separations of the two interfaces that vary over some 10 nm depending on the secondary ion selected. The shapes of these profiles are strongly governed by matrix effects, slightly weakened by a long wavelength roughening. The matrix effects are separately measured using homogeneous, known mixtures of these two materials. Removal of the matrix and roughening effects give consistent compositional profiles for all ions that are described by an integrated exponentially modified Gaussian (EMG) profile. Use of a simple integrated Gaussian may lead to significant errors. The average interface positions in the compositional profiles are determined to standard uncertainties of 0.19 and 0.14 nm, respectively, using the integrated EMG function. Alternatively, and more simply, it is shown that interface positions and profiles may be deduced from data for several secondary ions with measured matrix factors by simply extrapolating the result to Ξ = 0. Care must be taken in quoting interface resolutions since those measured for predominantly Gaussian interfaces with Ξ above or below zero, without correction, appear significantly better than the true resolution.

Basic fibroblast growth factor accelerates matrix degradation via a neuro-endocrine pathway in human adult articular chondrocytes.

PubMed

Im, Hee-Jeong; Li, Xin; Muddasani, Prasuna; Kim, Gun-Hee; Davis, Francesca; Rangan, Jayanthi; Forsyth, Christopher B; Ellman, Michael; Thonar, Eugene J M A

2008-05-01

Pain-related neuropeptides released from synovial fibroblasts, such as substance P, have been implicated in joint destruction. Substance P-induced inflammatory processes are mediated via signaling through a G-protein-coupled receptor, that is, neurokinin-1 tachykinin receptor (NK(1)-R). We determined the pathophysiological link between substance P and its receptor in human adult articular cartilage homeostasis. We further examined if catabolic growth factors such as basic fibroblast growth factor (bFGF or FGF-2) or IL-1beta accelerate matrix degradation via a neural pathway upregulation of substance P and NK(1)-R. We show here that substance P stimulates the production of cartilage-degrading enzymes, such as matrix metalloproteinase-13 (MMP-13), and suppresses proteoglycan deposition in human adult articular chondrocytes via NK(1)-R. Furthermore, we have demonstrated that substance P negates proteoglycan stimulation promoted by bone morphogenetic protein-7, suggesting the dual role of substance P as both a pro-catabolic and anti-anabolic mediator of cartilage homeostasis. We report that bFGF-mediated stimulation of substance P and its receptor NK(1)-R is, in part, through an IL-1beta-dependent pathway. (c) 2007 Wiley-Liss, Inc.

Basic Fibroblast Growth Factor Accelerates Matrix Degradation Via a Neuro-Endocrine Pathway in Human Adult Articular Chondrocytes

PubMed Central

IM, HEE-JEONG; LI, XIN; MUDDASANI, PRASUNA; KIM, GUN-HEE; DAVIS, FRANCESCA; RANGAN, JAYANTHI; FORSYTH, CHRISTOPHER B.; ELLMAN, MICHAEL; THONAR, EUGENE JMA

2010-01-01

Pain-related neuropeptides released from synovial fibroblasts, such as substance P, have been implicated in joint destruction. Substance P-induced inflammatory processes are mediated via signaling through a G-protein-coupled receptor, that is, neurokinin-1 tachykinin receptor (NK1-R). We determined the pathophysiological link between substance P and its receptor in human adult articular cartilage homeostasis. We further examined if catabolic growth factors such as basic fibroblast growth factor (bFGF or FGF-2) or IL-1β accelerate matrix degradation via a neural pathway upregulation of substance P and NK1-R. We show here that substance P stimulates the production of cartilage-degrading enzymes, such as matrix metalloproteinase-13 (MMP-13), and suppresses proteoglycan deposition in human adult articular chondrocytes via NK1-R. Furthermore, we have demonstrated that substance P negates proteoglycan stimulation promoted by bone morphogenetic protein-7, suggesting the dual role of substance P as both a pro-catabolic and anti-anabolic mediator of cartilage homeostasis. We report that bFGF-mediated stimulation of substance P and its receptor NK1-R is, in part, through an IL-1β-dependent pathway. PMID:17960584

Stiffness-dependent cellular internalization of matrix-bound BMP-2 and its relation to Smad and non-Smad signaling.

PubMed

Gilde, Flora; Fourel, Laure; Guillot, Raphael; Pignot-Paintrand, Isabelle; Okada, Takaharu; Fitzpatrick, Vincent; Boudou, Thomas; Albiges-Rizo, Corinne; Picart, Catherine

2016-12-01

Surface coatings delivering BMP are a promising approach to render biomaterials osteoinductive. In contrast to soluble BMPs which can interact with their receptors at the dorsal side of the cell, BMPs presented as an insoluble cue physically bound to a biomimetic matrix, called here matrix-bound (bBMP-2), are presented to cells by their ventral side. To date, BMP-2 internalization and signaling studies in cell biology have always been performed by adding soluble (sBMP-2) to cells adhered on cell culture plates or glass slides, which will be considered here as a "reference" condition. However, whether and how matrix-bound BMP-2 can be internalized by cells and its relation to canonical (SMAD) and non-canonical signaling (ALP) remain open questions. In this study, we investigated the uptake and processing of BMP-2 by C2C12 myoblasts. This BMP-2 was presented either embedded in polyelectrolyte multilayer films (matrix-bound presentation) or as soluble form. Using fluorescently labeled BMP-2, we showed that the amount of matrix-bound BMP-2 internalized is dependent on the level of crosslinking of the polyelectrolyte films. Cav-1-mediated internalization is related to both SMAD and ALP signaling, while clathrin-mediated is only related to ALP signaling. BMP-2 internalization was independent of the presentation mode (sBMP-2 versus bBMP-2) for low crosslinked films (soft, EDC10) in striking contrast with high crosslinked (stiff, EDC70) films where internalization was much lower and slower for bBMP-2. As anticipated, internalization of sBMP-2 barely depended on the underlying matrix. Taken together, these results indicate that BMP-2 internalization can be tuned by the underlying matrix and activates downstream BMP-2 signaling, which is key for the effective formation of bone tissue. The presentation of growth factors from material surfaces currently presents significant challenges in academic research, clinics and industry. Being able to deliver efficiently these growth factors by a biomaterial will open new perspectives for regenerative medicine. However, to date, very little is known about how matrix-bound growth factors are delivered to cells, especially whether they are internalized and how they are signaling to drive key differentiation events. These initial steps are crucial as they will guide the subsequent processes leading to tissue regeneration. In this work, we investigate the uptake and processing by cells of BMP-2 ligands embedded in polyelectrolyte multilayer films in comparison to soluble BMP-2. We show that BMP-2 responsive cells can internalize matrix-bound BMP-2 and that internalization is dependent on the cross-linking level of the polyelectrolyte films. In addition, we show that internalization is mediated by both clathrin- and caveolin-dependent pathways. While inhibiting clathrin-dependent endocytosis affects only non-canonical signaling, blocking caveolin-1-dependent endocytosis reduces both canonical and non-canonical BMP signaling. The signaling pathways found for matrix-bound BMP-2 are similar to those found for soluble BMP-2. These results highlight that BMP-2 presented by a biomaterial at the ventral side of the cell can trigger major endocytic and associated signaling pathways leading to bone regeneration. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

EMMPRIN co-expressed with matrix metalloproteinases predicts poor prognosis in patients with osteosarcoma.

PubMed

Futamura, Naohisa; Nishida, Yoshihiro; Urakawa, Hiroshi; Kozawa, Eiji; Ikuta, Kunihiro; Hamada, Shunsuke; Ishiguro, Naoki

2014-06-01

Several studies have focused on the relationships between the expression of extracellular matrix metalloproteinase inducer (EMMPRIN) and the prognosis of patients with malignant tumors. However, few of these have investigated the expression of EMMPRIN in osteosarcoma. We examined expression levels of EMMPRIN immunohistochemically in 53 cases of high-grade osteosarcoma of the extremities and analyzed the correlation of its expression with patient prognosis. The correlation between matrix metalloproteinases (MMPs) and EMMPRIN expression and the prognostic value of co-expression were also analyzed. Staining positivity for EMMPRIN was negative in 7 cases, low in 17, moderate in 19, and strong in 10. The overall and disease-free survivals (OS and DFS) in patients with higher EMMPRIN expression (strong-moderate) were significantly lower than those in the lower (weak-negative) group (0.037 and 0.024, respectively). In multivariate analysis, age (P=0.004), location (P=0.046), and EMMPRIN expression (P=0.038) were significant prognostic factors for overall survival. EMMPRIN expression (P=0.024) was also a significant prognostic factor for disease-free survival. Co-expression analyses of EMMPRIN and MMPs revealed that strong co-expression of EMMPRIN and membrane-type 1 (MT1)-MMP had a poor prognostic value (P=0.056 for DFS, P=0.006 for OS). EMMPRIN expression and co-expression with MMPs well predict the prognosis of patients with extremity osteosarcoma, making EMMPRIN a possible therapeutic target in these patients.

Confirmation and Identification of Salmonella spp., Cronobacter spp., and Other Gram-Negative Organisms by the Bruker MALDI Biotyper Method: Collaborative Study, First Action 2017.09.

PubMed

Bastin, Benjamin; Bird, Patrick; Benzinger, M Joseph; Crowley, Erin; Agin, James; Goins, David; Sohier, Daniele; Timke, Markus; Shi, Gongyi; Kostrzewa, Markus

2018-04-27

The Bruker MALDI Biotyper ® method utilizes matrix-assisted laser desorption/ionizationtime-of-flight (MALDI-TOF) MS for the rapid and accurate identification and confirmation of Gram-negative bacteria from select media types. The alternative method was evaluated using nonselective and selective agars to identify Cronobacter spp., Salmonella spp., and select Gram-negative bacteria. Results obtained by the Bruker MALDI Biotyper were compared to the traditional biochemical methods as prescribed in the appropriate reference methods. Two collaborative studies were organized, one in the United States focusing on Cronobacter spp. and other Gram-negative bacteria, and one in Europe focusing on Salmonella spp. and other Gram-negative bacteria. Fourteen collaborators from seven laboratories located within the United States participated in the first collaborative study for Cronobacter spp. Fifteen collaborators from 15 service laboratories located within Europe participated in the second collaborative study for Salmonella spp. For each target organism (either Salmonella spp. or Cronobacter spp.), a total of 24 blind-coded isolates were evaluated. In each set of 24 organisms, there were 16 inclusivity organisms ( Cronobacter spp. or Salmonella spp.) and 8 exclusivity organisms (closely related non- Cronobacter spp. and non- Salmonella spp. Gram-negative organisms). After testing was completed, the total percentage of correct identifications from each agar type for each strain was determined at a percentage of 100.0% to the genus level for the Cronobacter study and a percentage of 100.0% to the genus level for the Salmonella study. For both non- Cronobacter and non- Salmonella organisms, a percentage of 100.0% was correctly identified. The results indicated that the alternative method produced equivalent results when compared to the confirmatory procedures specified by each reference method.

Quantification of various growth factors in different demineralized bone matrix preparations.

PubMed

Wildemann, B; Kadow-Romacker, A; Haas, N P; Schmidmaier, G

2007-05-01

Besides autografts, allografts, and synthetic materials, demineralized bone matrix (DBM) is used for bone defect filling and treatment of non-unions. Different DBM formulations are introduced in clinic since years. However, little is known about the presents and quantities of growth factors in DBM. Aim of the present study was the quantification of eight growth factors important for bone healing in three different "off the shelf" DBM formulations, which are already in human use: DBX putty, Grafton DBM putty, and AlloMatrix putty. All three DBM formulations are produced from human donor tissue but they differ in the substitutes added. From each of the three products 10 different lots were analyzed. Protein was extracted from the samples with Guanidine HCL/EDTA method and human ELISA kits were used for growth factor quantification. Differences between the three different products were seen in total protein contend and the absolute growth factor values but also a large variability between the different lots was found. The order of the growth factors, however, is almost comparable between the materials. In the three investigated materials FGF basic and BMP-4 were not detectable in any analyzed sample. BMP-2 revealed the highest concentration extractable from the samples with approximately 3.6 microg/g tissue without a significant difference between the three DBM formulations. In DBX putty significantly more TGF-beta1 and FGFa were measurable compared to the two other DBMs. IGF-I revealed the significantly highest value in the AlloMatrix and PDGF in Grafton. No differences were accessed for VEGF. Due to the differences in the growth factor concentration between the individual samples, independently from the product formulation, further analyzes are required to optimize the clinical outcome of the used demineralized bone matrix. Copyright 2006 Wiley Periodicals, Inc.

EMMPRIN Is an Independent Negative Prognostic Factor for Patients with Astrocytic Glioma

PubMed Central

Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management. PMID:23516431

EMMPRIN is an independent negative prognostic factor for patients with astrocytic glioma.

PubMed

Tian, Li; Zhang, Yang; Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management.

High-Resolution, Non-Invasive Imaging of Upper Vocal Tract Articulators Compatible with Human Brain Recordings

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

Bouchard, Kristofer E.; Conant, David F.; Anumanchipalli, Gopala K.

A complete neurobiological understanding of speech motor control requires determination of the relationship between simultaneously recorded neural activity and the kinematics of the lips, jaw, tongue, and larynx. Many speech articulators are internal to the vocal tract, and therefore simultaneously tracking the kinematics of all articulators is nontrivial-especially in the context of human electrophysiology recordings. Here, we describe a noninvasive, multi-modal imaging system to monitor vocal tract kinematics, demonstrate this system in six speakers during production of nine American English vowels, and provide new analysis of such data. Classification and regression analysis revealed considerable variability in the articulator-to-acoustic relationship acrossmore » speakers. Non-negative matrix factorization extracted basis sets capturing vocal tract shapes allowing for higher vowel classification accuracy than traditional methods. Statistical speech synthesis generated speech from vocal tract measurements, and we demonstrate perceptual identification. We demonstrate the capacity to predict lip kinematics from ventral sensorimotor cortical activity. These results demonstrate a multi-modal system to non-invasively monitor articulator kinematics during speech production, describe novel analytic methods for relating kinematic data to speech acoustics, and provide the first decoding of speech kinematics from electrocorticography. These advances will be critical for understanding the cortical basis of speech production and the creation of vocal prosthetics.« less

High-Resolution, Non-Invasive Imaging of Upper Vocal Tract Articulators Compatible with Human Brain Recordings

PubMed Central

Anumanchipalli, Gopala K.; Dichter, Benjamin; Chaisanguanthum, Kris S.; Johnson, Keith; Chang, Edward F.

2016-01-01

A complete neurobiological understanding of speech motor control requires determination of the relationship between simultaneously recorded neural activity and the kinematics of the lips, jaw, tongue, and larynx. Many speech articulators are internal to the vocal tract, and therefore simultaneously tracking the kinematics of all articulators is nontrivial—especially in the context of human electrophysiology recordings. Here, we describe a noninvasive, multi-modal imaging system to monitor vocal tract kinematics, demonstrate this system in six speakers during production of nine American English vowels, and provide new analysis of such data. Classification and regression analysis revealed considerable variability in the articulator-to-acoustic relationship across speakers. Non-negative matrix factorization extracted basis sets capturing vocal tract shapes allowing for higher vowel classification accuracy than traditional methods. Statistical speech synthesis generated speech from vocal tract measurements, and we demonstrate perceptual identification. We demonstrate the capacity to predict lip kinematics from ventral sensorimotor cortical activity. These results demonstrate a multi-modal system to non-invasively monitor articulator kinematics during speech production, describe novel analytic methods for relating kinematic data to speech acoustics, and provide the first decoding of speech kinematics from electrocorticography. These advances will be critical for understanding the cortical basis of speech production and the creation of vocal prosthetics. PMID:27019106

High-Resolution, Non-Invasive Imaging of Upper Vocal Tract Articulators Compatible with Human Brain Recordings

DOE PAGES

Bouchard, Kristofer E.; Conant, David F.; Anumanchipalli, Gopala K.; ...

2016-03-28

A complete neurobiological understanding of speech motor control requires determination of the relationship between simultaneously recorded neural activity and the kinematics of the lips, jaw, tongue, and larynx. Many speech articulators are internal to the vocal tract, and therefore simultaneously tracking the kinematics of all articulators is nontrivial-especially in the context of human electrophysiology recordings. Here, we describe a noninvasive, multi-modal imaging system to monitor vocal tract kinematics, demonstrate this system in six speakers during production of nine American English vowels, and provide new analysis of such data. Classification and regression analysis revealed considerable variability in the articulator-to-acoustic relationship acrossmore » speakers. Non-negative matrix factorization extracted basis sets capturing vocal tract shapes allowing for higher vowel classification accuracy than traditional methods. Statistical speech synthesis generated speech from vocal tract measurements, and we demonstrate perceptual identification. We demonstrate the capacity to predict lip kinematics from ventral sensorimotor cortical activity. These results demonstrate a multi-modal system to non-invasively monitor articulator kinematics during speech production, describe novel analytic methods for relating kinematic data to speech acoustics, and provide the first decoding of speech kinematics from electrocorticography. These advances will be critical for understanding the cortical basis of speech production and the creation of vocal prosthetics.« less

CERA Attenuates Kidney Fibrogenesis in the db/db Mouse by Influencing the Renal Myofibroblast Generation

PubMed Central

Fischer, Christin; Deininger, Natalie; Wolf, Gunter; Loeffler, Ivonne

2018-01-01

Tubulointerstitial fibrosis (TIF) is a pivotal pathophysiological process in patients with diabetic nephropathy (DN). Multiple profibrotic factors and cell types, including transforming growth factor beta 1 (TGF-β1) and interstitial myofibroblasts, respectively, are responsible for the accumulation of extracellular matrix in the kidney. Matrix-producing myofibroblasts can originate from different sources and different mechanisms are involved in the activation process of the myofibroblasts in the fibrotic kidney. In this study, 16-week-old db/db mice, a model for type 2 DN, were treated for two weeks with continuous erythropoietin receptor activator (CERA), a synthetic erythropoietin variant with possible non-hematopoietic, tissue-protective effects. Non-diabetic and diabetic mice treated with placebo were used as controls. The effects of CERA on tubulointerstitial fibrosis (TIF) as well as on the generation of the matrix-producing myofibroblasts were evaluated by morphological, immunohistochemical, and molecular biological methods. The placebo-treated diabetic mice showed significant signs of beginning renal TIF (shown by picrosirius red staining; increased connective tissue growth factor (CTGF), fibronectin and collagen I deposition; upregulated KIM1 expression) together with an increased number of interstitial myofibroblasts (shown by different mesenchymal markers), while kidneys from diabetic mice treated with CERA revealed less TIF and fewer myofibroblasts. The mechanisms, in which CERA acts as an anti-fibrotic agent/drug, seem to be multifaceted: first, CERA inhibits the generation of matrix-producing myofibroblasts and second, CERA increases the ability for tissue repair. Many of these CERA effects can be explained by the finding that CERA inhibits the renal expression of the cytokine TGF-β1. PMID:29385703

CERA Attenuates Kidney Fibrogenesis in the db/db Mouse by Influencing the Renal Myofibroblast Generation.

PubMed

Fischer, Christin; Deininger, Natalie; Wolf, Gunter; Loeffler, Ivonne

2018-01-30

Tubulointerstitial fibrosis (TIF) is a pivotal pathophysiological process in patients with diabetic nephropathy (DN). Multiple profibrotic factors and cell types, including transforming growth factor beta 1 (TGF-β1) and interstitial myofibroblasts, respectively, are responsible for the accumulation of extracellular matrix in the kidney. Matrix-producing myofibroblasts can originate from different sources and different mechanisms are involved in the activation process of the myofibroblasts in the fibrotic kidney. In this study, 16-week-old db / db mice, a model for type 2 DN, were treated for two weeks with continuous erythropoietin receptor activator (CERA), a synthetic erythropoietin variant with possible non-hematopoietic, tissue-protective effects. Non-diabetic and diabetic mice treated with placebo were used as controls. The effects of CERA on tubulointerstitial fibrosis (TIF) as well as on the generation of the matrix-producing myofibroblasts were evaluated by morphological, immunohistochemical, and molecular biological methods. The placebo-treated diabetic mice showed significant signs of beginning renal TIF (shown by picrosirius red staining; increased connective tissue growth factor (CTGF), fibronectin and collagen I deposition; upregulated KIM1 expression) together with an increased number of interstitial myofibroblasts (shown by different mesenchymal markers), while kidneys from diabetic mice treated with CERA revealed less TIF and fewer myofibroblasts. The mechanisms, in which CERA acts as an anti-fibrotic agent/drug, seem to be multifaceted: first, CERA inhibits the generation of matrix-producing myofibroblasts and second, CERA increases the ability for tissue repair. Many of these CERA effects can be explained by the finding that CERA inhibits the renal expression of the cytokine TGF-β1.

Solute Transport of Negatively Charged Contrast Agents Across Articular Surface of Injured Cartilage.

PubMed

Kokkonen, H T; Chin, H C; Töyräs, J; Jurvelin, J S; Quinn, T M

2017-04-01

Solute transport through the extracellular matrix (ECM) is crucial to chondrocyte metabolism. Cartilage injury affects solute transport in cartilage due to alterations in ECM structure and solute-matrix interactions. Therefore, cartilage injury may be detected by using contrast agent-based clinical imaging. In the present study, effects of mechanical injury on transport of negatively charged contrast agents in cartilage were characterized. Using cartilage plugs injured by mechanical compression protocol, effective partition coefficients and diffusion fluxes of iodine- and gadolinium-based contrast agents were measured using high resolution microCT imaging. For all contrast agents studied, effective diffusion fluxes increased significantly, particularly at early times during the diffusion process (38 and 33% increase after 4 min, P < 0.05 for iodine and Gd-DTPA; and 76% increase after 10 min for diatrizoate, P < 0.05). Effective partition coefficients were unaffected in mechanically injured cartilage. Mechanical injury reduced PG content and collagen integrity in cartilage superficial zone. This study suggests that alterations in contrast agent diffusion flux, a non-equilibrium transport parameter, provides a more sensitive indicator for assessment of cartilage matrix integrity than partition coefficient and the equilibrium distribution of solute. These findings may help in developing clinical methods of contrast agent-based imaging to detect cartilage injury.

A Case of “en bloc” Excision of a Chest Wall Leiomyosarcoma and Closure of the Defect with Non-Cross-Linked Collagen Matrix (Egis®)

PubMed Central

Rastrelli, Marco; Tropea, Saveria; Spina, Romina; Costa, Alessandra; Stramare, Roberto; Mocellin, Simone; Bonavina, Maria Giuseppina; Rossi, Carlo Riccardo

2016-01-01

Sarcomas arising from the chest wall account for less than 20% of all soft tissue sarcomas, and at this site, primitive tumors are the most frequent to occur. Leiomyosarcoma is a malignant smooth muscle tumor and the best outcomes are achieved with wide surgical excision. Although advancements have been made in treatment protocols, leiomyosarcoma remains one of the more difficult soft tissue sarcoma to treat. Currently, general local control is obtained with surgical treatment with wide negative margins. We describe the case of a 50-year-old man who underwent a chest wall resection involving a wide portion of the pectoralis major and minor muscle, the serratus and part of the second, third and fourth ribs of the left side. The full-thickness chest wall defect of 10 × 8 cm was closed using a non-cross-linked acellular dermal matrix (Egis®) placed in two layers, beneath the rib plane and over it. A successful repair was achieved with no incisional herniation and with complete tissue regeneration, allowing natural respiratory movements. No complications were observed in the postoperative course. Biological non-cross-linked matrix, derived from porcine dermis, behaves like a scaffold supporting tissue regeneration; it can be successfully used as an alternative to synthetic mesh for chest wall reconstruction. PMID:27920698

Quantum kinetic expansion in the spin-boson model: Matrix formulation and system-bath factorized initial state.

PubMed

Gong, Zhihao; Tang, Zhoufei; Wang, Haobin; Wu, Jianlan

2017-12-28

Within the framework of the hierarchy equation of motion (HEOM), the quantum kinetic expansion (QKE) method of the spin-boson model is reformulated in the matrix representation. The equivalence between the two formulations (HEOM matrices and quantum operators) is numerically verified from the calculation of the time-integrated QKE rates. The matrix formulation of the QKE is extended to the system-bath factorized initial state. Following a one-to-one mapping between HEOM matrices and quantum operators, a quantum kinetic equation is rederived. The rate kernel is modified by an extra term following a systematic expansion over the site-site coupling. This modified QKE is numerically tested for its reliability by calculating the time-integrated rate and non-Markovian population kinetics. For an intermediate-to-strong dissipation strength and a large site-site coupling, the population transfer is found to be significantly different when the initial condition is changed from the local equilibrium to system-bath factorized state.

Monocyte activation by smooth muscle cell-derived matrices.

PubMed

Kaufmann, J; Jorgensen, R W; Martin, B M; Franzblau, C

1990-12-01

Mononuclear phagocytes adhere to and penetrate the vessel wall endothelium and contact the subendothelial space prior to the development of the atherosclerotic plaque. In an attempt to model the early events of plaque development we used an elastin-rich, multicomponent, cell-derived matrix from neonatal rat aortic smooth muscle cells as a substratum for monocytes. Using this model, we show that human monocyte morphology and metabolism are markedly altered by the matrix substratum. When a mixed mononuclear cell population is seeded on matrix or plastic, only monocytes adhere to the matrix surface. In contrast, lymphocytes as well as monocytes adhere to the plastic surface. The matrix-adherent monocytes develop large intracellular granules and form extensive clusters of individual cells. Metabolically, these cells develop sodium fluoride resistant non-specific esterase activity and their media contain more growth factor activity and PGE2. Although total protein synthesis is equivalent in both cultures, the matrix contact induces an increase in specific proteins in the media. We also show that a purified alpha-elastin substratum induces some, but not all, of the monocyte changes seen when using the matrix substratum. Using the alpha-elastin substratum, there is selective adhesion of monocytes and increased growth factor activity, however, the cells are morphologically different from the matrix-adherent cells. Thus, the use of the smooth muscle cell-derived matrix, in conjunction with purified matrix components, serves as a model that can provide insight into the mechanisms of monocyte adhesion and stimulation by the matrix environment that exists in vivo. Such mechanisms may be particularly important in atherogenesis.

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS.

PubMed

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-04-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H] - ) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. Graphical Abstract ᅟ.

Skin Rejuvenation with Non-Invasive Pulsed Electric Fields

NASA Astrophysics Data System (ADS)

Golberg, Alexander; Khan, Saiqa; Belov, Vasily; Quinn, Kyle P.; Albadawi, Hassan; Felix Broelsch, G.; Watkins, Michael T.; Georgakoudi, Irene; Papisov, Mikhail; Mihm, Martin C., Jr.; Austen, William G., Jr.; Yarmush, Martin L.

2015-05-01

Degenerative skin diseases affect one third of individuals over the age of sixty. Current therapies use various physical and chemical methods to rejuvenate skin; but since the therapies affect many tissue components including cells and extracellular matrix, they may also induce significant side effects, such as scarring. Here we report on a new, non-invasive, non-thermal technique to rejuvenate skin with pulsed electric fields. The fields destroy cells while simultaneously completely preserving the extracellular matrix architecture and releasing multiple growth factors locally that induce new cells and tissue growth. We have identified the specific pulsed electric field parameters in rats that lead to prominent proliferation of the epidermis, formation of microvasculature, and secretion of new collagen at treated areas without scarring. Our results suggest that pulsed electric fields can improve skin function and thus can potentially serve as a novel non-invasive skin therapy for multiple degenerative skin diseases.

Implication of the oligomeric state of the N-terminal PTX3 domain in cumulus matrix assembly

PubMed Central

Ievoli, Elena; Lindstedt, Ragnar; Inforzato, Antonio; Camaioni, Antonella; Palone, Francesca; Day, Anthony J.; Mantovani, Alberto; Salvatori, Giovanni; Salustri, Antonietta

2011-01-01

Pentraxin 3 (PTX3) plays a key role in the formation of the hyaluronan-rich matrix of the cumulus oophorus surrounding ovulated eggs that is required for successful fertilization and female fertility. PTX3 is a multimeric protein consisting of eight identical protomers held together by a combination of non-covalent interactions and disulfide bonds. Recent findings suggest that the oligomeric status of PTX3 is important for stabilizing the cumulus matrix. Because the role of PTX3 in the cumulus resides in the unique N-terminal sequence of the protomer, we investigated further this issue by testing the ability of distinct Cys/Ser mutants of recombinant N-terminal region of PTX3 (N_PTX3) with different oligomeric arrangement to promote in vitro normal expansion in cumuli from Ptx3-null mice. Here we report that the dimer of the N_PTX3 is unable to rescue cumulus matrix organization, and that the tetrameric assembly of the protein is the minimal oligomeric state required for accomplishing this function. We have previously demonstrated that PTX3 binds to HCs of IαI and TSG-6, which are essential for cumulus matrix formation and able to interact with hyaluronan. Interestingly, here we show by solid-phase binding experiments that the dimer of the N_PTX3 retains the ability to bind to both IαI and TSG-6, suggesting that the octameric structure of PTX3 provides multiple binding sites for each of these ligands. These findings support the hypothesis that PTX3 contributes to cumulus matrix organization by cross-linking HA polymers through interactions with multiple HCs of IαI and/or TSG-6. The N-terminal PTX3 tetrameric oligomerization was recently reported to be also required for recognition and inhibition of FGF2. Given that this growth factor has been detected in the mammalian preovulatory follicle, we wondered whether FGF2 negatively influences cumulus expansion and PTX3 may also serve in vivo to antagonize its activity. We found that a molar excess of FGF2, above PTX3 binding capacity, does not affect in vitro cumulus matrix formation thus ruling out this possibility. In conclusion, the data strength the view that PTX3 acts as a nodal molecule in cross-linking HA in the matrix. PMID:21619930

Triple-negative (ER, PgR, HER-2/neu) breast cancer in Indian women

PubMed Central

Patil, Vinayak W; Singhai, Rajeev; Patil, Amit V; Gurav, Prakash D

2011-01-01

The aim of our study was to analyze triple-negative (TN) breast cancer, which is defined as being negative for the estrogen receptor (ER), the progesterone receptor (PgR), and the human epidermal growth factor receptor 2 (HER-2/neu) and which represents a subset of breast cancer with different biologic behavior. We investigated the clinicopathological characteristics and prognostic indicators of lymph node-negative TN breast cancer. Medical records were reviewed from patients with node-negative breast cancer who underwent curative surgery at Grant Medical College and Sir JJ Group of Hospitals, Mumbai, India, from May 2007 to October 2010. Clinicopathological variables and clinical outcomes were evaluated. Among 683 patients included, 136 had TN breast cancer and 529 had non-TN breast cancer. TN breast cancer correlated with younger age (<35 years, P = 0.003) and a higher histopathologic and nuclear grade (P < 0.001). It also correlated with a molecular profile associated with biological aggressiveness: negative for Bcl-2 expression (P < 0.001), positive for the epidermal growth factor receptor (P = 0.003), and a high level of p53 (P < 0.001) and Ki-67 expression (P < 0.00). The relapse rates during the follow-up period (median 56.8 months) were 14.7% for TN breast cancer and 6.6% for non-TN breast cancer (P = 0.004). Relapse-free survival (RFS) was significantly shorter among patients with TN breast cancer compared with those with non-TN breast cancer: 3.5-year RFS rate 85.5% versus 94.2%, respectively; P = 0.001. On multivariate analysis, young age, close resection margin, and triple negativity were independent predictors of shorter RFS. TN breast cancer had a higher relapse rate and more aggressive clinicopathological characteristics than non-TN in node-negative breast cancer. Thus, TN breast cancer should be integrated into risk factor analysis for node-negative breast cancer. PMID:24367172

Matrix superpotentials

NASA Astrophysics Data System (ADS)

Nikitin, Anatoly G.; Karadzhov, Yuri

2011-07-01

We present a collection of matrix-valued shape invariant potentials which give rise to new exactly solvable problems of SUSY quantum mechanics. It includes all irreducible matrix superpotentials of the generic form W=kQ+\\frac{1}{k} R+P, where k is a variable parameter, Q is the unit matrix multiplied by a real-valued function of independent variable x, and P and R are the Hermitian matrices depending on x. In particular, we recover the Pron'ko-Stroganov 'matrix Coulomb potential' and all known scalar shape invariant potentials of SUSY quantum mechanics. In addition, five new shape invariant potentials are presented. Three of them admit a dual shape invariance, i.e. the related Hamiltonians can be factorized using two non-equivalent superpotentials. We find discrete spectrum and eigenvectors for the corresponding Schrödinger equations and prove that these eigenvectors are normalizable.

Leukocyte- and platelet-rich fibrin (L-PRF) for long-term delivery of growth factor in rotator cuff repair: review, preliminary results and future directions.

PubMed

Zumstein, Matthias A; Berger, Simon; Schober, Martin; Boileau, Pascal; Nyffeler, Richard W; Horn, Michael; Dahinden, Clemens A

2012-06-01

Surgical repair of the rotator cuff repair is one of the most common procedures in orthopedic surgery. Despite it being the focus of much research, the physiological tendon-bone insertion is not recreated following repair and there is an anatomic non-healing rate of up to 94%. During the healing phase, several growth factors are upregulated that induce cellular proliferation and matrix deposition. Subsequently, this provisional matrix is replaced by the definitive matrix. Leukocyte- and platelet-rich fibrin (L-PRF) contain growth factors and has a stable dense fibrin matrix. Therefore, use of LPRF in rotator cuff repair is theoretically attractive. The aim of the present study was to determine 1) the optimal protocol to achieve the highest leukocyte content; 2) whether L-PRF releases growth factors in a sustained manner over 28 days; 3) whether standard/gelatinous or dry/compressed matrix preparation methods result in higher growth factor concentrations. 1) The standard L-PRF centrifugation protocol with 400 x g showed the highest concentration of platelets and leukocytes. 2) The L-PRF clots cultured in medium showed a continuous slow release with an increase in the absolute release of growth factors TGF-β1, VEGF and MPO in the first 7 days, and for IGF1, PDGF-AB and platelet activity (PF4=CXCL4) in the first 8 hours, followed by a decrease to close to zero at 28 days. Significantly higher levels of growth factor were expressed relative to the control values of normal blood at each culture time point. 3) Except for MPO and the TGFβ-1, there was always a tendency towards higher release of growth factors (i.e., CXCL4, IGF-1, PDGF-AB, and VEGF) in the standard/gelatinous- compared to the dry/compressed group. L-PRF in its optimal standard/gelatinous-type matrix can store and deliver locally specific healing growth factors for up to 28 days and may be a useful adjunct in rotator cuff repair.

Negative Intrusive Thoughts and Dissociation as Risk Factors for Self-Harm

ERIC Educational Resources Information Center

Batey, Helen; May, Jon; Andrade, Jackie

2010-01-01

Relationships between self-harm and vulnerability factors were studied in a general population of 432 participants, of whom 30% reported some experience of self-harm. This group scored higher on dissociation and childhood trauma, had lower self-worth, and reported more negative intrusive thoughts. Among the non-harming group, 10% scored similarly…

[Tuberculin test responses of tuberculosis patients].

PubMed

Pina, J M; Domínguez, A; Alcaide, J; Alvarez, J; Camps, N; Díez, M; Godoy, P; Jansá, J M; Minguell, S

2002-12-01

To determine the response of tuberculosis patients to tuberculin skin tests. The results of skin tests used for initial assessment of tuberculosis patients in Catalonia were reviewed (Multicenter Tuberculosis Research Project). Negative skin tests were those with indurations < 5 mm; positive tests were those with indurations measuring > or = 5 mm. Individuals were classed as having or not having risk factors for developing tuberculosis and those without risk factors were classified by age, location and extension of tuberculosis. Negative skin tests were seen in 1,566 patients (23%). Negative tests were more common in patients with risk factors, significantly so in those undergoing immunosuppressant therapy (50%) or with HIV infection (61%). Negative tests were less prevalent in patients with no risk factors (13%) and, among them, in children (1%), in patients between 15 and 29 years of age (10%) or in those with non-pulmonary forms (10%). Negative tests were significantly more prevalent among patients 60 to 74 years of age (27%), those over 74 (44%), and those whose disease was pulmonary and extrapulmonary (26%) or disseminated (64%). No significant differences in induration size of positive skin tests were observed for patients with and without risk factors (including HIV infection or non-infection). A normal distribution of induration size was observed in all groups. A negative tuberculin skin test for initial assessment should be interpreted in function of the presence or absence of risk factors, age, location or extension of tuberculosis. When a skin test is positive, the response will be similar whether or not an immunodepressant factor is present.

Continued-fraction representation of the Kraus map for non-Markovian reservoir damping

NASA Astrophysics Data System (ADS)

van Wonderen, A. J.; Suttorp, L. G.

2018-04-01

Quantum dissipation is studied for a discrete system that linearly interacts with a reservoir of harmonic oscillators at thermal equilibrium. Initial correlations between system and reservoir are assumed to be absent. The dissipative dynamics as determined by the unitary evolution of system and reservoir is described by a Kraus map consisting of an infinite number of matrices. For all Laplace-transformed Kraus matrices exact solutions are constructed in terms of continued fractions that depend on the pair correlation functions of the reservoir. By performing factorizations in the Kraus map a perturbation theory is set up that conserves in arbitrary perturbative order both positivity and probability of the density matrix. The latter is determined by an integral equation for a bitemporal matrix and a finite hierarchy for Kraus matrices. In the lowest perturbative order this hierarchy reduces to one equation for one Kraus matrix. Its solution is given by a continued fraction of a much simpler structure as compared to the non-perturbative case. In the lowest perturbative order our non-Markovian evolution equations are applied to the damped Jaynes–Cummings model. From the solution for the atomic density matrix it is found that the atom may remain in the state of maximum entropy for a significant time span that depends on the initial energy of the radiation field.

Micro-mechanics of fiber reinforced bounded and unbounded solids: effective local and non-local thermo-elastic properties, stress concentration factors, and edge effect

DTIC Science & Technology

2005-07-01

second order tensors of local eigenstresses and eigenstrains (transformation fields) which may arise by thermal expansion, plastic deformation, phase...with properties different from those of the homogeneous matrix) can be related to specified eigenstrain *( )e x by replacing the inhomogeneities...homogeneous matrix material only. rλ and mλ could be isotropic or anisotropic if the eigenstrain field *( )e x is uniform in Iv . So the strain at

Tumor grade and matrix metalloproteinase 2 expression in stromal fibroblasts help to stratify the high-risk group of patients with early breast cancer identified on the basis of st Gallen recommendations.

PubMed

Niemiec, Joanna; Adamczyk, Agnieszka; Małecki, Krzysztof; Ambicka, Aleksandra; Ryś, Janusz

2013-04-01

It is still being discussed if the assessment of basal markers or if adhesion molecules expression contributes additional prognostic information to the classic prognostic factors and hence should be included into standard morphologic reports. The aim of the study was to assess the prognostic significance of: (i) classification recommended by St Gallen experts (ii) tumor grade, expression of (iii) basal markers, (iv) adhesion molecules, and (v) matrix metalloproteinase 2 (MMP-2) in patients with T1-T2 N0M0 chemotherapy-naive ductal breast cancer. In 79 patients with tumors characterized by estrogen receptor (ER) and progesterone receptor (PgR) positive, human epidermal growth factor receptor 2 negative (HER2) phenotype and MIB-1 labeling index (MIB-l) LI ≤ 15% (low-risk group) cumulative 17-year breast cancer-specific survival probability was 100% and was significantly higher than in 95 patients from the high-risk group (ER(-)/PgR(-)/HER2(-) or HER2(+) or MIB-1 LI > 15%) (72.5%). We found that MMP-2 fibroblast expression indicated 2 subgroups with significantly different survival rates in women with grade 3 tumor (88.9% for MMP-2 positivity and 56.0% for negativity). Cox multivariate analysis revealed that both grade 3 combined with stromal fibroblast MMP-2(-) and a high-risk group according to St Gallen recommendations are independent negative prognostic factors that influence survival of patients with breast cancer. To the best of our knowledge, we have shown for the first time that MMP-2(-) in stromal fibroblasts might indicate poor survivors in the group of patients with grade 3 tumors and that the cumulative effect of both above-mentioned parameters might be helpful in selecting the high-risk individuals from the group of patients with luminal B subtype/HER2(+)/triple negative phenotype identified according to St Gallen recommendations. Copyright © 2013 Elsevier Inc. All rights reserved.

Method for making 2-electron response reduced density matrices approximately N-representable

NASA Astrophysics Data System (ADS)

Lanssens, Caitlin; Ayers, Paul W.; Van Neck, Dimitri; De Baerdemacker, Stijn; Gunst, Klaas; Bultinck, Patrick

2018-02-01

In methods like geminal-based approaches or coupled cluster that are solved using the projected Schrödinger equation, direct computation of the 2-electron reduced density matrix (2-RDM) is impractical and one falls back to a 2-RDM based on response theory. However, the 2-RDMs from response theory are not N-representable. That is, the response 2-RDM does not correspond to an actual physical N-electron wave function. We present a new algorithm for making these non-N-representable 2-RDMs approximately N-representable, i.e., it has the right symmetry and normalization and it fulfills the P-, Q-, and G-conditions. Next to an algorithm which can be applied to any 2-RDM, we have also developed a 2-RDM optimization procedure specifically for seniority-zero 2-RDMs. We aim to find the 2-RDM with the right properties which is the closest (in the sense of the Frobenius norm) to the non-N-representable 2-RDM by minimizing the square norm of the difference between this initial response 2-RDM and the targeted 2-RDM under the constraint that the trace is normalized and the 2-RDM, Q-matrix, and G-matrix are positive semidefinite, i.e., their eigenvalues are non-negative. Our method is suitable for fixing non-N-representable 2-RDMs which are close to being N-representable. Through the N-representability optimization algorithm we add a small correction to the initial 2-RDM such that it fulfills the most important N-representability conditions.

Serum matrix metalloproteinase 3 in detecting remitting seronegative symmetrical synovitis with pitting edema syndrome: A case report.

PubMed

Kenzaka, Tsuneaki; Goda, Ken

2018-05-16

We report a case of remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome in a 71-year-old woman. She referred to our hospital with finger stiffness, edema of both hands and feet, pain of bilateral shoulder, wrist, metacarpophalangeal, proximal interphalangeal, and ankle joints. Rheumatoid factor was negative, human leukocyte antigen -B7 antigen was positive. Moreover, matrix metalloproteinase 3 (MMP-3) was high. She was diagnosed with RS3PE syndrome, and treatment with prednisolone (15 mg/d) was started. One week after prednisolone treatment initiation, CRP decreased to negative, and joint pain was almost completely resolved. However, hand stiffness persisted, and MMP-3 level was still high. Thus, prednisolone dose was increased to 20 mg/d, and the stiffness resolved. Twenty days after treatment initiation, MMP-3 was normalized. MMP-3 was more indicative of RS3PE syndrome symptoms than CRP. Thus, MMP-3 seems to be more sensitive to RS3PE syndrome symptoms.

Serum matrix metalloproteinase 3 in detecting remitting seronegative symmetrical synovitis with pitting edema syndrome: A case report

PubMed Central

Kenzaka, Tsuneaki; Goda, Ken

2018-01-01

We report a case of remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome in a 71-year-old woman. She referred to our hospital with finger stiffness, edema of both hands and feet, pain of bilateral shoulder, wrist, metacarpophalangeal, proximal interphalangeal, and ankle joints. Rheumatoid factor was negative, human leukocyte antigen -B7 antigen was positive. Moreover, matrix metalloproteinase 3 (MMP-3) was high. She was diagnosed with RS3PE syndrome, and treatment with prednisolone (15 mg/d) was started. One week after prednisolone treatment initiation, CRP decreased to negative, and joint pain was almost completely resolved. However, hand stiffness persisted, and MMP-3 level was still high. Thus, prednisolone dose was increased to 20 mg/d, and the stiffness resolved. Twenty days after treatment initiation, MMP-3 was normalized. MMP-3 was more indicative of RS3PE syndrome symptoms than CRP. Thus, MMP-3 seems to be more sensitive to RS3PE syndrome symptoms. PMID:29774220

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS

NASA Astrophysics Data System (ADS)

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-01-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H]-) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. [Figure not available: see fulltext.

SHIP, a novel factor to ameliorate extracellular matrix accumulation via suppressing PI3K/Akt/CTGF signaling in diabetic kidney disease.

PubMed

Li, Fan; Li, Lisha; Cheng, Meijuan; Wang, Xiumin; Hao, Jun; Liu, Shuxia; Duan, Huijun

2017-01-22

Tubular interstitial extracellular matrix accumulation, which plays a key role in the pathogenesis and progression of diabetic kidney disease (DKD), is believed to be mediated by activation of PI3K/Akt signal pathway. However, it is still not clear whether SH2 domain-containing inositol 5'-phosphatase (SHIP), known as a negative regulator of PI3K/Akt pathway is also involved in extracellular matrix metabolism of diabetic kidney. In the present study, decreased SHIP and increased phospho-Akt (Ser 473, Thr 308) were found in renal tubular cells of diabetic mice accompanied by overexpression of connective tissue growth factor (CTGF) and extracellular matrix deposition versus normal mice. Again, high glucose attenuated SHIP expression in a time-dependent manner, concomitant with activation of PI3K/Akt signaling and extracellular matrix production in human renal proximal tubular epithelial cells (HK2) cultured in vitro, which was significantly prevented by transfection of M90-SHIP vector. Furthermore, in vivo delivery of rAd-INPP5D vector (SHIP expression vector) via intraperitoneal injection in diabetic mice increased SHIP expression by 3.36 times followed by 65.26%, 70.38% and 46.71% decreases of phospho-Akt (Ser 473), phospho-Akt (Thr 308) and CTGF expression versus diabetic mice receiving rAd-EGFP vector. Meanwhile, increased renal extracellular matrix accumulation of diabetic mice was also inhibited with intraperitoneal injection of rAd-INPP5D vector. These above data suggested that overexpression of SHIP might be a potent method to lessen renal extracellular matrix accumulation via inactivation of PI3K/Akt pathway and suppression of CTGF expression in DKD. Copyright © 2016 Elsevier Inc. All rights reserved.

Evaluation of risk factors for false-negative results with an antigen-specific peripheral blood-based quantitative T cell assay (T-SPOT®. TB) in the diagnosis of active tuberculosis: A large-scale retrospective study in China.

PubMed

Yang, Chi; Zhang, Shaojun; Yao, Lan; Fan, Lin

2018-05-01

Objective To investigate the diagnostic efficacy of an interferon-γ release assay, T-SPOT ® . TB, for diagnosing active tuberculosis (TB) and to identify risk factors for false-negative results. Methods This retrospective study enrolled consecutive patients with active TB and with non-TB respiratory diseases to evaluate the risk factors for false-negative results when using the T-SPOT ® . TB assay for the diagnosis of active TB. Patients with active TB were categorized as having confirmed pulmonary TB, clinically diagnosed pulmonary TB or extrapulmonary TB (EPTB). Results This study analysed 4964 consecutive patients; 2425 with active TB and 2539 with non-TB respiratory diseases. Multivariate logistic regression analyses identified the following five factors that were all associated with an increased false-negative rate with the T-SPOT ® . TB assay: increased age (odds ratio [OR] 1.018; 95% confidence interval [CI] 1.013, 1.024); decreased CD8+ count (OR 0.307; 95% CI 0.117, 0.803); negative sputum acid-fast bacilli (AFB) smear staining (OR 1.821; 95% CI 1.338, 2.477); negative mycobacterial cultures (OR 1.379; 95% CI 1.043, 1.824); and absence of EPTB (OR 1.291; 95% CI 1.026, 1.623). Conclusions Increased age, decreased CD8+ count, negative sputum AFB smear results, negative sputum mycobacterial cultures and absence of EPTB might lead to an increased false-negative rate when using the T-SPOT ® . TB assay.

Risk for excessive alcohol use and drinking-related problems in college student athletes

PubMed Central

Yusko, David A.; Buckman, Jennifer F.; White, Helene R.; Pandina, Robert J.

2008-01-01

There is compelling evidence that college student athletes engage in frequent episodes of heavy drinking and are prone to negative consequences resulting from such use. This study sought to identify risk and protective factors associated with student-athlete drinking and determine if student-athlete risk factors differed from those of non-athletes. Athletes compared to non-athletes reported more exaggerated perceptions of peer heavy drinking and lower sensation seeking and coping and enhancement motives for drinking, suggesting a risk profile distinct from non-athletes. In the overall sample, higher sensation seeking, overestimation of peer heavy drinking, non-use of protective behaviors while drinking, and higher enhancement and coping drinking motives were associated with greater frequency of heavy episodic drinking and more negative drinking consequences. In athletes compared to non-athletes, sensation seeking was more strongly associated with heavy episodic drinking and drinking to cope was more strongly associated with negative alcohol-related consequences. Overall, the results suggest that already proven brief intervention strategies, with minor adaptations related to the roles of sensation seeking and drinking to cope, may be helpful for student athletes. PMID:18752900

shiftNMFk 1.1: Robust Nonnegative matrix factorization with kmeans clustering and signal shift, for allocation of unknown physical sources, toy version for open sourcing with publications

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

Alexandrov, Boian S.; Lliev, Filip L.; Stanev, Valentin G.

This code is a toy (short) version of CODE-2016-83. From a general perspective, the code represents an unsupervised adaptive machine learning algorithm that allows efficient and high performance de-mixing and feature extraction of a multitude of non-negative signals mixed and recorded by a network of uncorrelated sensor arrays. The code identifies the number of the mixed original signals and their locations. Further, the code also allows deciphering of signals that have been delayed in regards to the mixing process in each sensor. This code is high customizable and it can be efficiently used for a fast macro-analyses of data. Themore » code is applicable to a plethora of distinct problems: chemical decomposition, pressure transient decomposition, unknown sources/signal allocation, EM signal decomposition. An additional procedure for allocation of the unknown sources is incorporated in the code.« less

Seismic signature analysis for discrimination of people from animals

NASA Astrophysics Data System (ADS)

Damarla, Thyagaraju; Mehmood, Asif; Sabatier, James M.

2013-05-01

Cadence analysis has been the main focus for discriminating between the seismic signatures of people and animals. However, cadence analysis fails when multiple targets are generating the signatures. We analyze the mechanism of human walking and the signature generated by a human walker, and compare it with the signature generated by a quadruped. We develop Fourier-based analysis to differentiate the human signatures from the animal signatures. We extract a set of basis vectors to represent the human and animal signatures using non-negative matrix factorization, and use them to separate and classify both the targets. Grazing animals such as deer, cows, etc., often produce sporadic signals as they move around from patch to patch of grass and one must characterize them so as to differentiate their signatures from signatures generated by a horse steadily walking along a path. These differences in the signatures are used in developing a robust algorithm to distinguish the signatures of animals from humans. The algorithm is tested on real data collected in a remote area.

Optical biopsy using fluorescence spectroscopy for prostate cancer diagnosis

NASA Astrophysics Data System (ADS)

Wu, Binlin; Gao, Xin; Smith, Jason; Bailin, Jacob

2017-02-01

Native fluorescence spectra are acquired from fresh normal and cancerous human prostate tissues. The fluorescence data are analyzed using a multivariate analysis algorithm such as non-negative matrix factorization. The nonnegative spectral components are retrieved and attributed to the native fluorophores such as collagen, reduced nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD) in tissue. The retrieved weights of the components, e.g. NADH and FAD are used to estimate the relative concentrations of the native fluorophores and the redox ratio. A machine learning algorithm such as support vector machine (SVM) is used for classification to distinguish normal and cancerous tissue samples based on either the relative concentrations of NADH and FAD or the redox ratio alone. The classification performance is shown based on statistical measures such as sensitivity, specificity, and accuracy, along with the area under receiver operating characteristic (ROC) curve. A cross validation method such as leave-one-out is used to evaluate the predictive performance of the SVM classifier to avoid bias due to overfitting.

EVIDENCE OF SPREADING LAYER EMISSION IN A THERMONUCLEAR SUPERBURST

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

Koljonen, K. I. I.; Kajava, J. J. E.; Kuulkers, E., E-mail: karri.koljonen@nyu.edu

2016-10-01

When a neutron star (NS) accretes matter from a companion star in a low-mass X-ray binary, the accreted gas settles onto the stellar surface through a boundary/spreading layer. On rare occasions the accumulated gas undergoes a powerful thermonuclear superburst powered by carbon burning deep below the NS atmosphere. In this paper, we apply the non-negative matrix factorization spectral decomposition technique to show that the spectral variations during a superburst from 4U 1636–536 can be explained by two distinct components: (1) the superburst emission characterized by a variable temperature blackbody radiation component and (2) a quasi-Planckian component with a constant, ∼2.5more » keV, temperature varying by a factor of ∼15 in flux. The spectrum of the quasi-Planckian component is identical in shape and characteristics to the frequency-resolved spectra observed in the accretion/persistent spectrum of NS low-mass X-ray binaries and agrees well with the predictions of the spreading layer model by Inogamov and Sunyaev. Our results provide yet more observational evidence that superbursts—and possibly also normal X-ray bursts—induce changes in the disc–star boundary.« less

The sales of antidepressants and suicide rates in Norway and its counties 1980-2004.

PubMed

Bramness, Jørgen G; Walby, Fredrik A; Tverdal, Aage

2007-09-01

Suicide is a major public health problem and depression is among the most important risk factors for suicide. Treatment of depression might prevent suicide. To study this hypothesis further we conducted an ecological study. An ecological study using sales data for antidepressants and numbers of suicides in Norway and Norwegian counties 1980-2004 was performed. Data on alcohol consumption and unemployment rates were registered and taken into account. Data were analyzed using Cochrane-Orcutt time series for the country as a whole. The county specific data were analyzed with a random coefficient model with county as subject and intercept and time (slope) as random variables using an unstructured covariance matrix. Sales of non-tricyclic antidepressants (non-TCAs) and suicide were clearly negatively related, even when controlling for alcohol and unemployment (adjusted r(2): 0.57). There was an effect modification between time and level of sales of non-TCAs. Studying the relationship between the sales of non-TCAs and the suicide rate, we found that it was significant and stronger for the low sales figures, but non-existent for the high sales figures. Ecological studies cannot infer causality. The fall in suicide rates in Norway and its counties was related to the increased sales of non-TCAs. The effect was mostly a result of a sales increase in the lower sales segment, indicating that a change from the more toxic TCAs, or heightened awareness of depression and its treatment, could explain the relationship found between sales of newer antidepressants and a decrease in suicide rate.

A review and prospects for Nb3Sn superconductor development

NASA Astrophysics Data System (ADS)

Xu, Xingchen

2017-09-01

Nb3Sn superconductors have significant applications in constructing high-field (>10 T) magnets. This article briefly reviews development of Nb3Sn superconductor and proposes prospects for further improvement. It is shown that significant improvement of critical current density (J c) is needed for future accelerator magnets. After a brief review of the development of Nb3Sn superconductors, the factors controlling J c are summarized and correlated with their microstructure and chemistry. The non-matrix J c of Nb3Sn conductors is mainly determined by three factors: the fraction of current-carrying Nb3Sn phase in the non-matrix area, the upper critical field B c2, and the flux line pinning capacity. Then prospects to improve the three factors are discussed respectively. An analytic model was developed to show how the ratios of precursors determine the phase fractions after heat treatment, based on which it is predicted that the limit of current-carrying Nb3Sn fraction in subelements is ∼65%. Then, since B c2 is largely determined by the Nb3Sn stoichiometry, a thermodynamic/kinetic theory is presented to show what essentially determines the Sn content of Nb3Sn conductors. This theory explains the influences of Sn sources and Ti addition on stoichiometry and growth rate of Nb3Sn layers. Next, to improve flux pinning, previous efforts in this community to introduce additional pinning centers to Nb3Sn wires are reviewed, and an internal oxidation technique is described. Finally, prospects for further improvement of non-matrix J c of Nb3Sn conductors are discussed, and it is seen that the only opportunity for further significantly improving J c lies in improving flux pinning.

A review and prospects for Nb 3Sn superconductor development

DOE PAGES

Xu, Xingchen

2017-08-03

Nb 3Sn superconductors have significant applications in constructing high-field (> 10 T) magnets. This article briefly reviews development of Nb 3Sn superconductor and proposes prospects for further improvement. It is shown that significant improvement of critical current density (J c) is needed for future accelerator magnets. After a brief review of the development of Nb 3Sn superconductors, the factors controlling J c are summarized and correlated with their microstructure and chemistry. The non-matrix J c of Nb 3Sn conductors is mainly determined by three factors: the fraction of current-carrying Nb 3Sn phase in the non-matrix area, the upper critical fieldmore » B c2, and the flux-line pinning capacity. Then prospects to improve the three factors are discussed respectively. An analytic model was developed to show how the ratios of precursors determine the phase fractions after heat treatment, based on which it is predicted that the limit of current-carrying Nb 3Sn fraction in subelements is ~65%. Then, since B c2 is largely determined by the Nb 3Sn stoichiometry, a thermodynamic/kinetic theory was presented to show what essentially determines the Sn content of Nb 3Sn conductors. This theory explains the influences of Sn sources and Ti addition on stoichiometry and growth rate of Nb 3Sn layers. Next, to improve flux pinning, previous efforts in this community to introduce additional pinning centers (APC) to Nb 3Sn wires are reviewed, and an internal oxidation technique is described. Lastly, prospects for further improvement of non-matrix J c of Nb 3Sn conductors are discussed, and it is seen that the only opportunity for further significantly improving J c lies in improving the flux pinning.« less

CD147 and matrix-metalloproteinase-2 expression in metastatic and non-metastatic uveal melanomas.

PubMed

Lüke, Julia; Vukoja, Vlatka; Brandenbusch, Tim; Nassar, Khaled; Rohrbach, Jens Martin; Grisanti, Salvatore; Lüke, Matthias; Tura, Aysegül

2016-06-03

Extracellular matrix remodelling regulated by matrix-metalloproteinase (MMP) inducer (CD147) is a crucial process during tumor cell invasion and regulation of blood supply. In this study, we evaluated the correlation of CD147 and MMP-2 expression with major prognostic factors for uveal melanoma and the development of metastasis. The expression of CD147 and MMP-2 was analyzed in 49 samples of uveal melanomas. Triple immunofluorescence stainings using markers against glial cells (GFAP), endothelial cells (CD34) and macrophages (CD68) were performed to further analyse the exact localisation of CD147 and MMP-2 positivity. In 28 cases clinical metastatic disease were found. The remaining 21 cases showed no signs of metastatic disease for an average follow-up of 10 years. Correlation analysis (Pearson correlation) was performed to analyse the association of CD147 and MMP-2 expression with known prognostic factors, vasculogenic mimicry (VM), the mature vasculature (von Willebrand Factor) and tumor induced angiogenesis (by means of Endoglin expression). CD147 and MMP-2 were expressed in 47 (96.0 %) of the uveal melanomas. CD147 up-regulation was significantly correlated with a higher MMP-2 expression. The overall expression analysis revealed no significant difference in the metastatic (p = 0.777) and non-metastatic subgroup (p = 0.585). No correlation of CD147 expression and any system of blood supply was evident. In the non-metastatic sub-group a significant correlation of clustered CD147 positive cells with largest basal diameter (p = 0.039), height (p = 0.047) and TNM-stage (p = 0.013) was evident. These data may indicate that CD147 regulates MMP-2 expression in uveal melanoma cells.

The neural basis of emotions varies over time: different regions go with onset- and offset-bound processes underlying emotion intensity.

PubMed

Résibois, Maxime; Verduyn, Philippe; Delaveau, Pauline; Rotgé, Jean-Yves; Kuppens, Peter; Van Mechelen, Iven; Fossati, Philippe

2017-08-01

According to theories of emotion dynamics, emotions unfold across two phases in which different types of processes come to the fore: emotion onset and emotion offset. Differences in onset-bound processes are reflected by the degree of explosiveness or steepness of the response at onset, and differences in offset-bound processes by the degree of accumulation or intensification of the subsequent response. Whether onset- and offset-bound processes have distinctive neural correlates and, hence, whether the neural basis of emotions varies over time, still remains unknown. In the present fMRI study, we address this question using a recently developed paradigm that allows to disentangle explosiveness and accumulation. Thirty-one participants were exposed to neutral and negative social feedback, and asked to reflect on its contents. Emotional intensity while reading and thinking about the feedback was measured with an intensity profile tracking approach. Using non-negative matrix factorization, the resulting profile data were decomposed in explosiveness and accumulation components, which were subsequently entered as continuous regressors of the BOLD response. It was found that the neural basis of emotion intensity shifts as emotions unfold over time with emotion explosiveness and accumulation having distinctive neural correlates. © The Author (2017). Published by Oxford University Press.

The neural basis of emotions varies over time: different regions go with onset- and offset-bound processes underlying emotion intensity

PubMed Central

Verduyn, Philippe; Delaveau, Pauline; Rotgé, Jean-Yves; Kuppens, Peter; Van Mechelen, Iven; Fossati, Philippe

2017-01-01

Abstract According to theories of emotion dynamics, emotions unfold across two phases in which different types of processes come to the fore: emotion onset and emotion offset. Differences in onset-bound processes are reflected by the degree of explosiveness or steepness of the response at onset, and differences in offset-bound processes by the degree of accumulation or intensification of the subsequent response. Whether onset- and offset-bound processes have distinctive neural correlates and, hence, whether the neural basis of emotions varies over time, still remains unknown. In the present fMRI study, we address this question using a recently developed paradigm that allows to disentangle explosiveness and accumulation. Thirty-one participants were exposed to neutral and negative social feedback, and asked to reflect on its contents. Emotional intensity while reading and thinking about the feedback was measured with an intensity profile tracking approach. Using non-negative matrix factorization, the resulting profile data were decomposed in explosiveness and accumulation components, which were subsequently entered as continuous regressors of the BOLD response. It was found that the neural basis of emotion intensity shifts as emotions unfold over time with emotion explosiveness and accumulation having distinctive neural correlates. PMID:28402478

Matrix product representation of the stationary state of the open zero range process

NASA Astrophysics Data System (ADS)

Bertin, Eric; Vanicat, Matthieu

2018-06-01

Many one-dimensional lattice particle models with open boundaries, like the paradigmatic asymmetric simple exclusion process (ASEP), have their stationary states represented in the form of a matrix product, with matrices that do not explicitly depend on the lattice site. In contrast, the stationary state of the open 1D zero-range process (ZRP) takes an inhomogeneous factorized form, with site-dependent probability weights. We show that in spite of the absence of correlations, the stationary state of the open ZRP can also be represented in a matrix product form, where the matrices are site-independent, non-commuting and determined from algebraic relations resulting from the master equation. We recover the known distribution of the open ZRP in two different ways: first, using an explicit representation of the matrices and boundary vectors; second, from the sole knowledge of the algebraic relations satisfied by these matrices and vectors. Finally, an interpretation of the relation between the matrix product form and the inhomogeneous factorized form is proposed within the framework of hidden Markov chains.

Complementary Effects of Negative-Pressure Wound Therapy and Pulsed Radiofrequency Energy on Cutaneous Wound Healing in Diabetic Mice.

PubMed

Chen, Bin; Kao, Huang-Kai; Dong, Ziqing; Jiang, Zhaohua; Guo, Lifei

2017-01-01

Negative-pressure wound therapy and pulsed radiofrequency energy are two clinical modalities used to treat soft-tissue wounds. They are purported to affect healing differently. The aim of this experimental study was to contrast the two modalities at a mechanistic level and to investigate whether their combined therapy could achieve additive and complementary effects on wound healing. Full-thickness dorsal cutaneous wounds of diabetic, db/db, mice were treated with either negative-pressure wound therapy, pulsed radiofrequency energy, or combined therapies. Macroscopic healing kinetics were examined. Epidermal regeneration (proliferation rate and length of reepithelialization) and neovascularization (blood vessel density) were investigated. Messenger RNA levels indicative of angiogenic (basic fibroblast growth factor), profibrotic (transforming growth factor-β), epidermal proliferative (keratinocyte growth factor), and extracellular matrix remodeling (collagen 1) processes were measured in wound tissues. All three treatment groups displayed faster wound healing. The negative-pressure wound therapy/pulsed radiofrequency energy combined therapy led to significantly faster healing than either the negative-pressure wound therapy or pulsed radiofrequency energy therapy alone. Epidermal regeneration and neovascularization were enhanced in all three groups. The two negative-pressure wound therapy groups (alone and combined with pulsed radiofrequency energy) demonstrated more significant increases in expression of all assayed growth factors than the pulsed radiofrequency energy group. Furthermore, the combined therapy exhibited a more profound elevation in collagen 1 expression than either of the two therapies alone. Combining the negative-pressure wound therapy and pulsed radiofrequency energy modalities can achieve additive benefits in cutaneous healing, and the two therapies can be easily used together to complement each other in clinical wound treatments.

Precise stacking of decellularized extracellular matrix based 3D cell-laden constructs by a 3D cell printing system equipped with heating modules.

PubMed

Ahn, Geunseon; Min, Kyung-Hyun; Kim, Changhwan; Lee, Jeong-Seok; Kang, Donggu; Won, Joo-Yun; Cho, Dong-Woo; Kim, Jun-Young; Jin, Songwan; Yun, Won-Soo; Shim, Jin-Hyung

2017-08-17

Three-dimensional (3D) cell printing systems allow the controlled and precise deposition of multiple cells in 3D constructs. Hydrogel materials have been used extensively as printable bioinks owing to their ability to safely encapsulate living cells. However, hydrogel-based bioinks have drawbacks for cell printing, e.g. inappropriate crosslinking and liquid-like rheological properties, which hinder precise 3D shaping. Therefore, in this study, we investigated the influence of various factors (e.g. bioink concentration, viscosity, and extent of crosslinking) on cell printing and established a new 3D cell printing system equipped with heating modules for the precise stacking of decellularized extracellular matrix (dECM)-based 3D cell-laden constructs. Because the pH-adjusted bioink isolated from native tissue is safely gelled at 37 °C, our heating system facilitated the precise stacking of dECM bioinks by enabling simultaneous gelation during printing. We observed greater printability compared with that of a non-heating system. These results were confirmed by mechanical testing and 3D construct stacking analyses. We also confirmed that our heating system did not elicit negative effects, such as cell death, in the printed cells. Conclusively, these results hold promise for the application of 3D bioprinting to tissue engineering and drug development.

Structural analysis of N-glycans by the glycan-labeling method using 3-aminoquinoline-based liquid matrix in negative-ion MALDI-MS.

PubMed

Nishikaze, Takashi; Kaneshiro, Kaoru; Kawabata, Shin-ichirou; Tanaka, Koichi

2012-11-06

Negative-ion fragmentation of underivatized N-glycans has been proven to be more informative than positive-ion fragmentation. Fluorescent labeling via reductive amination is often employed for glycan analysis, but little is known about the influence of the labeling group on negative-ion fragmentation. We previously demonstrated that the on-target glycan-labeling method using 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid (3AQ/CHCA) liquid matrix enables highly sensitive, rapid, and quantitative N-glycan profiling analysis. The current study investigates the suitability of 3AQ-labeled N-glycans for structural analysis based on negative-ion collision-induced dissociation (CID) spectra. 3AQ-labeled N-glycans exhibited simple and informative CID spectra similar to those of underivatized N-glycans, with product ions due to cross-ring cleavages of the chitobiose core and ions specific to two antennae (D and E ions). The interpretation of diagnostic fragment ions suggested for underivatized N-glycans could be directly applied to the 3AQ-labeled N-glycans. However, fluorescently labeled N-glycans by conventional reductive amination, such as 2-aminobenzamide (2AB)- and 2-pyrydilamine (2PA)-labeled N-glycans, exhibited complicated CID spectra consisting of numerous signals formed by dehydration and multiple cleavages. The complicated spectra of 2AB- and 2PA-labeled N-glycans was found to be due to their open reducing-terminal N-acetylglucosamine (GlcNAc) ring, rather than structural differences in the labeling group in the N-glycan derivative. Finally, as an example, the on-target 3AQ labeling method followed by negative-ion CID was applied to structurally analyze neutral N-glycans released from human epidermal growth factor receptor type 2 (HER2) protein. The glycan-labeling method using 3AQ-based liquid matrix should facilitate highly sensitive quantitative and qualitative analyses of glycans.

Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer.

PubMed

Krams, Indrikis A; Niemelä, Petri T; Trakimas, Giedrius; Krams, Ronalds; Burghardt, Gordon M; Krama, Tatjana; Kuusik, Aare; Mänd, Marika; Rantala, Markus J; Mänd, Raivo; Kekäläinen, Jukka; Sirkka, Ilkka; Luoto, Severi; Kortet, Raine

2017-03-29

The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer , selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the sign of the covariation, we applied structural equation models to an individual-level covariance matrix to examine whether the RMR generates covariation between the measured behaviours. All traits showed among-individual variation and covariation: RMR and boldness were positively correlated, RMR and exploration were negatively correlated, and boldness and exploration were negatively correlated. However, the RMR was not a causal factor generating covariation between boldness and exploration. Instead, the covariation between all three traits was explained by another, unmeasured mechanism. The selection lines differed from each other in all measured traits and significantly affected the covariance matrix structure between the traits, suggesting that there is a genetic component in the trait integration. Our results emphasize that interpretations made solely from the correlation matrix might be misleading. © 2017 The Author(s).

Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer

PubMed Central

Trakimas, Giedrius; Krams, Ronalds; Burghardt, Gordon M.; Krama, Tatjana; Kuusik, Aare; Mänd, Marika; Rantala, Markus J.; Mänd, Raivo; Sirkka, Ilkka; Luoto, Severi; Kortet, Raine

2017-01-01

The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer, selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the sign of the covariation, we applied structural equation models to an individual-level covariance matrix to examine whether the RMR generates covariation between the measured behaviours. All traits showed among-individual variation and covariation: RMR and boldness were positively correlated, RMR and exploration were negatively correlated, and boldness and exploration were negatively correlated. However, the RMR was not a causal factor generating covariation between boldness and exploration. Instead, the covariation between all three traits was explained by another, unmeasured mechanism. The selection lines differed from each other in all measured traits and significantly affected the covariance matrix structure between the traits, suggesting that there is a genetic component in the trait integration. Our results emphasize that interpretations made solely from the correlation matrix might be misleading. PMID:28330918

Spin-1 Particles and Perturbative QCD

NASA Astrophysics Data System (ADS)

de Melo, J. P. B. C.; Frederico, T.; Ji, Chueng-Ryong

2018-07-01

Due to the angular condition in the light-front dynamics (LFD), the extraction of the electromagnetic form factors for spin-1 particles can be uniquely determined taking into account implicitly non-valence and/or the zero-mode contributions to the matrix elements of the electromagnetic current. No matter which matrix elements of the electromagnetic current is used to extract the electromagnetic form factors, the same unique result is obtained. As physical observables, the electromagnetic form factors obtained from matrix elements of the current in LFD must be equal to those obtained in the instant form calculations. Recently, the Babar collaboration (Phys Rev D 78:071103, 2008) has analyzed the reaction e^+ + e^-→ ρ ^+ + ρ ^- at √{s}=10.58 GeV to measure the cross section as well as the ratios of the helicity amplitudes F_{λ 'λ }. We present our recent analysis of the Babar data for the rho meson considering the angular condition in LFD to put a stringent test on the onset of asymptotic perturbative QCD and predict the energy regime where the subleading contributions are still considerable.

The molecular biology in wound healing & non-healing wound.

PubMed

Qing, Chun

2017-08-01

The development of molecular biology and other new biotechnologies helps us to recognize the wound healing and non-healing wound of skin in the past 30 years. This review mainly focuses on the molecular biology of many cytokines (including growth factors) and other molecular factors such as extracellular matrix (ECM) on wound healing. The molecular biology in cell movement such as epidermal cells in wound healing was also discussed. Moreover many common chronic wounds such as pressure ulcers, leg ulcers, diabetic foot wounds, venous stasis ulcers, etc. usually deteriorate into non-healing wounds. Therefore the molecular biology such as advanced glycation end products (AGEs) and other molecular factors in diabetes non-healing wounds were also reviewed. Copyright © 2017 Daping Hospital and the Research Institute of Surgery of the Third Military Medical University. Production and hosting by Elsevier B.V. All rights reserved.

Exploring the Relationship between Negative Urgency and Dysregulated Eating: Etiologic Associations and the Role of Negative Affect

PubMed Central

Racine, Sarah E.; Keel, Pamela K.; Burt, S. Alexandra; Sisk, Cheryl L.; Neale, Michael; Boker, Steven; Klump, Kelly L.

2013-01-01

Negative urgency (i.e., the tendency to engage in rash action in response to negative affect) has emerged as a critical personality trait contributing to individual differences in binge eating. However, studies investigating the extent to which genetic and/or environmental influences underlie the effects of negative urgency on binge eating are lacking. Moreover, it remains unclear whether negative urgency-binge eating associations are simply due to the well-established role of negative affect in the development/maintenance of binge eating. The current study addresses these gaps by examining phenotypic and etiologic associations between negative urgency, negative affect, and dysregulated eating (i.e., binge eating, emotional eating) in a sample of 222 same-sex female twin pairs from the Michigan State Twin Registry. Negative urgency was significantly associated with both dysregulated eating symptoms, even after controlling for the effects of negative affect. Genetic factors accounted for the majority (62–77%) of this phenotypic association, although a significant proportion of this genetic covariation was due to genetic influences in common with negative affect. Non-shared environmental factors accounted for a relatively smaller (23–38%) proportion of the association, but these non-shared environmental effects were independent of negative affect. Findings suggest that the presence of emotion-based rash action, combined with high levels of negative affect, may significantly increase genetic risk for dysregulated eating. PMID:23356217

Measuring consciousness in dreams: the lucidity and consciousness in dreams scale.

PubMed

Voss, Ursula; Schermelleh-Engel, Karin; Windt, Jennifer; Frenzel, Clemens; Hobson, Allan

2013-03-01

In this article, we present results from an interdisciplinary research project aimed at assessing consciousness in dreams. For this purpose, we compared lucid dreams with normal non-lucid dreams from REM sleep. Both lucid and non-lucid dreams are an important contrast condition for theories of waking consciousness, giving valuable insights into the structure of conscious experience and its neural correlates during sleep. However, the precise differences between lucid and non-lucid dreams remain poorly understood. The construction of the Lucidity and Consciousness in Dreams scale (LuCiD) was based on theoretical considerations and empirical observations. Exploratory factor analysis of the data from the first survey identified eight factors that were validated in a second survey using confirmatory factor analysis: INSIGHT, CONTROL, THOUGHT, REALISM, MEMORY, DISSOCIATION, NEGATIVE EMOTION, and POSITIVE EMOTION. While all factors are involved in dream consciousness, realism and negative emotion do not differentiate between lucid and non-lucid dreams, suggesting that lucid insight is separable from both bizarreness in dreams and a change in the subjectively experienced realism of the dream. Copyright © 2012 Elsevier Inc. All rights reserved.

eap Gene as novel target for specific identification of Staphylococcus aureus.

PubMed

Hussain, Muzaffar; von Eiff, Christof; Sinha, Bhanu; Joost, Insa; Herrmann, Mathias; Peters, Georg; Becker, Karsten

2008-02-01

The cell surface-associated extracellular adherence protein (Eap) mediates adherence of Staphylococcus aureus to host extracellular matrix components and inhibits inflammation, wound healing, and angiogenesis. A well-characterized collection of S. aureus and non-S. aureus staphylococcal isolates (n = 813) was tested for the presence of the Eap-encoding gene (eap) by PCR to investigate the use of the eap gene as a specific diagnostic tool for identification of S. aureus. Whereas all 597 S. aureus isolates were eap positive, this gene was not detectable in 216 non-S. aureus staphylococcal isolates comprising 47 different species and subspecies of coagulase-negative staphylococci and non-S. aureus coagulase-positive or coagulase-variable staphylococci. Furthermore, non-S. aureus isolates did not express Eap homologs, as verified on the transcriptional and protein levels. Based on these data, the sensitivity and specificity of the newly developed PCR targeting the eap gene were both 100%. Thus, the unique occurrence of Eap in S. aureus offers a promising tool particularly suitable for molecular diagnostics of this pathogen.

A DATA-DRIVEN MODEL FOR SPECTRA: FINDING DOUBLE REDSHIFTS IN THE SLOAN DIGITAL SKY SURVEY

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

Tsalmantza, P.; Hogg, David W., E-mail: vivitsal@mpia.de

2012-07-10

We present a data-driven method-heteroscedastic matrix factorization, a kind of probabilistic factor analysis-for modeling or performing dimensionality reduction on observed spectra or other high-dimensional data with known but non-uniform observational uncertainties. The method uses an iterative inverse-variance-weighted least-squares minimization procedure to generate a best set of basis functions. The method is similar to principal components analysis (PCA), but with the substantial advantage that it uses measurement uncertainties in a responsible way and accounts naturally for poorly measured and missing data; it models the variance in the noise-deconvolved data space. A regularization can be applied, in the form of a smoothnessmore » prior (inspired by Gaussian processes) or a non-negative constraint, without making the method prohibitively slow. Because the method optimizes a justified scalar (related to the likelihood), the basis provides a better fit to the data in a probabilistic sense than any PCA basis. We test the method on Sloan Digital Sky Survey (SDSS) spectra, concentrating on spectra known to contain two redshift components: these are spectra of gravitational lens candidates and massive black hole binaries. We apply a hypothesis test to compare one-redshift and two-redshift models for these spectra, utilizing the data-driven model trained on a random subset of all SDSS spectra. This test confirms 129 of the 131 lens candidates in our sample and all of the known binary candidates, and turns up very few false positives.« less

Efficient l1 -norm-based low-rank matrix approximations for large-scale problems using alternating rectified gradient method.

PubMed

Kim, Eunwoo; Lee, Minsik; Choi, Chong-Ho; Kwak, Nojun; Oh, Songhwai

2015-02-01

Low-rank matrix approximation plays an important role in the area of computer vision and image processing. Most of the conventional low-rank matrix approximation methods are based on the l2 -norm (Frobenius norm) with principal component analysis (PCA) being the most popular among them. However, this can give a poor approximation for data contaminated by outliers (including missing data), because the l2 -norm exaggerates the negative effect of outliers. Recently, to overcome this problem, various methods based on the l1 -norm, such as robust PCA methods, have been proposed for low-rank matrix approximation. Despite the robustness of the methods, they require heavy computational effort and substantial memory for high-dimensional data, which is impractical for real-world problems. In this paper, we propose two efficient low-rank factorization methods based on the l1 -norm that find proper projection and coefficient matrices using the alternating rectified gradient method. The proposed methods are applied to a number of low-rank matrix approximation problems to demonstrate their efficiency and robustness. The experimental results show that our proposals are efficient in both execution time and reconstruction performance unlike other state-of-the-art methods.

Persistently Auxetic Materials: Engineering the Poisson Ratio of 2D Self-Avoiding Membranes under Conditions of Non-Zero Anisotropic Strain.

PubMed

Ulissi, Zachary W; Govind Rajan, Ananth; Strano, Michael S

2016-08-23

Entropic surfaces represented by fluctuating two-dimensional (2D) membranes are predicted to have desirable mechanical properties when unstressed, including a negative Poisson's ratio ("auxetic" behavior). Herein, we present calculations of the strain-dependent Poisson ratio of self-avoiding 2D membranes demonstrating desirable auxetic properties over a range of mechanical strain. Finite-size membranes with unclamped boundary conditions have positive Poisson's ratio due to spontaneous non-zero mean curvature, which can be suppressed with an explicit bending rigidity in agreement with prior findings. Applying longitudinal strain along a singular axis to this system suppresses this mean curvature and the entropic out-of-plane fluctuations, resulting in a molecular-scale mechanism for realizing a negative Poisson's ratio above a critical strain, with values significantly more negative than the previously observed zero-strain limit for infinite sheets. We find that auxetic behavior persists over surprisingly high strains of more than 20% for the smallest surfaces, with desirable finite-size scaling producing surfaces with negative Poisson's ratio over a wide range of strains. These results promise the design of surfaces and composite materials with tunable Poisson's ratio by prestressing platelet inclusions or controlling the surface rigidity of a matrix of 2D materials.

Shifts in bryophyte carbon isotope ratio across an elevation × soil age matrix on Mauna Loa, Hawaii: do bryophytes behave like vascular plants?

PubMed

Waite, Mashuri; Sack, Lawren

2011-05-01

The carbon isotope ratio (δ(13)C) of vascular plant leaf tissue is determined by isotope discrimination, primarily mediated by stomatal and mesophyll diffusion resistances and by photosynthetic rate. These effects lead to predictable trends in leaf δ(13)C across natural gradients of elevation, irradiance and nutrient supply. Less is known about shifts in δ(13)C for bryophytes at landscape scale, as bryophytes lack stomata in the dominant gametophyte phase, and thus lack active control over CO(2) diffusion. Twelve bryophyte species were sampled across a matrix of elevation and soil ages on Mauna Loa, Hawaii Island. We tested hypotheses based on previous findings for vascular plants, which tend to have less negative δ(13)C at higher elevations or irradiances, and for leaves with higher leaf mass per area (LMA). Across the matrix, bryophytes spanned the range of δ(13)C values typical of C(3) vascular plants. Bryophytes were remarkably similar to vascular plants in exhibiting less negative δ(13)C with increasing elevation, and with lower overstory cover; additionally δ(13)C was related to bryophyte canopy projected mass per area, a trait analogous to LMA in vascular plants, also correlated negatively with overstory cover. The similarity of responses of δ(13)C in bryophytes and vascular plants to environmental factors, despite differing morphologies and diffusion pathways, points to a strong direct role of photosynthetic rate in determining δ(13)C variation at the landscape scale.

Study of melanoma invasion by FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Yang, Y.; Sulé-Suso, J.; Sockalingum, G. D.

2008-02-01

Compared to other forms of skin cancer, a malignant melanoma has a high risk of spreading to other parts of the body. Melanoma invasion is a complex process involving changes in cell-extracellular matrix (ECM) interaction and cell-cell interactions. To fully understand the factors which control the invasion process, a human skin model system was reconstructed. HBL (a commercially available cell line) melanoma cells were seeded on a skin model with and without the presence of keratinocytes and/or fibroblasts. After 14 days culture, the skin specimens were fixed, parafin embedded and cut into 7 µm sections. The de-parafinised sections were investigated by synchrotron Fourier transformed infrared (FTIR) microspectroscopy to study skin cell invasion behaviour. The advantage of using FTIR is its ability to obtain the fingerprint information of the invading cells in terms of protein secondary structure in comparison to non-invading cells and the concentration of the enzyme (matrix-metalloproteinase) which digests protein matrix, near the invading cells. With aid of the spectral mapping images, it is possible to pinpoint the cells in non-invasion and invasion area and analyse the respective spectra. It has been observed that the protein bands in cells and matrix shifted between non-invasive and invasive cells in the reconstructed skin model. We hypothesise that by careful analysis of the FTIR data and validation by other models, FTIR studies can reveal information on which type of cells and proteins are involved in melanoma invasion. Thus, it is possible to trace the cell invasion path by mapping the spectra along the interface of cell layer and matrix body by FTIR spectroscopy.

Prognostic significance of surgical extranodal extension in head and neck squamous cell carcinoma patients.

PubMed

Matsumoto, Fumihiko; Mori, Taisuke; Matsumura, Satoko; Matsumoto, Yoshifumi; Fukasawa, Masahiko; Teshima, Masanori; Kobayashi, Kenya; Yoshimoto, Seiichi

2017-08-01

Lymph node metastasis with extranodal extension represents one of the most important adverse prognostic factors for survival in patients with head and neck squamous cell carcinoma. We propose that extranodal extension occurs to differing extents. The aim of this study was to determine the prognostic significance of extranodal extension in patients with head and neck squamous cell carcinoma. Two hundred and ninety-eight patients with head and neck squamous cell carcinoma who underwent surgical resection and neck dissection were included. Cervical lymph nodes were classified into four categories: (i) pathological N negative, (ii) extranodal extension negative, (iii) non-surgical extranodal extension and (iv) surgical extranodal extension. Lymph node metastases were detected in 67.1% of laryngeal/hypopharyngeal cancer patients and 52.7% of oral cancer patients. The 3-year disease-specific survival rates for patients in the pathological N negative, extranodal extension negative, non-surgical extranodal extension and surgical extranodal extension groups were 90.9%, 79.6%, 63.8% and 48.3%, respectively. In laryngeal/hypopharyngeal cancer patients, surgical extranodal extension was associated with a significantly poorer disease-specific survival than a pathological N negative, extranodal extension negative or non-surgical extranodal extension status. In oral cancer patients, no significant differences were observed between the non-surgical and surgical extranodal extension groups. However, non-surgical extranodal extension was associated with a poorer disease-specific survival than a pathological N negative or extranodal extension negative status. Surgical extranodal extension was a poor prognostic factor in patients with head and neck squamous cell carcinoma. The prognostic significance of surgical extranodal extension differed between laryngeal/hypopharyngeal and oral cancer patients. The clinical significance of surgical extranodal extension was much greater for patients with laryngeal/hypopharyngeal cancer than oral cancer. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of processing on recovery and variability associated with immunochemical analytical methods for multiple allergens in a single matrix: sugar cookies.

PubMed

Khuda, Sefat; Slate, Andrew; Pereira, Marion; Al-Taher, Fadwa; Jackson, Lauren; Diaz-Amigo, Carmen; Bigley, Elmer C; Whitaker, Thomas; Williams, Kristina M

2012-05-02

Among the major food allergies, peanut, egg, and milk are the most common. The immunochemical detection of food allergens depends on various factors, such as the food matrix and processing method, which can affect allergen conformation and extractability. This study aimed to (1) develop matrix-specific incurred reference materials for allergen testing, (2) determine whether multiple allergens in the same model food can be simultaneously detected, and (3) establish the effect of processing on reference material stability and allergen detection. Defatted peanut flour, whole egg powder, and spray-dried milk were added to cookie dough at seven incurred levels before baking. Allergens were measured using five commercial enzyme-linked immunosorbent assay (ELISA) kits. All kits showed decreased recovery of all allergens after baking. Analytical coefficients of variation for most kits increased with baking time, but decreased with incurred allergen level. Thus, food processing negatively affects the recovery and variability of peanut, egg, and milk detection in a sugar cookie matrix when using immunochemical methods.

Cathepsin B is the driving force of esophageal cell invasion in a fibroblast-dependent manner.

PubMed

Andl, Claudia D; McCowan, Kelsey M; Allison, Gillian L; Rustgi, Anil K

2010-06-01

Esophageal cancer, which frequently exhibits coordinated loss of E-cadherin (Ecad) and transforming growth factor beta (TGFbeta) receptor II (TbetaRII), has a high mortality rate. In a three-dimensional organotypic culture model system, esophageal keratinocytes expressing dominant-negative mutant versions of both Ecad and TbetaRII (ECdnT) invade into the underlying matrix embedded with fibroblasts. We also find that cathepsin B induction is necessary for fibroblast-mediated invasion. Furthermore, the ECdnT cells in this physiological context activate fibroblasts through the secretion of TGFbeta1, which, in turn, is activated by cathepsin B. These results suggest that the interplay between the epithelial compartment and the surrounding microenvironment is crucial to invasion into the extracellular matrix.

Separating OR, SUM, and XOR Circuits.

PubMed

Find, Magnus; Göös, Mika; Järvisalo, Matti; Kaski, Petteri; Koivisto, Mikko; Korhonen, Janne H

2016-08-01

Given a boolean n × n matrix A we consider arithmetic circuits for computing the transformation x ↦ Ax over different semirings. Namely, we study three circuit models: monotone OR-circuits, monotone SUM-circuits (addition of non-negative integers), and non-monotone XOR-circuits (addition modulo 2). Our focus is on separating OR-circuits from the two other models in terms of circuit complexity: We show how to obtain matrices that admit OR-circuits of size O ( n ), but require SUM-circuits of size Ω( n 3/2 /log 2 n ).We consider the task of rewriting a given OR-circuit as a XOR-circuit and prove that any subquadratic-time algorithm for this task violates the strong exponential time hypothesis.

The emerging role of skeletal muscle extracellular matrix remodelling in obesity and exercise.

PubMed

Martinez-Huenchullan, S; McLennan, S V; Verhoeven, A; Twigg, S M; Tam, C S

2017-07-01

Skeletal muscle extracellular matrix remodelling has been proposed as a new feature associated with obesity and metabolic dysfunction. Exercise training improves muscle function in obesity, which may be mediated by regulatory effects on the muscle extracellular matrix. This review examined available literature on skeletal muscle extracellular matrix remodelling during obesity and the effects of exercise. A non-systematic literature review was performed on PubMed of publications from 1970 to 2015. A total of 37 studies from humans and animals were retained. Studies reported overall increases in gene and protein expression of different types of collagen, growth factors and enzymatic regulators of the skeletal muscle extracellular matrix in obesity. Only two studies investigated the effects of exercise on skeletal muscle extracellular matrix during obesity, with both suggesting a regulatory effect of exercise. The effects of exercise on muscle extracellular matrix seem to be influenced by the duration and type of exercise training with variable effects from a single session compared with a longer duration of exercise. More studies are needed to elucidate the mechanisms behind skeletal muscle extracellular matrix remodelling during obesity and the effects of exercise. © 2017 World Obesity Federation.

[The Relationship of Deficit Syndrome with Clinical Symptoms, Summer Births and Heritability in Patients with Schizophrenia].

PubMed

Mete, Levent; Sarıkaya, Özyıl; Erol, Almıla

2015-01-01

The aim of this study was to compare deficit schizophrenia patients with non-deficit schizophrenia patients for negative and positive symptome scores, rate of summer births, and rate of familial history of psychosis. 110 patients with schizophrenia diagnosed via Structured Clinical Interview for DSM-IV (SCID-I) aged between 18-65 were included in the study. All the patients were evaluated using the Scale for the Assessment of Negative Symptoms (SANS), Scale for the Assessment of Positive Symptoms (SAPS), and The Schedule for the Deficit Syndrome (SDS), and sociodemographic information was obtained. The deficit syndrome group had higher negative and positive scores compared to the non-deficit group. The rate of summer births were higher in the deficit group. Although the rate of positive family history for psychosis was higher in deficit group compared with the non-deficit group, the difference did not achieve statistical significance. Our results that depict higher severity of negative and positive symptom scores and higher rate of summer births with deficit schizophrenia, provides more evidence that deficit and non-deficit schizophrenia are different subtypes having different pathophysiologies. But statistically nonsignificant difference of positive familial history between two groups suggests that the thesis of deficit schizophrenia may be related to genetic factors more than enviromental factors needs to be invesigated further.

Approximate method of variational Bayesian matrix factorization/completion with sparse prior

NASA Astrophysics Data System (ADS)

Kawasumi, Ryota; Takeda, Koujin

2018-05-01

We derive the analytical expression of a matrix factorization/completion solution by the variational Bayes method, under the assumption that the observed matrix is originally the product of low-rank, dense and sparse matrices with additive noise. We assume the prior of a sparse matrix is a Laplace distribution by taking matrix sparsity into consideration. Then we use several approximations for the derivation of a matrix factorization/completion solution. By our solution, we also numerically evaluate the performance of a sparse matrix reconstruction in matrix factorization, and completion of a missing matrix element in matrix completion.

Obsessive-Compulsive Tendencies, Self/Other Perception, Personality, and Suicidal Ideation in a Non-clinical Sample.

PubMed

Iliceto, Paolo; D'Antuono, Laura; Cassarà, Luisa; Giacolini, Teodosio; Sabatello, Ugo; Candilera, Gabriella

2017-06-01

Research on the risk factors for SI in adults with OC tendencies is limited, and it is still unclear whether the association between OC tendencies and SI in non-clinical individuals exists. The goal of the present study was to test the associations between OC tendencies, self/other perception, personality traits, depressive symptoms and SI among a non-clinical adult population. We investigated an Italian sample of 337 adults, who were administered a set of self-report questionnaires to assess obsessive-compulsive tendencies, depression, self/other perception, personality traits, and hopelessness. Confirmatory factor analyses (CFA) were performed. In the final model we found that personality, obsessive-compulsive factor and suicidal ideation were significantly correlated with each other: personality correlated negatively with obsessive-compulsive factor and suicidal ideation, while obsessive-compulsive factor and suicidal ideation resulted as strongly positively associated. Our results highlight the importance of assessing OC tendencies, negative self/other perception and SI. Understanding their role and interplay will allow for the development and implementation of more advanced prevention and treatment policies.

N-(1-Naphthyl) Ethylenediamine Dinitrate: A New Matrix for Negative Ion MALDI-TOF MS Analysis of Small Molecules

NASA Astrophysics Data System (ADS)

Chen, Rui; Chen, Suming; Xiong, Caiqiao; Ding, Xunlei; Wu, Chih-Che; Chang, Huan-Cheng; Xiong, Shaoxiang; Nie, Zongxiu

2012-09-01

An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules ( m/z < 1000) such as oligosaccharides, peptides, metabolites and explosives using negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range ( m/z < 200) consist of only nitrate and nitric acid cluster ions, making the matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.

[Uncommon non-fermenting Gram-negative rods as pathogens of lower respiratory tract infection].

PubMed

Juhász, Emese; Iván, Miklós; Pongrácz, Júlia; Kristóf, Katalin

2018-01-01

Glucose non-fermenting Gram-negative bacteria are ubiquitous environmental organisms. Most of them are identified as opportunistic, nosocomial pathogens in patients. Uncommon species are identified accurately, mainly due to the introduction of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology practice. Most of these uncommon non-fermenting rods are isolated from lower respiratory tract samples. Their significance in lower respiratory tract infections, such as rules of their testing are not clarified yet. The aim of this study was to review the clinical microbiological features of these bacteria, especially their roles in lower respiratory tract infections and antibiotic treatment options. Lower respiratory tract samples of 3589 patients collected in a four-year period (2013-2016) were analyzed retrospectively at Semmelweis University (Budapest, Hungary). Identification of bacteria was performed by MALDI-TOF MS, the antibiotic susceptibility was tested by disk diffusion method. Stenotrophomonas maltophilia was revealed to be the second, whereas Acinetobacter baumannii the third most common non-fermenting rod in lower respiratory tract samples, behind the most common Pseudomonas aeruginosa. The total number of uncommon non-fermenting Gram-negative isolates was 742. Twenty-three percent of isolates were Achromobacter xylosoxidans. Beside Chryseobacterium, Rhizobium, Delftia, Elizabethkingia, Ralstonia and Ochrobactrum species, and few other uncommon species were identified among our isolates. The accurate identification of this species is obligatory, while most of them show intrinsic resistance to aminoglycosides. Resistance to ceftazidime, cefepime, piperacillin-tazobactam and carbapenems was frequently observed also. Ciprofloxacin, levofloxacin and trimethoprim-sulfamethoxazole were found to be the most effective antibiotic agents. Orv Hetil. 2018; 159(1): 23-30.

Changes in chemical composition of bone matrix in ovariectomized (OVX) rats detected by Raman spectroscopy and multivariate analysis

NASA Astrophysics Data System (ADS)

Oshima, Yusuke; Iimura, Tadahiro; Saitou, Takashi; Imamura, Takeshi

2015-02-01

Osteoporosis is a major bone disease that connotes the risk of fragility fractures resulting from alterations to bone quantity and/or quality to mechanical competence. Bone strength arises from both bone quantity and quality. Assessment of bone quality and bone quantity is important for prediction of fracture risk. In spite of the two factors contribute to maintain the bone strength, only one factor, bone mineral density is used to determine the bone strength in the current diagnosis of osteoporosis. On the other hand, there is no practical method to measure chemical composition of bone tissue including hydroxyapatite and collagen non-invasively. Raman spectroscopy is a powerful technique to analyze chemical composition and material properties of bone matrix non-invasively. Here we demonstrated Raman spectroscopic analysis of the bone matrix in osteoporosis model rat. Ovariectomized (OVX) rat was made and the decalcified sections of tibias were analyzed by a Raman microscope. In the results, Raman bands of typical collagen appeared in the obtained spectra. Although the typical mineral bands at 960 cm-1 (Phosphate) was absent due to decalcified processing, we found that Raman peak intensities of amide I and C-C stretching bands were significantly different between OVX and sham-operated specimens. These differences on the Raman spectra were statistically compared by multivariate analyses, principal component analysis (PCA) and liner discrimination analysis (LDA). Our analyses suggest that amide I and C-C stretching bands can be related to stability of bone matrix which reflects bone quality.

Clinical correlates of resilience factors in geriatric depression.

PubMed

Laird, Kelsey T; Lavretsky, Helen; Paholpak, Pattharee; Vlasova, Roza M; Roman, Michael; St Cyr, Natalie; Siddarth, Prabha

2018-01-16

Traditional perspectives conceptualize resilience as a trait and depression as resulting from resilience deficiency. However, research indicates that resilience varies substantially even among adults who are clinically depressed, as well as across the lifespan of an individual. Few studies have investigated resilience in depression, and even fewer have examined resilience in depressed older adults. Three hundred thirty-seven adults ≥60 years with major depressive disorder completed the Connor-Davidson Resilience Scale (CD-RISC) and measures of mental health, quality of life (QOL), and medical comorbidity. Exploratory factor analysis was used to explore the factor structure of the CD-RISC. Correlations and general linear models were used to examine associations between resilience and other variables. The rotated component matrix indicated a four-factor model. Sorting of items by highest factor loading revealed constructs associated with (1) grit, (2) active coping self-efficacy, (3) accommodative coping self-efficacy, and (4) spirituality. Resilience was significantly correlated with increased age, lower cognitive functioning, greater cerebrovascular risk, and greater medical comorbidity. Resilience was negatively associated with mental health symptoms (depression, apathy, and anxiety) and positively associated with QOL. The final optimal model identified less depression, less apathy, greater medical comorbidity, higher QOL, and minority (non-White) race as factors that significantly explained variability in resilience. Resilience was significantly associated with a range of mental health constructs in a sample of older adults with depression. Future clinical trials and dismantling studies may help determine whether interventions targeting grit, active coping, accommodative coping, and spirituality can increase resilience and help prevent and treat depression in older adults.

Emotion socialization in anxious youth: Parenting buffers emotional reactivity to peer negative events

PubMed Central

Oppenheimer, Caroline W.; Ladouceur, Cecile D.; Waller, Jennifer M.; Ryan, Neal D.; Allen, Kristy Benoit; Sheeber, Lisa; Forbes, Erika E; Dahl, Ronald E.; Silk, Jennifer S.

2016-01-01

Anxious youth exhibit heightened emotional reactivity, particularly to social-evaluative threat, such as peer evaluation and feedback, compared to non-anxious youth. Moreover, normative developmental changes during the transition into adolescence may exacerbate emotional reactivity to peer negative events, particularly for anxious youth. Therefore, it is important to investigate factors that may buffer emotional reactivity within peer contexts among anxious youth. The current study examined the role of parenting behaviors in child emotional reactivity to peer and non-peer negative events among 86 anxious youth in middle childhood to adolescence (Mean age = 11.29, 54% girls). Parenting behavior and affect was observed during a social-evaluative laboratory speech task for youth, and ecological momentary assessment (EMA) methods were used to examine youth emotional reactivity to typical daily negative events within peer and non-peer contexts. Results showed that parent positive behaviors, and low levels of parent anxious affect, during the stressful laboratory task for youth buffered youth negative emotional reactivity to real-world negative peer events, but not non-peer events. Findings inform our understanding of parenting influences on anxious youth's emotional reactivity to developmentally salient negative events during the transition into adolescence. PMID:26783026

Emotion Socialization in Anxious Youth: Parenting Buffers Emotional Reactivity to Peer Negative Events.

PubMed

Oppenheimer, Caroline W; Ladouceur, Cecile D; Waller, Jennifer M; Ryan, Neal D; Allen, Kristy Benoit; Sheeber, Lisa; Forbes, Erika E; Dahl, Ronald E; Silk, Jennifer S

2016-10-01

Anxious youth exhibit heightened emotional reactivity, particularly to social-evaluative threat, such as peer evaluation and feedback, compared to non-anxious youth. Moreover, normative developmental changes during the transition into adolescence may exacerbate emotional reactivity to peer negative events, particularly for anxious youth. Therefore, it is important to investigate factors that may buffer emotional reactivity within peer contexts among anxious youth. The current study examined the role of parenting behaviors in child emotional reactivity to peer and non-peer negative events among 86 anxious youth in middle childhood to adolescence (Mean age = 11.29, 54 % girls). Parenting behavior and affect was observed during a social-evaluative laboratory speech task for youth, and ecological momentary assessment (EMA) methods were used to examine youth emotional reactivity to typical daily negative events within peer and non-peer contexts. Results showed that parent positive behaviors, and low levels of parent anxious affect, during the stressful laboratory task for youth buffered youth negative emotional reactivity to real-world negative peer events, but not non-peer events. Findings inform our understanding of parenting influences on anxious youth's emotional reactivity to developmentally salient negative events during the transition into adolescence.

Psychometric Properties and Validation of the Positive and Negative Suicide Ideation (PANSI) Inventory in an Outpatient Clinical Population in Malaysia.

PubMed

Sinniah, Aishvarya; Oei, Tian P S; Chinna, Karuthan; Shah, Shamsul A; Maniam, T; Subramaniam, Ponnusamy

2015-01-01

The PANSI is a measure designed to assess the risk and protective factors related to suicidal behaviors. The present study evaluated the psychometric properties and factor structure of the Positive and Negative Suicide Ideation (PANSI) Inventory in a sample of clinical outpatients at a major hospital in Malaysia. In this study, 283 psychiatric patients and 200 medical (non-psychiatric) patients participated. All the patients completed the PANSI and seven other self-report instruments. Confirmative factor analysis supported the 2-factor oblique model. The internal consistency of the two subscales of PANSI-Negative and the PANSI-Positive were 0.93 and 0.84, respectively. In testing construct validity, PANSI showed sizable correlation with the other seven scales. Criterion validity was supported by scores on PANSI which differentiated psychiatric patients from medical patients. Logistic regression analyses showed PANSI can be used to classify the patients into suicidal or non-suicidal. The PANSI is a reliable and valid instrument to measure the severity of suicidal ideation among clinical outpatients in Malaysia.

Psychometric Properties and Validation of the Positive and Negative Suicide Ideation (PANSI) Inventory in an Outpatient Clinical Population in Malaysia

PubMed Central

Sinniah, Aishvarya; Oei, Tian P. S.; Chinna, Karuthan; Shah, Shamsul A.; Maniam, T.; Subramaniam, Ponnusamy

2015-01-01

The PANSI is a measure designed to assess the risk and protective factors related to suicidal behaviors. The present study evaluated the psychometric properties and factor structure of the Positive and Negative Suicide Ideation (PANSI) Inventory in a sample of clinical outpatients at a major hospital in Malaysia. In this study, 283 psychiatric patients and 200 medical (non-psychiatric) patients participated. All the patients completed the PANSI and seven other self-report instruments. Confirmative factor analysis supported the 2-factor oblique model. The internal consistency of the two subscales of PANSI-Negative and the PANSI-Positive were 0.93 and 0.84, respectively. In testing construct validity, PANSI showed sizable correlation with the other seven scales. Criterion validity was supported by scores on PANSI which differentiated psychiatric patients from medical patients. Logistic regression analyses showed PANSI can be used to classify the patients into suicidal or non-suicidal. The PANSI is a reliable and valid instrument to measure the severity of suicidal ideation among clinical outpatients in Malaysia. PMID:26733920

Sclerostin as a potential novel biomarker for aortic valve calcification: an in-vivo and ex-vivo study.

PubMed

Koos, Ralf; Brandenburg, Vincent; Mahnken, Andreas Horst; Schneider, Rebekka; Dohmen, Guido; Autschbach, Rüdiger; Marx, Nikolaus; Kramann, Rafael

2013-05-01

Sclerostin is a key negative regulator of bone formation. It was hypothesized that sclerostin might also play a potential role in the development of aortic valve calcification (AVC). The study aim was to evaluate serum sclerostin levels in patients with different degrees of AVC compared to a healthy control group, and to investigate local sclerostin expression in explanted calcified and non-calcified aortic valves. A prospective cross-sectional study was performed in 115 patients (mean age 74 +/- 7 years) with echocardiographically proven AVC. Sclerostin serum levels were measured using ELISA and compared to values obtained from a healthy control population. For quantification of AVC, all patients of the study cohort underwent non-contrast-enhanced dual-source computed tomography (DSCT). Immunohistochemistry (IHC) staining for sclerostin and mRNA sclerostin expression was analyzed in 10 calcified aortic valves and 10 non-calcified age-matched control valves. Patients with AVC showed significantly higher sclerostin serum levels as compared to healthy controls (0.94 +/- 0.45 versus 0.58 +/- 0.26 ng/ml, p < 0.001). A significant correlation between sclerostin serum levels and Agatston AVC scores as assessed by DSCT was observed (r = 0.62, p < 0.001) in the study cohort. IHC revealed positive sclerostin staining in nine calcified valves, in contrast to negative staining for sclerostin in all non-calcified valves. Quantitative real-time PCR confirmed the increased sclerostin expression on mRNA level, with a significant up-regulation of sclerostin mRNA (fold change 150 +/- 52, p < 0.001) expression being shown in calcified aortic valves compared to non-calcified control valves. Co-staining experiments revealed that sclerostin-expressing cells co-express the major osteogenic transcription factor Runx2 and the extracellular matrix protein osteocalcin. Patients with AVC showed increased sclerostin serum levels compared to a healthy reference population, and it was revealed that the severity of AVC may be linked to increased sclerostin serum levels. Moreover, the PCR and staining data demonstrated an increased sclerostin expression in parallel to prototypic markers of osteogenic transdifferentiation, indicating a role of sclerostin in the valvular calcification process.

Contributions of a Child’s Built, Natural, and Social Environments to Their General Cognitive Ability: A Systematic Scoping Review

DOE PAGES

Ruiz, Jazmin Del Carmen; Quackenboss, James J.; Tulve, Nicolle S.; ...

2016-02-03

The etiology of a child’s cognitive ability is complex, with research suggesting that it is not attributed to a single determinant or even a defined period of exposure. Rather, cognitive development is the product of cumulative interactions with the environment, both negative and positive, over the life course. The aim of this systematic scoping review was to collate evidence associated with children’s cognitive health, including inherent factors as well as chemical and non-chemical stressors from the built, natural, and social environments. Three databases were used to identify recent epidemiological studies (2003–2013) that examined exposure factors associated with general cognitive abilitymore » in children. Over 100 factors were evaluated from 258 eligible studies. We found that recent literature mainly assessed the hypothesized negative effects of either inherent factors or chemical exposures present in the physical environment. Prenatal growth, sleep health, lead and water pollutants showed consistent negative effects. Of the few studies that examined social stressors, results consistently showed cognitive development to be influenced by both positive and negative social interactions at home, in school or the community. Among behavioral factors related to diet and lifestyle choices of the mother, breastfeeding was the most studied, showing consistent positive associations with cognitive ability. There were mostly inconsistent results for both chemical and non-chemical stressors. The majority of studies utilized traditional exposure assessments, evaluating chemical and non-chemical stressors separately. Collective evidence from a limited number of studies revealed that cumulative exposure assessment that incorporates multiple chemical and non-chemical stressors over the life course may unravel the variability in effect on cognitive development and help explain the inconsistencies across studies. Here, future research examining the interactions of multiple stressors within a child’s total environment, depicting a more real-world exposure, will aid in understanding the cumulative effects associated with a child’s ability to learn.« less

Contributions of a Child’s Built, Natural, and Social Environments to Their General Cognitive Ability: A Systematic Scoping Review

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

Ruiz, Jazmin Del Carmen; Quackenboss, James J.; Tulve, Nicolle S.

The etiology of a child’s cognitive ability is complex, with research suggesting that it is not attributed to a single determinant or even a defined period of exposure. Rather, cognitive development is the product of cumulative interactions with the environment, both negative and positive, over the life course. The aim of this systematic scoping review was to collate evidence associated with children’s cognitive health, including inherent factors as well as chemical and non-chemical stressors from the built, natural, and social environments. Three databases were used to identify recent epidemiological studies (2003–2013) that examined exposure factors associated with general cognitive abilitymore » in children. Over 100 factors were evaluated from 258 eligible studies. We found that recent literature mainly assessed the hypothesized negative effects of either inherent factors or chemical exposures present in the physical environment. Prenatal growth, sleep health, lead and water pollutants showed consistent negative effects. Of the few studies that examined social stressors, results consistently showed cognitive development to be influenced by both positive and negative social interactions at home, in school or the community. Among behavioral factors related to diet and lifestyle choices of the mother, breastfeeding was the most studied, showing consistent positive associations with cognitive ability. There were mostly inconsistent results for both chemical and non-chemical stressors. The majority of studies utilized traditional exposure assessments, evaluating chemical and non-chemical stressors separately. Collective evidence from a limited number of studies revealed that cumulative exposure assessment that incorporates multiple chemical and non-chemical stressors over the life course may unravel the variability in effect on cognitive development and help explain the inconsistencies across studies. Here, future research examining the interactions of multiple stressors within a child’s total environment, depicting a more real-world exposure, will aid in understanding the cumulative effects associated with a child’s ability to learn.« less

Contributions of a Child’s Built, Natural, and Social Environments to Their General Cognitive Ability: A Systematic Scoping Review

PubMed Central

Ruiz, Jazmin Del Carmen; Quackenboss, James J.; Tulve, Nicolle S.

2016-01-01

The etiology of a child’s cognitive ability is complex, with research suggesting that it is not attributed to a single determinant or even a defined period of exposure. Rather, cognitive development is the product of cumulative interactions with the environment, both negative and positive, over the life course. The aim of this systematic scoping review was to collate evidence associated with children’s cognitive health, including inherent factors as well as chemical and non-chemical stressors from the built, natural, and social environments. Three databases were used to identify recent epidemiological studies (2003–2013) that examined exposure factors associated with general cognitive ability in children. Over 100 factors were evaluated from 258 eligible studies. We found that recent literature mainly assessed the hypothesized negative effects of either inherent factors or chemical exposures present in the physical environment. Prenatal growth, sleep health, lead and water pollutants showed consistent negative effects. Of the few studies that examined social stressors, results consistently showed cognitive development to be influenced by both positive and negative social interactions at home, in school or the community. Among behavioral factors related to diet and lifestyle choices of the mother, breastfeeding was the most studied, showing consistent positive associations with cognitive ability. There were mostly inconsistent results for both chemical and non-chemical stressors. The majority of studies utilized traditional exposure assessments, evaluating chemical and non-chemical stressors separately. Collective evidence from a limited number of studies revealed that cumulative exposure assessment that incorporates multiple chemical and non-chemical stressors over the life course may unravel the variability in effect on cognitive development and help explain the inconsistencies across studies. Future research examining the interactions of multiple stressors within a child’s total environment, depicting a more real-world exposure, will aid in understanding the cumulative effects associated with a child’s ability to learn. PMID:26840411

Evaluation of Shape and Textural Features from CT as Prognostic Biomarkers in Non-small Cell Lung Cancer.

PubMed

Bianconi, Francesco; Fravolini, Mario Luca; Bello-Cerezo, Raquel; Minestrini, Matteo; Scialpi, Michele; Palumbo, Barbara

2018-04-01

We retrospectively investigated the prognostic potential (correlation with overall survival) of 9 shape and 21 textural features from non-contrast-enhanced computed tomography (CT) in patients with non-small-cell lung cancer. We considered a public dataset of 203 individuals with inoperable, histologically- or cytologically-confirmed NSCLC. Three-dimensional shape and textural features from CT were computed using proprietary code and their prognostic potential evaluated through four different statistical protocols. Volume and grey-level run length matrix (GLRLM) run length non-uniformity were the only two features to pass all four protocols. Both features correlated negatively with overall survival. The results also showed a strong dependence on the evaluation protocol used. Tumour volume and GLRLM run-length non-uniformity from CT were the best predictor of survival in patients with non-small-cell lung cancer. We did not find enough evidence to claim a relationship with survival for the other features. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Soluble Factors from Biofilms of Wound Pathogens Modulate Human Bone Marrow-derived Stromal Cell Differentiation, Migration, Angiogenesis, and Cytokine Secretion

DTIC Science & Technology

2015-03-28

Becerra, Christopher R Rathbone and Joseph C Wenke Abstract Background: Chronic, non- healing wounds are often characterized by the persistence of bacteria...within biofilms - aggregations of cells encased within a self -produced polysaccharide matrix. Biofilm bacteria exhibit unique characteristics from...modulation of host-immune responses by secreting factors that promote wound healing . While these characteristics make MSCs an attractive therapeutic

Classification Techniques for Multivariate Data Analysis.

DTIC Science & Technology

1980-03-28

analysis among biologists, botanists, and ecologists, while some social scientists may refer "typology". Other frequently encountered terms are pattern...the determinantal equation: lB -XW 0 (42) 49 The solutions X. are the eigenvalues of the matrix W-1 B 1 as in discriminant analysis. There are t non...Statistical Package for Social Sciences (SPSS) (14) subprogram FACTOR was used for the principal components analysis. It is designed both for the factor

Modulation of Stem Cell Differentiation and Myostatin as an Approach to Counteract Fibrosis in Muscle Dystrophy and Regeneration after Injury

DTIC Science & Technology

2011-03-01

Duchenne muscular dystrophy (DMD). To examine whether counteracting myostatin, a negative regulator of muscle mass and a pro-lipofibrotic factor...extracellular matrix, and fat, characterizes muscle dystrophy , and in particular Duchenne muscular dystrophy (DMD) (1,2), as seen also in its animal model...stem cells (MDSC) into myogenic as opposed to lipofibrogenic lineages is a promising therapeutic strategy for Duchenne muscular dystrophy (DMD). To

EGFR-Dependent Regulation of Matrix-Independent Epithelial Cell Survival. Addendum

DTIC Science & Technology

2007-04-01

of the original proposal. The results obtained have identified key players that coordinate keratinocyte survival dependent on soluble growth factors...2004;6:203–8. 4. Duffey DC, Chen Z, Dong G, et al. Expression of a dominant-negative mutant inhibitor- nBa of nuclear fac- tor-nB in human head and neck...Attempts to treat such tumors with EGFR antagonists have met with remarkable initial successes , particularly when EGFR antagonists were used in

Gender differences in negative affect during acute tobacco abstinence differ between African American and White adult cigarette smokers.

PubMed

Pang, Raina D; Bello, Mariel S; Liautaud, Madalyn M; Weinberger, Andrea H; Leventhal, Adam M

2018-06-15

Prior studies have found heightened negative affect following tobacco abstinence in women compared to men. However, experimental work addressing whether these findings generalize across racial groups is scarce. The current study investigated whether race (Non-Hispanic White vs. Non-Hispanic African American) moderated gender differences in abstinence-induced negative affect and smoking behavior. Data were collected from 2010 to 2017 from two separate laboratory studies investigating experimentally manipulated tobacco abstinence. Following a baseline session, adult daily smokers (10 cigarettes per day; women: n=297, 83.8% Non-Hispanic African American; men: n=492, 86.2% Non-Hispanic African American) attended two counterbalanced lab sessions (16 hours abstinent vs. non-abstinent) and completed self-report measures of negative affect followed by a laboratory analogue smoking reinstatement task. We found a gender race interaction for several negative affect states and composite negative affect (ßs=-.12 to -.16, ps<.05). Analyses stratified by race showed that Non-Hispanic White women compared to Non-Hispanic White men exhibited greater abstinence-induced increases in anger, anxiety, and composite negative affect (ßs=-.20 to -.29, ps<.05). No significant gender differences in abstinence-induced negative affect were found for Non-Hispanic African American smokers (ßs=.00 to -.04, ps>.05). These findings suggest that negative affect during acute tobacco abstinence may be a clinically important and intervenable factor that can inform cessation interventions specifically for Non-Hispanic White women smokers. Further empirical exploration of mechanisms underlying interactions of gender and race in tobacco addiction may benefit smoking cessation efforts in Non-Hispanic African American women smokers. The current study contributes to a scant body of research examining the intersectional influence of race and gender on abstinence-induced negative affect-a central, motivationally prepotent feature of tobacco withdrawal. Using a laboratory-based design to experimentally manipulate abstinence, we provide evidence of a gender race interaction on negative affect-related withdrawal. Our findings suggest that gender differences in abstinence-induced negative affect observed among Non-Hispanic White smokers may not generalize to Non-Hispanic African American smokers, highlighting the need for future work to address potential mechanisms underlying the racially discrepant impact of gender on affective tobacco withdrawal.

Understanding Antipsychotic Drug Treatment Effects: A Novel Method to Reduce Pseudospecificity of the Positive and Negative Syndrome Scale (PANSS) Factors.

PubMed

Hopkins, Seth C; Ogirala, Ajay; Loebel, Antony; Koblan, Kenneth S

2017-12-01

The Positive and Negative Syndrome Scale (PANSS) is the most widely used efficacy measure in acute treatment studies of schizophrenia. However, interpretation of the efficacy of antipsychotics in improving specific symptom domains is confounded by moderate-to-high correlations among standard (Marder) PANSS factors. The authors review the results of an uncorrelated PANSS score matrix (UPSM) transform designed to reduce pseudospecificity in assessment of symptom change in patients with schizophrenia. Based on a factor analysis of five pooled, placebo-controlled lurasidone clinical trials (N=1,710 patients), a UPSM transform was identified that generated PANSS factors with high face validity (good correlation with standard Marder PANSS factors), and high specificity/orthogonality (low levels of between-factor correlation measuring change during treatment). Between-factor correlations were low at baseline for both standard (Marder) PANSS factors and transformed PANSS factors. However, when measured change in symptom severity was measured during treatment (in a pooled 5-study analysis), there was a notable difference for standard PANSS factors, where changes across factors were found to be highly correlated (factors exhibited pseudospecificity), compared to transformed PANSS factors, where factor change scores exhibited the same low levels of between-factor correlation observed at baseline. At Week 6-endpoint, correlations among PANSS factor severity scores were moderate-to-high for standard factors (0.34-0.68), but continued to be low for the transformed factors (-0.22-0.20). As an additional validity check, we analyzed data from one of the original five pooled clinical trials that included other well-validated assessment scales (MADRS, Negative Symptom Assessment scale [NSA]). In this baseline analysis, UPSM-transformed PANSS factor severity scores (negative and depression factors) were found to correlate well with the MADRS and NSA. The availability of transformed PANSS factors with a high degree of orthogonality/specificity, but which retain a high degree of concurrent and face validity, can reduce pseudospecificity as a measurement confound, and should facilitate the drug development process, permitting a more accurate characterization of the efficacy of putative new agents in targeting specific symptom domains in patients with psychotic illness.

Both gas chromatography and an electronic nose reflect chemical polymorphism of juniper shrubs browsed or avoided by sheep.

PubMed

Markó, Gábor; Novák, Ildikó; Bernáth, Jeno; Altbäcker, Vilmos

2011-07-01

Chemical polymorphism may contribute to variation in browsing damage by mammalian herbivores. Earlier, we demonstrated that essential oil concentration in juniper, Juniperus communis, was negatively associated with herbivore browsing. The aim of the present study was to characterize the volatile chemical composition of browsed and non-browsed J. communis. By using either gas chromatography with flame ionization detection (GC-FID) or an electronic nose device, we could separate sheep-browsed or non-browsed juniper shrubs by their essential oil pattern and complex odor matrix. The main components of the essential oil from J. communis were monoterpenes. We distinguished three chemotypes, dominated either by α-pinene, sabinene, or δ-3-carene. Shrubs belonging to the α-pinene- or sabinene-dominated groups were browsed, whereas all individuals with the δ-3-carene chemotype were unused by the local herbivores. The electronic nose also separated the browsed and non-browsed shrubs indicating that their odor matrix could guide sheep browsing. Responses of sheep could integrate the post-ingestive effects of plant secondary metabolites with sensory experience that stems from odor-phytotoxin interactions. Chemotype diversity could increase the survival rate in the present population of J. communis as certain shrubs could benefit from relatively better chemical protection against the herbivores.

Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours

PubMed Central

2012-01-01

Background In-vivo single voxel proton magnetic resonance spectroscopy (SV 1H-MRS), coupled with supervised pattern recognition (PR) methods, has been widely used in clinical studies of discrimination of brain tumour types and follow-up of patients bearing abnormal brain masses. SV 1H-MRS provides useful biochemical information about the metabolic state of tumours and can be performed at short (< 45 ms) or long (> 45 ms) echo time (TE), each with particular advantages. Short-TE spectra are more adequate for detecting lipids, while the long-TE provides a much flatter signal baseline in between peaks but also negative signals for metabolites such as lactate. Both, lipids and lactate, are respectively indicative of specific metabolic processes taking place. Ideally, the information provided by both TE should be of use for clinical purposes. In this study, we characterise the performance of a range of Non-negative Matrix Factorisation (NMF) methods in two respects: first, to derive sources correlated with the mean spectra of known tissue types (tumours and normal tissue); second, taking the best performing NMF method for source separation, we compare its accuracy for class assignment when using the mixing matrix directly as a basis for classification, as against using the method for dimensionality reduction (DR). For this, we used SV 1H-MRS data with positive and negative peaks, from a widely tested SV 1H-MRS human brain tumour database. Results The results reported in this paper reveal the advantage of using a recently described variant of NMF, namely Convex-NMF, as an unsupervised method of source extraction from SV1H-MRS. Most of the sources extracted in our experiments closely correspond to the mean spectra of some of the analysed tumour types. This similarity allows accurate diagnostic predictions to be made both in fully unsupervised mode and using Convex-NMF as a DR step previous to standard supervised classification. The obtained results are comparable to, or more accurate than those obtained with supervised techniques. Conclusions The unsupervised properties of Convex-NMF place this approach one step ahead of classical label-requiring supervised methods for the discrimination of brain tumour types, as it accounts for their increasingly recognised molecular subtype heterogeneity. The application of Convex-NMF in computer assisted decision support systems is expected to facilitate further improvements in the uptake of MRS-derived information by clinicians. PMID:22401579

Factors associated with smoking in Asian American adults: a systematic review.

PubMed

Zhang, Jing; Wang, Zhongmiao

2008-05-01

This review systematically examined the factors associated with smoking in Asian American adults (aged > or =17 years). A total of 21 quantitative studies published in peer-reviewed journals from 1997 to 2006 were reviewed and abstracted using the matrix method. Statistically significant factors reported by the studies were summarized. Methodological quality of the studies also was assessed (maximum possible score = 10). Acculturation and education were the most frequently reported factors (n = 10, 47.6%). Acculturation was negatively associated with men's smoking but was positively associated with women's smoking. Education was uniformly found to be negatively related to smoking. Age was reported to have either a positive or a negative relationship with smoking (n = 9, 42.9%). Men were more likely to smoke than women (n = 7, 33.3%). The mean methodological score of the reviewed studies was 4.14 (on a scale of 1-10 points; SD = 1.62; range = 2-8). Health promotion professionals need to consider the summarized factors associated with Asian American adults' smoking behavior when planning smoking prevention programs and when recruiting participants for smoking cessation programs. When addressing acculturation, program planners should design different health education materials and use different strategies for men and women. To identify, understand, and incorporate essential factors into effective interventions, future studies should aim at higher methodological quality by using longitudinal design and increasing the use of theory, the test of data validity and reliability, and the report of effect sizes.

Canonical form of master equations and characterization of non-Markovianity

NASA Astrophysics Data System (ADS)

Hall, Michael J. W.; Cresser, James D.; Li, Li; Andersson, Erika

2014-04-01

Master equations govern the time evolution of a quantum system interacting with an environment, and may be written in a variety of forms. Time-independent or memoryless master equations, in particular, can be cast in the well-known Lindblad form. Any time-local master equation, Markovian or non-Markovian, may in fact also be written in a Lindblad-like form. A diagonalization procedure results in a unique, and in this sense canonical, representation of the equation, which may be used to fully characterize the non-Markovianity of the time evolution. Recently, several different measures of non-Markovianity have been presented which reflect, to varying degrees, the appearance of negative decoherence rates in the Lindblad-like form of the master equation. We therefore propose using the negative decoherence rates themselves, as they appear in the canonical form of the master equation, to completely characterize non-Markovianity. The advantages of this are especially apparent when more than one decoherence channel is present. We show that a measure proposed by Rivas et al. [Phys. Rev. Lett. 105, 050403 (2010), 10.1103/PhysRevLett.105.050403] is a surprisingly simple function of the canonical decoherence rates, and give an example of a master equation that is non-Markovian for all times t >0, but to which nearly all proposed measures are blind. We also give necessary and sufficient conditions for trace distance and volume measures to witness non-Markovianity, in terms of the Bloch damping matrix.

Trade-Off Analysis between Concerns Based on Aspect-Oriented Requirements Engineering

NASA Astrophysics Data System (ADS)

Laurito, Abelyn Methanie R.; Takada, Shingo

The identification of functional and non-functional concerns is an important activity during requirements analysis. However, there may be conflicts between the identified concerns, and they must be discovered and resolved through trade-off analysis. Aspect-Oriented Requirements Engineering (AORE) has trade-off analysis as one of its goals, but most AORE approaches do not actually offer support for trade-off analysis; they focus on describing concerns and generating their composition. This paper proposes an approach for trade-off analysis based on AORE using use cases and the Requirements Conflict Matrix (RCM) to represent compositions. RCM shows the positive or negative effect of non-functional concerns over use cases and other non-functional concerns. Our approach is implemented within a tool called E-UCEd (Extended Use Case Editor). We also show the results of evaluating our tool.

Heterologous expression of Streptococcus mutans Cnm in Lactococcus lactis promotes intracellular invasion, adhesion to human cardiac tissues and virulence.

PubMed

Freires, Irlan A; Avilés-Reyes, Alejandro; Kitten, Todd; Simpson-Haidaris, P J; Swartz, Michael; Knight, Peter A; Rosalen, Pedro L; Lemos, José A; Abranches, Jacqueline

2017-01-02

In S. mutans, the expression of the surface glycoprotein Cnm mediates binding to extracellular matrix proteins, endothelial cell invasion and virulence in the Galleria mellonella invertebrate model. To further characterize Cnm as a virulence factor, the cnm gene from S. mutans strain OMZ175 was expressed in the non-pathogenic Lactococcus lactis NZ9800 using a nisin-inducible system. Despite the absence of the machinery necessary for Cnm glycosylation, Western blot and immunofluorescence microscopy analyses demonstrated that Cnm was effectively expressed and translocated to the cell wall of L. lactis. Similar to S. mutans, expression of Cnm in L. lactis enabled robust binding to collagen and laminin, invasion of human coronary artery endothelial cells and increased virulence in G. mellonella. Using an ex vivo human heart tissue colonization model, we showed that Cnm-positive strains of either S. mutans or L. lactis outcompete their Cnm-negative counterparts for tissue colonization. Finally, Cnm expression facilitated L. lactis adhesion and colonization in a rabbit model of infective endocarditis. Collectively, our results provide unequivocal evidence that binding to extracellular matrices mediated by Cnm is an important virulence attribute of S. mutans and confirm the usefulness of the L. lactis heterologous system for further characterization of bacterial virulence factors.

Gestational Age is Dimensionally Associated with Structural Brain Network Abnormalities Across Development.

PubMed

Nassar, Rula; Kaczkurkin, Antonia N; Xia, Cedric Huchuan; Sotiras, Aristeidis; Pehlivanova, Marieta; Moore, Tyler M; Garcia de La Garza, Angel; Roalf, David R; Rosen, Adon F G; Lorch, Scott A; Ruparel, Kosha; Shinohara, Russell T; Davatzikos, Christos; Gur, Ruben C; Gur, Raquel E; Satterthwaite, Theodore D

2018-04-21

Prematurity is associated with diverse developmental abnormalities, yet few studies relate cognitive and neurostructural deficits to a dimensional measure of prematurity. Leveraging a large sample of children, adolescents, and young adults (age 8-22 years) studied as part of the Philadelphia Neurodevelopmental Cohort, we examined how variation in gestational age impacted cognition and brain structure later in development. Participants included 72 preterm youth born before 37 weeks' gestation and 206 youth who were born at term (37 weeks or later). Using a previously-validated factor analysis, cognitive performance was assessed in three domains: (1) executive function and complex reasoning, (2) social cognition, and (3) episodic memory. All participants completed T1-weighted neuroimaging at 3 T to measure brain volume. Structural covariance networks were delineated using non-negative matrix factorization, an advanced multivariate analysis technique. Lower gestational age was associated with both deficits in executive function and reduced volume within 11 of 26 structural covariance networks, which included orbitofrontal, temporal, and parietal cortices as well as subcortical regions including the hippocampus. Notably, the relationship between lower gestational age and executive dysfunction was accounted for in part by structural network deficits. Together, these findings emphasize the durable impact of prematurity on cognition and brain structure, which persists across development.

Isolated effects of external bath osmolality, solute concentration, and electrical charge on solute transport across articular cartilage.

PubMed

Pouran, Behdad; Arbabi, Vahid; Zadpoor, Amir A; Weinans, Harrie

2016-12-01

The metabolic function of cartilage primarily depends on transport of solutes through diffusion mechanism. In the current study, we use contrast enhanced micro-computed tomography to determine equilibrium concentration of solutes through different cartilage zones and solute flux in the cartilage, using osteochondral plugs from equine femoral condyles. Diffusion experiments were performed with two solutes of different charge and approximately equal molecular weight, namely iodixanol (neutral) and ioxaglate (charge=-1) in order to isolate the effects of solute's charge on diffusion. Furthermore, solute concentrations as well as bath osmolality were changed to isolate the effects of steric hindrance on diffusion. Bath concentration and bath osmolality only had minor effects on the diffusion of the neutral solute through cartilage at the surface, middle and deep zones, indicating that the diffusion of the neutral solute was mainly Fickian. The negatively charged solute diffused considerably slower through cartilage than the neutral solute, indicating a large non-Fickian contribution in the diffusion of charged molecules. The numerical models determined maximum solute flux in the superficial zone up to a factor of 2.5 lower for the negatively charged solutes (charge=-1) as compared to the neutral solutes confirming the importance of charge-matrix interaction in diffusion of molecules across cartilage. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

VIP: Vortex Image Processing Package for High-contrast Direct Imaging

NASA Astrophysics Data System (ADS)

Gomez Gonzalez, Carlos Alberto; Wertz, Olivier; Absil, Olivier; Christiaens, Valentin; Defrère, Denis; Mawet, Dimitri; Milli, Julien; Absil, Pierre-Antoine; Van Droogenbroeck, Marc; Cantalloube, Faustine; Hinz, Philip M.; Skemer, Andrew J.; Karlsson, Mikael; Surdej, Jean

2017-07-01

We present the Vortex Image Processing (VIP) library, a python package dedicated to astronomical high-contrast imaging. Our package relies on the extensive python stack of scientific libraries and aims to provide a flexible framework for high-contrast data and image processing. In this paper, we describe the capabilities of VIP related to processing image sequences acquired using the angular differential imaging (ADI) observing technique. VIP implements functionalities for building high-contrast data processing pipelines, encompassing pre- and post-processing algorithms, potential source position and flux estimation, and sensitivity curve generation. Among the reference point-spread function subtraction techniques for ADI post-processing, VIP includes several flavors of principal component analysis (PCA) based algorithms, such as annular PCA and incremental PCA algorithms capable of processing big datacubes (of several gigabytes) on a computer with limited memory. Also, we present a novel ADI algorithm based on non-negative matrix factorization, which comes from the same family of low-rank matrix approximations as PCA and provides fairly similar results. We showcase the ADI capabilities of the VIP library using a deep sequence on HR 8799 taken with the LBTI/LMIRCam and its recently commissioned L-band vortex coronagraph. Using VIP, we investigated the presence of additional companions around HR 8799 and did not find any significant additional point source beyond the four known planets. VIP is available at http://github.com/vortex-exoplanet/VIP and is accompanied with Jupyter notebook tutorials illustrating the main functionalities of the library.

New insights into the roles of matrix metalloproteinases in colorectal cancer development and progression.

PubMed

Leeman, Matthew F; Curran, Stephanie; Murray, Graeme I

2003-12-01

This review outlines new concepts that are emerging for the functions of matrix metalloproteinases in colorectal cancer development and progression. The two main concepts that will be discussed are the role of matrix metalloproteinases in the early stages of colorectal tumour development and the functional mechanisms by which matrix metalloproteinases contribute to colorectal tumour invasion and metastasis. The matrix metalloproteinases are a group of enzymes, which have been best characterized for their ability to degrade extracellular matrix proteins and thus they have been extensively studied in tumour invasion. It is now becoming recognized that the matrix metalloproteinases have key roles in a variety of biological processes that are distinct from their well-defined role in matrix degradation. This group of enzymes has been shown to interact with a broad range of non-matrix proteins including growth factors and their receptors, mediators of apoptosis, and cell adhesion molecules. The elucidation of novel biological roles for the matrix metalloproteinases also challenges the current predominant concept of matrix metalloproteinases as enzymes only involved in matrix degradation. Recent studies have shown that several matrix metalloproteinases, especially matrilysin (MMP-7), interact with the specific molecular genetic and signalling pathways involved in colorectal cancer development. In particular, matrilysin is activated at an early stage of colorectal tumourigenesis by the beta-catenin signalling pathway. Furthermore, studies are now elucidating specific mechanisms by which individual matrix metalloproteinases, especially membrane-type matrix metalloproteinases, interact with specific cell adhesion molecules and cytoskeletal proteins and thus contribute dynamically to colorectal tumour invasion. Copyright 2003 John Wiley & Sons, Ltd.

Niche Extracellular Matrix Components and Their Influence on HSC.

PubMed

Domingues, Mélanie J; Cao, Huimin; Heazlewood, Shen Y; Cao, Benjamin; Nilsson, Susan K

2017-08-01

Maintenance of hematopoietic stem cells (HSC) takes place in a highly specialized microenvironment within the bone marrow. Technological improvements, especially in the field of in vivo imaging, have helped unravel the complexity of the niche microenvironment and have completely changed the classical concept from what was previously believed to be a static supportive platform, to a dynamic microenvironment tightly regulating HSC homeostasis through the complex interplay between diverse cell types, secreted factors, extracellular matrix molecules, and the expression of different transmembrane receptors. To add to the complexity, non-protein based metabolites have also been recognized as a component of the bone marrow niche. The objective of this review is to discuss the current understanding on how the different extracellular matrix components of the niche regulate HSC fate, both during embryonic development and in adulthood. Special attention will be provided to the description of non-protein metabolites, such as lipids and metal ions, which contribute to the regulation of HSC behavior. J. Cell. Biochem. 118: 1984-1993, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The use of type 1 collagen scaffold containing stromal cell-derived factor-1 to create a matrix environment conducive to partial-thickness cartilage defects repair.

PubMed

Zhang, Wei; Chen, Jialin; Tao, Jiadong; Jiang, Yangzi; Hu, Changchang; Huang, Lu; Ji, Junfeng; Ouyang, Hong Wei

2013-01-01

Despite the presence of cartilage-derived mesenchymal stem cells (C-MSCs) and synovial membrane-derived mesenchymal stem cells (SM-MSCs) populations, partial-thickness cartilage defects, in contrast to the full-thickness defects, are devoid of spontaneous repair capacity. This study aims to create an in situ matrix environment conducive to C-MSCs and SM-MSCs to promote cartilage self-repair. Spontaneous repair with MSCs migration into the defect area was observed in full-thickness defects, but not in partial-thickness defects in rabbit model. Ex vivo and in vitro studies showed that subchondral bone or type 1 collagen (col1) scaffold was more permissive for MSCs adhesion than cartilage or type 2 collagen (col2) scaffold and induced robust stromal cell-derived factors-1 (SDF-1) dependent migration of MSCs. Furthermore, creating a matrix environment with col1 scaffold containing SDF-1 enhanced in situ self-repair of partial-thickness defects in rabbit 6 weeks post-injury. Hence, the inferior self-repair capacity in partial-thickness defects is partially owing to the non-permissive matrix environment. Creating an in situ matrix environment conducive to C-MSCs and SM-MSCs migration and adhesion with col1 scaffold containing SDF-1 can be exploited to improve self-repair capacity of cartilage. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bilinear Factor Matrix Norm Minimization for Robust PCA: Algorithms and Applications.

PubMed

Shang, Fanhua; Cheng, James; Liu, Yuanyuan; Luo, Zhi-Quan; Lin, Zhouchen

2017-09-04

The heavy-tailed distributions of corrupted outliers and singular values of all channels in low-level vision have proven effective priors for many applications such as background modeling, photometric stereo and image alignment. And they can be well modeled by a hyper-Laplacian. However, the use of such distributions generally leads to challenging non-convex, non-smooth and non-Lipschitz problems, and makes existing algorithms very slow for large-scale applications. Together with the analytic solutions to Lp-norm minimization with two specific values of p, i.e., p=1/2 and p=2/3, we propose two novel bilinear factor matrix norm minimization models for robust principal component analysis. We first define the double nuclear norm and Frobenius/nuclear hybrid norm penalties, and then prove that they are in essence the Schatten-1/2 and 2/3 quasi-norms, respectively, which lead to much more tractable and scalable Lipschitz optimization problems. Our experimental analysis shows that both our methods yield more accurate solutions than original Schatten quasi-norm minimization, even when the number of observations is very limited. Finally, we apply our penalties to various low-level vision problems, e.g. moving object detection, image alignment and inpainting, and show that our methods usually outperform the state-of-the-art methods.

The etiology of the association between child antisocial behavior and maternal negativity varies across aggressive and non-aggressive rule-breaking forms of antisocial behavior

PubMed Central

Klahr, Ashlea M.; Klump, Kelly L.; Burt, S. Alexandra

2014-01-01

There is a robust association between negative parenting and child antisocial behavior problems. However, the etiology of this association remains unclear. Extant literature has reported strikingly different conclusions across studies, with some highlighting genetic mediation and others highlighting environmental mediation. One possible reason for these discrepancies across studies may be the failure to differentiate between aggressive and non-aggressive (rule-breaking) dimensions of childhood antisocial behavior, given their notably different etiologies and developmental trajectories (Burt, 2012). The current study sought to examine the phenotypic and etiologic associations of maternal negativity with aggressive and rule-breaking antisocial behavior, respectively. Participants included 824 mothers and their twin children between the ages of 6 and 10. Our results highlighted clear etiologic distinctions in the associations of aggression and rule-breaking with maternal negativity. Aggression was associated with maternal negativity via both genetic and environmental factors, whereas the association between non-aggressive rule-breaking and maternal negativity was entirely environmental in origin. These findings provide additional support for the presence of meaningful distinctions between aggressive and non-aggressive forms of antisocial behavior, and highlight the complex relationship between parenting and child outcome. PMID:24906982

Separating OR, SUM, and XOR Circuits☆

PubMed Central

Find, Magnus; Göös, Mika; Järvisalo, Matti; Kaski, Petteri; Koivisto, Mikko; Korhonen, Janne H.

2017-01-01

Given a boolean n × n matrix A we consider arithmetic circuits for computing the transformation x ↦ Ax over different semirings. Namely, we study three circuit models: monotone OR-circuits, monotone SUM-circuits (addition of non-negative integers), and non-monotone XOR-circuits (addition modulo 2). Our focus is on separating OR-circuits from the two other models in terms of circuit complexity: We show how to obtain matrices that admit OR-circuits of size O(n), but require SUM-circuits of size Ω(n3/2/log2n).We consider the task of rewriting a given OR-circuit as a XOR-circuit and prove that any subquadratic-time algorithm for this task violates the strong exponential time hypothesis. PMID:28529379

Physical, Spatial, and Molecular Aspects of Extracellular Matrix of In Vivo Niches and Artificial Scaffolds Relevant to Stem Cells Research

PubMed Central

Akhmanova, Maria; Osidak, Egor; Domogatsky, Sergey; Rodin, Sergey; Domogatskaya, Anna

2015-01-01

Extracellular matrix can influence stem cell choices, such as self-renewal, quiescence, migration, proliferation, phenotype maintenance, differentiation, or apoptosis. Three aspects of extracellular matrix were extensively studied during the last decade: physical properties, spatial presentation of adhesive epitopes, and molecular complexity. Over 15 different parameters have been shown to influence stem cell choices. Physical aspects include stiffness (or elasticity), viscoelasticity, pore size, porosity, amplitude and frequency of static and dynamic deformations applied to the matrix. Spatial aspects include scaffold dimensionality (2D or 3D) and thickness; cell polarity; area, shape, and microscale topography of cell adhesion surface; epitope concentration, epitope clustering characteristics (number of epitopes per cluster, spacing between epitopes within cluster, spacing between separate clusters, cluster patterns, and level of disorder in epitope arrangement), and nanotopography. Biochemical characteristics of natural extracellular matrix molecules regard diversity and structural complexity of matrix molecules, affinity and specificity of epitope interaction with cell receptors, role of non-affinity domains, complexity of supramolecular organization, and co-signaling by growth factors or matrix epitopes. Synergy between several matrix aspects enables stem cells to retain their function in vivo and may be a key to generation of long-term, robust, and effective in vitro stem cell culture systems. PMID:26351461

The ADRA2B gene in the production of false memories for affective information in healthy female volunteers.

PubMed

Fairfield, Beth; Mammarella, Nicola; Di Domenico, Alberto; D'Aurora, Marco; Stuppia, Liborio; Gatta, Valentina

2017-08-30

False memories are common memory distortions in everyday life and seem to increase with affectively connoted complex information. In line with recent studies showing a significant interaction between the noradrenergic system and emotional memory, we investigated whether healthy volunteer carriers of the deletion variant of the ADRA2B gene that codes for the α2b-adrenergic receptor are more prone to false memories than non-carriers. In this study, we collected genotype data from 212 healthy female volunteers; 91 ADRA2B carriers and 121 non-carriers. To assess gene effects on false memories for affective information, factorial mixed model analysis of variances (ANOVAs) were conducted with genotype as the between-subjects factor and type of memory error as the within-subjects factor. We found that although carriers and non-carriers made comparable numbers of false memory errors, they showed differences in the direction of valence biases, especially for inferential causal errors. Specifically, carriers produced fewer causal false memory errors for scripts with a negative outcome, whereas non-carriers showed a more general emotional effect and made fewer causal errors with both positive and negative outcomes. These findings suggest that putatively higher levels of noradrenaline in deletion carriers may enhance short-term consolidation of negative information and lead to fewer memory distortions when facing negative events. Copyright © 2017 Elsevier B.V. All rights reserved.

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

FISSA: A neuropil decontamination toolbox for calcium imaging signals.

PubMed

Keemink, Sander W; Lowe, Scott C; Pakan, Janelle M P; Dylda, Evelyn; van Rossum, Mark C W; Rochefort, Nathalie L

2018-02-22

In vivo calcium imaging has become a method of choice to image neuronal population activity throughout the nervous system. These experiments generate large sequences of images. Their analysis is computationally intensive and typically involves motion correction, image segmentation into regions of interest (ROIs), and extraction of fluorescence traces from each ROI. Out of focus fluorescence from surrounding neuropil and other cells can strongly contaminate the signal assigned to a given ROI. In this study, we introduce the FISSA toolbox (Fast Image Signal Separation Analysis) for neuropil decontamination. Given pre-defined ROIs, the FISSA toolbox automatically extracts the surrounding local neuropil and performs blind-source separation with non-negative matrix factorization. Using both simulated and in vivo data, we show that this toolbox performs similarly or better than existing published methods. FISSA requires only little RAM, and allows for fast processing of large datasets even on a standard laptop. The FISSA toolbox is available in Python, with an option for MATLAB format outputs, and can easily be integrated into existing workflows. It is available from Github and the standard Python repositories.

Multispectral analysis tools can increase utility of RGB color images in histology

NASA Astrophysics Data System (ADS)

Fereidouni, Farzad; Griffin, Croix; Todd, Austin; Levenson, Richard

2018-04-01

Multispectral imaging (MSI) is increasingly finding application in the study and characterization of biological specimens. However, the methods typically used come with challenges on both the acquisition and the analysis front. MSI can be slow and photon-inefficient, leading to long imaging times and possible phototoxicity and photobleaching. The resulting datasets can be large and complex, prompting the development of a number of mathematical approaches for segmentation and signal unmixing. We show that under certain circumstances, just three spectral channels provided by standard color cameras, coupled with multispectral analysis tools, including a more recent spectral phasor approach, can efficiently provide useful insights. These findings are supported with a mathematical model relating spectral bandwidth and spectral channel number to achievable spectral accuracy. The utility of 3-band RGB and MSI analysis tools are demonstrated on images acquired using brightfield and fluorescence techniques, as well as a novel microscopy approach employing UV-surface excitation. Supervised linear unmixing, automated non-negative matrix factorization and phasor analysis tools all provide useful results, with phasors generating particularly helpful spectral display plots for sample exploration.

Methods for biological data integration: perspectives and challenges

PubMed Central

Gligorijević, Vladimir; Pržulj, Nataša

2015-01-01

Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

ShiftNMFk 1.2

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

Alexandrov, Boian S.; Vesselinov, Velimir V.; Stanev, Valentin

The ShiftNMFk1.2 code, or as we call it, GreenNMFk, represents a hybrid algorithm combining unsupervised adaptive machine learning and Green's function inverse method. GreenNMFk allows an efficient and high performance de-mixing and feature extraction of a multitude of nonnegative signals that change their shape propagating through the medium. The signals are mixed and recorded by a network of uncorrelated sensors. The code couples Non-negative Matrix Factorization (NMF) and inverse-analysis Green's functions method. GreenNMF synergistically performs decomposition of the recorded mixtures, finds the number of the unknown sources and uses the Green's function of the governing partial differential equation to identifymore » the unknown sources and their charecteristics. GreenNMF can be applied directly to any problem controlled by a known partial-differential parabolic equation where mixtures of an unknown number of sources are measured at multiple locations. Full GreenNMFk method is a subject LANL U.S. Patent application S133364.000 August, 2017. The ShiftNMFk 1.2 version here is a toy version of this method that can work with a limited number of unknown sources (4 or less).« less

Wavelet-based unsupervised learning method for electrocardiogram suppression in surface electromyograms.

PubMed

Niegowski, Maciej; Zivanovic, Miroslav

2016-03-01

We present a novel approach aimed at removing electrocardiogram (ECG) perturbation from single-channel surface electromyogram (EMG) recordings by means of unsupervised learning of wavelet-based intensity images. The general idea is to combine the suitability of certain wavelet decomposition bases which provide sparse electrocardiogram time-frequency representations, with the capacity of non-negative matrix factorization (NMF) for extracting patterns from images. In order to overcome convergence problems which often arise in NMF-related applications, we design a novel robust initialization strategy which ensures proper signal decomposition in a wide range of ECG contamination levels. Moreover, the method can be readily used because no a priori knowledge or parameter adjustment is needed. The proposed method was evaluated on real surface EMG signals against two state-of-the-art unsupervised learning algorithms and a singular spectrum analysis based method. The results, expressed in terms of high-to-low energy ratio, normalized median frequency, spectral power difference and normalized average rectified value, suggest that the proposed method enables better ECG-EMG separation quality than the reference methods. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Robust demarcation of basal cell carcinoma by dependent component analysis-based segmentation of multi-spectral fluorescence images.

PubMed

Kopriva, Ivica; Persin, Antun; Puizina-Ivić, Neira; Mirić, Lina

2010-07-02

This study was designed to demonstrate robust performance of the novel dependent component analysis (DCA)-based approach to demarcation of the basal cell carcinoma (BCC) through unsupervised decomposition of the red-green-blue (RGB) fluorescent image of the BCC. Robustness to intensity fluctuation is due to the scale invariance property of DCA algorithms, which exploit spectral and spatial diversities between the BCC and the surrounding tissue. Used filtering-based DCA approach represents an extension of the independent component analysis (ICA) and is necessary in order to account for statistical dependence that is induced by spectral similarity between the BCC and surrounding tissue. This generates weak edges what represents a challenge for other segmentation methods as well. By comparative performance analysis with state-of-the-art image segmentation methods such as active contours (level set), K-means clustering, non-negative matrix factorization, ICA and ratio imaging we experimentally demonstrate good performance of DCA-based BCC demarcation in two demanding scenarios where intensity of the fluorescent image has been varied almost two orders of magnitude. Copyright 2010 Elsevier B.V. All rights reserved.

Orbit-product representation and correction of Gaussian belief propagation

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

Johnson, Jason K; Chertkov, Michael; Chernyak, Vladimir

We present a new interpretation of Gaussian belief propagation (GaBP) based on the 'zeta function' representation of the determinant as a product over orbits of a graph. We show that GaBP captures back-tracking orbits of the graph and consider how to correct this estimate by accounting for non-backtracking orbits. We show that the product over non-backtracking orbits may be interpreted as the determinant of the non-backtracking adjacency matrix of the graph with edge weights based on the solution of GaBP. An efficient method is proposed to compute a truncated correction factor including all non-backtracking orbits up to a specified length.

Matrix precipitation: a general strategy to eliminate matrix interference for pharmaceutical toxic impurities analysis.

PubMed

Yang, Xiaojing; Xiong, Xuewu; Cao, Ji; Luan, Baolei; Liu, Yongjun; Liu, Guozhu; Zhang, Lei

2015-01-30

Matrix interference, which can lead to false positive/negative results, contamination of injector or separation column, incompatibility between sample solution and the selected analytical instrument, and response inhibition or even quenching, is commonly suffered for the analysis of trace level toxic impurities in drug substance. In this study, a simple matrix precipitation strategy is proposed to eliminate or minimize the above stated matrix interference problems. Generally, a sample of active pharmaceutical ingredients (APIs) is dissolved in an appropriate solvent to achieve the desired high concentration and then an anti-solvent is added to precipitate the matrix substance. As a result, the target analyte is extracted into the mixed solution with very less residual of APIs. This strategy has the characteristics of simple manipulation, high recovery and excellent anti-interference capability. It was found that the precipitation ratio (R, representing the ability to remove matrix substance) and the proportion of solvent (the one used to dissolve APIs) in final solution (P, affecting R and also affecting the method sensitivity) are two important factors of the precipitation process. The correlation between R and P was investigated by performing precipitation with various APIs in different solvent/anti-solvent systems. After a detailed mathematical reasoning process, P=20% was proved to be an effective and robust condition to perform the precipitation strategy. The precipitation method with P=20% can be used as a general strategy for toxic impurity analysis in APIs. Finally, several typical examples are described in this article, where the challenging matrix interference issues have been resolved successfully. Copyright © 2014 Elsevier B.V. All rights reserved.

Osteogenic potential of mesenchymal cells embedded in the provisional matrix after a 6-week healing period in augmented and non-augmented extraction sockets: an immunohistochemical prospective pilot study in humans.

PubMed

Heberer, Susanne; Wustlich, Alexander; Lage, Hermann; Nelson, John J; Nelson, Katja

2012-01-01

The aim of the present clinical study was the evaluation of the osteogenic potential of mesenchymal cells embedded in the provisional matrix of non-augmented and with Bio-Oss collagen-augmented human extraction sockets after 6 weeks of healing time. Twenty-five patients with 47 extraction sites participated in the present study. After tooth removal, the extraction sockets were augmented with Bio-Oss collagen or not augmented. At implant placement, bone biopsies of the extraction sockets were obtained. The immunohistochemical analysis of the osteogenic potential of the mesenchymal cells in the provisional matrix was performed using three monoclonal antibodies: core-binding factor α1 (Cbfa1)/runt-related protein (Runx)2, osteonectin (OSN/secreted protein acidic and rich in cyst [SPARC]) and osteocalcin (OC). The statistical analysis was performed using two-factorial analysis for repeated measures, Mann-Whitney U-test and Spearman's rank-order correlation coefficient. Of 47 extraction sockets examined, 17 sockets demonstrated an almost complete ossification. Hence, the provisional matrix of the 30 remaining extraction sockets (21 non-augmented, 9 augmented) was immunohistochemically investigated. No evidence of acute or chronic inflammation was noted in any of the specimens. In the provisional matrix of the non-grafted socket, the median amount of Cbfa1/Runx2-positive cells was 72.3%, of OSN (SPARC) 66.9% and of OC 23.4%, whereas in the grafted sockets the median rate of immunopositive cells staining with Cbfa1/Runx2 was 73.3%, of OSN (SPARC) 61.4% and of OC 20.1%. There was no significant difference in the proportion of positive cells expressed by Cbfa1/Runx2, OSN/SPARC and OC between the grafted and non-grafted socket. Furthermore, the cell density did not correlate to the quantity of stained cells independent of the used proteins. After a 6-week healing period, the provisional matrix was demonstrated to have a high proportion of cells displaying a maturation of mature osteoprogenitor cells to osteoblasts. The grafting procedure did not influence the quantity of osteogenic cells in the extraction socket. © 2011 John Wiley & Sons A/S.

Comparative Analysis of the Reinforcement of Polymers with 2D-Nanofillers: Organoclay and Boron Nitride

NASA Astrophysics Data System (ADS)

Kozlov, G. V.; Kuvshinova, S. A.; Dolbin, I. V.; Koifman, O. I.

2018-03-01

Using the percolation reinforcement model, it has been shown that the main factor governing the degree of reinforcement of polymer/2D-nanofiller composites is the ability of a nanofiller to generate interfacial regions. This parameter is interrelated with two fundamental structural characteristics of a nanocomposite, i.e., the fractal dimension of its structure and the content of polymer matrix/nanofiller interfacial surfaces. The negative effect of high nanofiller anisotropy on the elasticity modulus of a nanocomposite is demonstrated.

Evaluation and prevention of the negative matrix effect of terpenoids on pesticides in apples quantification by gas chromatography-tandem mass spectrometry.

PubMed

Giacinti, Géraldine; Raynaud, Christine; Capblancq, Sophie; Simon, Valérie

2016-12-21

The sample matrix can enhance the gas chromatography signal of pesticide residues relative to that obtained with the same concentration of pesticide in solvent. This paper is related to negative matrix effects observed in coupled gas chromatography-mass spectrometry ion trap (GC/MS 2 ) quantification of pesticides in concentrated extracts of apple peel prepared by the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) method. It is focused on the pesticides most frequently used on the apple varieties studied, throughout the crop cycle, right up to harvest, to combat pests and diseases and to improve fruit storage properties. Extracts from the fleshy receptacle (flesh), the epiderm (peel) and fruit of three apple varieties were studied by high-performance thin-layer chromatography hyphenated with UV-vis light detection (HPTLC/UV visible). The peel extracts had high concentrations of triterpenic acids (oleanolic and ursolic acids), reaching 25mgkg -1 , whereas these compounds were not detected in the flesh extracts (<0.05mgkg -1 ). A significant relationship has been found between the levels of these molecules and negative matrix effects in GC/MS 2 . The differences in the behavior of pesticides with respect to matrix effects can be accounted for by the physicochemical characteristics of the molecules (lone pairs, labile hydrogen, conjugation). The HPTLC/UV visible method developed here for the characterization of QuEChERS extracts acts as a complementary clean-up method, aimed to decrease the negative matrix effects of such extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation and prevention of the negative matrix effect of terpenoids on pesticides in apples quantification by gas chromatography-tandem mass spectrometry.

PubMed

Giacinti, Géraldine; Raynaud, Christine; Capblancq, Sophie; Simon, Valérie

2017-02-03

The sample matrix can enhance the gas chromatography signal of pesticide residues relative to that obtained with the same concentration of pesticide in solvent. This paper is related to negative matrix effects observed in coupled gas chromatography-mass spectrometry ion trap (GC/MS 2 ) quantification of pesticides in concentrated extracts of apple peel prepared by the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) method. It is focused on the pesticides most frequently used on the apple varieties studied, throughout the crop cycle, right up to harvest, to combat pests and diseases and to improve fruit storage properties. Extracts from the fleshy receptacle (flesh), the epiderm (peel) and fruit of three apple varieties were studied by high-performance thin-layer chromatography hyphenated with UV-vis light detection (HPTLC/UV visible). The peel extracts had high concentrations of triterpenic acids (oleanolic and ursolic acids), reaching 25mgkg -1 , whereas these compounds were not detected in the flesh extracts (<0.05mgkg -1 ). A significant relationship has been found between the levels of these molecules and negative matrix effects in GC/MS 2 . The differences in the behavior of pesticides with respect to matrix effects can be accounted for by the physicochemical characteristics of the molecules (lone pairs, labile hydrogen, conjugation). The HPTLC/UV visible method developed here for the characterization of QuEChERS extracts acts as a complementary clean-up method, aimed to decrease the negative matrix effects of such extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Optimizing indomethacin-loaded chitosan nanoparticle size, encapsulation, and release using Box-Behnken experimental design.

PubMed

Abul Kalam, Mohd; Khan, Abdul Arif; Khan, Shahanavaj; Almalik, Abdulaziz; Alshamsan, Aws

2016-06-01

Indomethacin chitosan nanoparticles (NPs) were developed by ionotropic gelation and optimized by concentrations of chitosan and tripolyphosphate (TPP) and stirring time by 3-factor 3-level Box-Behnken experimental design. Optimal concentration of chitosan (A) and TPP (B) were found 0.6mg/mL and 0.4mg/mL with 120min stirring time (C), with applied constraints of minimizing particle size (R1) and maximizing encapsulation efficiency (R2) and drug release (R3). Based on obtained 3D response surface plots, factors A, B and C were found to give synergistic effect on R1, while factor A has a negative impact on R2 and R3. Interaction of AB was negative on R1 and R2 but positive on R3. The factor AC was having synergistic effect on R1 and on R3, while the same combination had a negative effect on R2. The interaction BC was positive on the all responses. NPs were found in the size range of 321-675nm with zeta potentials (+25 to +32mV) after 6 months storage. Encapsulation, drug release, and content were in the range of 56-79%, 48-73% and 98-99%, respectively. In vitro drug release data were fitted in different kinetic models and pattern of drug release followed Higuchi-matrix type. Copyright © 2016 Elsevier B.V. All rights reserved.

Shaping eosinophil identity in the tissue contexts of development, homeostasis, and disease.

PubMed

Abdala-Valencia, Hiam; Coden, Mackenzie E; Chiarella, Sergio E; Jacobsen, Elizabeth A; Bochner, Bruce S; Lee, James J; Berdnikovs, Sergejs

2018-04-14

Eosinophils play homeostatic roles in different tissues and are found in several organs at a homeostatic baseline, though their tissue numbers increase significantly in development and disease. The morphological, phenotypical, and functional plasticity of recruited eosinophils are influenced by the dynamic tissue microenvironment changes between homeostatic, morphogenetic, and disease states. Activity of the epithelial-mesenchymal interface, extracellular matrix, hormonal inputs, metabolic state of the environment, as well as epithelial and mesenchymal-derived innate cytokines and growth factors all have the potential to regulate the attraction, retention, in situ hematopoiesis, phenotype, and function of eosinophils. This review examines the reciprocal relationship between eosinophils and such tissue factors, specifically addressing: (1) tissue microenvironments associated with the presence and activity of eosinophils; (2) non-immune tissue ligands regulatory for eosinophil accumulation, hematopoiesis, phenotype, and function (with an emphasis on the extracellular matrix and epithelial-mesenchymal interface); (3) the contribution of eosinophils to regulating tissue biology; (4) eosinophil phenotypic heterogeneity in different tissue microenvironments, classifying eosinophils as progenitors, steady state eosinophils, and Type 1 and 2 activated phenotypes. An appreciation of eosinophil regulation by non-immune tissue factors is necessary for completing the picture of eosinophil immune activation and understanding the functional contribution of these cells to development, homeostasis, and disease. ©2018 Society for Leukocyte Biology.

A Gaussian random field model for similarity-based smoothing in Bayesian disease mapping.

PubMed

Baptista, Helena; Mendes, Jorge M; MacNab, Ying C; Xavier, Miguel; Caldas-de-Almeida, José

2016-08-01

Conditionally specified Gaussian Markov random field (GMRF) models with adjacency-based neighbourhood weight matrix, commonly known as neighbourhood-based GMRF models, have been the mainstream approach to spatial smoothing in Bayesian disease mapping. In the present paper, we propose a conditionally specified Gaussian random field (GRF) model with a similarity-based non-spatial weight matrix to facilitate non-spatial smoothing in Bayesian disease mapping. The model, named similarity-based GRF, is motivated for modelling disease mapping data in situations where the underlying small area relative risks and the associated determinant factors do not vary systematically in space, and the similarity is defined by "similarity" with respect to the associated disease determinant factors. The neighbourhood-based GMRF and the similarity-based GRF are compared and accessed via a simulation study and by two case studies, using new data on alcohol abuse in Portugal collected by the World Mental Health Survey Initiative and the well-known lip cancer data in Scotland. In the presence of disease data with no evidence of positive spatial correlation, the simulation study showed a consistent gain in efficiency from the similarity-based GRF, compared with the adjacency-based GMRF with the determinant risk factors as covariate. This new approach broadens the scope of the existing conditional autocorrelation models. © The Author(s) 2016.

Molecular signaling in live cells studied by FRET

NASA Astrophysics Data System (ADS)

Chien, Shu; Wang, Yingxiao

2011-11-01

Genetically encoded biosensors based on fluorescence resonance energy transfer (FRET) enables visualization of signaling events in live cells with high spatiotemporal resolution. We have used FRET to assess temporal and spatial characteristics for signaling molecules, including tyrosine kinases Src and FAK, small GTPase Rac, calcium, and a membrane-bound matrix metalloproteinase MT1-MMP. Activations of Src and Rac by platelet derived growth factor (PDGF) led to distinct subcellular patterns during cell migration on micropatterned surface, and these two enzymes interact with each other to form a feedback loop with differential regulations at different subcellular locations. We have developed FRET biosensors to monitor FAK activities at rafts vs. non-raft regions of plasma membrane in live cells. In response to cell adhesion on matrix proteins or stimulation by PDGF, the raft-targeting FAK biosensor showed a stronger FRET response than that at non-rafts. The FAK activation at rafts induced by PDGF is mediated by Src. In contrast, the FAK activation at rafts induced by adhesion is independent of Src activity, but rather is essential for Src activation. Thus, Src is upstream to FAK in response to chemical stimulation (PDGF), but FAK is upstream to Src in response to mechanical stimulation (adhesion). A novel biosensor has been developed to dynamically visualize the activity of membrane type-1-matrix metalloproteinase (MT1-MMP), which proteolytically remodels the extracellular matrix. Epidermal growth factor (EGF) directed active MT1-MMP to the leading edge of migrating live cancer cells with local accumulation of EGF receptor via a process dependent on an intact cytoskeletal network. In summary, FRET-based biosensors enable the elucidation of molecular processes and hierarchies underlying spatiotemporal regulation of biological and pathological processes, thus advancing our knowledge on how cells perceive mechanical/chemical cues in space and time to coordinate molecular/cellular functions.

Molecular signaling in live cells studied by FRET

NASA Astrophysics Data System (ADS)

Chien, Shu; Wang, Yingxiao

2012-03-01

Genetically encoded biosensors based on fluorescence resonance energy transfer (FRET) enables visualization of signaling events in live cells with high spatiotemporal resolution. We have used FRET to assess temporal and spatial characteristics for signaling molecules, including tyrosine kinases Src and FAK, small GTPase Rac, calcium, and a membrane-bound matrix metalloproteinase MT1-MMP. Activations of Src and Rac by platelet derived growth factor (PDGF) led to distinct subcellular patterns during cell migration on micropatterned surface, and these two enzymes interact with each other to form a feedback loop with differential regulations at different subcellular locations. We have developed FRET biosensors to monitor FAK activities at rafts vs. non-raft regions of plasma membrane in live cells. In response to cell adhesion on matrix proteins or stimulation by PDGF, the raft-targeting FAK biosensor showed a stronger FRET response than that at non-rafts. The FAK activation at rafts induced by PDGF is mediated by Src. In contrast, the FAK activation at rafts induced by adhesion is independent of Src activity, but rather is essential for Src activation. Thus, Src is upstream to FAK in response to chemical stimulation (PDGF), but FAK is upstream to Src in response to mechanical stimulation (adhesion). A novel biosensor has been developed to dynamically visualize the activity of membrane type-1-matrix metalloproteinase (MT1-MMP), which proteolytically remodels the extracellular matrix. Epidermal growth factor (EGF) directed active MT1-MMP to the leading edge of migrating live cancer cells with local accumulation of EGF receptor via a process dependent on an intact cytoskeletal network. In summary, FRET-based biosensors enable the elucidation of molecular processes and hierarchies underlying spatiotemporal regulation of biological and pathological processes, thus advancing our knowledge on how cells perceive mechanical/chemical cues in space and time to coordinate molecular/cellular functions.

Low-temperature anomalies in the dynamic elastic moduli of cubic AIIBVI crystals with 3d-transition metal impurities

NASA Astrophysics Data System (ADS)

Lonchakov, A. T.

2011-04-01

A negative paramagnetic contribution to the dynamic elastic moduli is identified in AIIBVI:3d wide band-gap compounds for the first time. It appears as a paramagnetic elastic, or, briefly, paraelastic, susceptibility. These compounds are found to have a linear temperature dependence for the inverse paraelastic susceptibility. This is explained by a contribution from the diagonal matrix elements of the orbit-lattice interaction operators in the energy of the spin-orbital states of the 3d-ion as a function of applied stress (by analogy with the Curie contribution to the magnetic susceptibility). The inverse paraelastic susceptibility of AIIBVI crystals containing non-Kramers 3d-ions is found to deviate from linearity with decreasing temperature and reaches saturation. This effect is explained by a contribution from nondiagonal matrix elements (analogous to the well known van Vleck contribution to the magnetic susceptibility of paramagnets).

Mitochondrial function in engineered cardiac tissues is regulated by extracellular matrix elasticity and tissue alignment.

PubMed

Lyra-Leite, Davi M; Andres, Allen M; Petersen, Andrew P; Ariyasinghe, Nethika R; Cho, Nathan; Lee, Jezell A; Gottlieb, Roberta A; McCain, Megan L

2017-10-01

Mitochondria in cardiac myocytes are critical for generating ATP to meet the high metabolic demands associated with sarcomere shortening. Distinct remodeling of mitochondrial structure and function occur in cardiac myocytes in both developmental and pathological settings. However, the factors that underlie these changes are poorly understood. Because remodeling of tissue architecture and extracellular matrix (ECM) elasticity are also hallmarks of ventricular development and disease, we hypothesize that these environmental factors regulate mitochondrial function in cardiac myocytes. To test this, we developed a new procedure to transfer tunable polydimethylsiloxane disks microcontact-printed with fibronectin into cell culture microplates. We cultured Sprague-Dawley neonatal rat ventricular myocytes within the wells, which consistently formed tissues following the printed fibronectin, and measured oxygen consumption rate using a Seahorse extracellular flux analyzer. Our data indicate that parameters associated with baseline metabolism are predominantly regulated by ECM elasticity, whereas the ability of tissues to adapt to metabolic stress is regulated by both ECM elasticity and tissue alignment. Furthermore, bioenergetic health index, which reflects both the positive and negative aspects of oxygen consumption, was highest in aligned tissues on the most rigid substrate, suggesting that overall mitochondrial function is regulated by both ECM elasticity and tissue alignment. Our results demonstrate that mitochondrial function is regulated by both ECM elasticity and myofibril architecture in cardiac myocytes. This provides novel insight into how extracellular cues impact mitochondrial function in the context of cardiac development and disease. NEW & NOTEWORTHY A new methodology has been developed to measure O 2 consumption rates in engineered cardiac tissues with independent control over tissue alignment and matrix elasticity. This led to the findings that matrix elasticity regulates basal mitochondrial function, whereas both matrix elasticity and tissue alignment regulate mitochondrial stress responses. Copyright © 2017 the American Physiological Society.

Direct Analyses of Secondary Metabolites by Mass Spectrometry Imaging (MSI) from Sunflower (Helianthus annuus L.) Trichomes.

PubMed

Brentan Silva, Denise; Aschenbrenner, Anna-Katharina; Lopes, Norberto Peporine; Spring, Otmar

2017-05-10

Helianthus annuus (sunflower) displays non-glandular trichomes (NGT), capitate glandular trichomes (CGT), and linear glandular trichomes (LGT), which reveal different chemical compositions and locations in different plant tissues. With matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging (MSI) techniques, efficient methods were developed to analyze the tissue distribution of secondary metabolites (flavonoids and sesquiterpenes) and proteins inside of trichomes. Herein, we analyzed sesquiterpene lactones, present in CGT, from leaf transversal sections using the matrix 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) (mixture 1:1) with sodium ions added to increase the ionization in positive ion mode. The results observed for sesquiterpenes and polymethoxylated flavones from LGT were similar. However, upon desiccation, LGT changed their shape in the ionization source, complicating analyses by MSI mainly after matrix application. An alternative method could be applied to LGT regions by employing LDI (without matrix) in negative ion mode. The polymethoxylated flavones were easily ionized by LDI, producing images with higher resolution, but the sesquiterpenes were not observed in spectra. Thus, the application and viability of MALDI imaging for the analyses of protein and secondary metabolites inside trichomes were confirmed, highlighting the importance of optimization parameters.

Self-Determination: A Buffer against Suicide Ideation

ERIC Educational Resources Information Center

Bureau, Julien S.; Mageau, Genevieve A.; Vallerand, Robert J.; Rousseau, Francois L.; Otis, Joanne

2012-01-01

Self-determination was examined as a protective factor against the detrimental impact of negative life events on suicide ideation in adolescents. It is postulated that for highly self-determined adolescents, negative life events have a weaker impact on both hopelessness and suicide ideation than for non-self-determined adolescents. In turn,…

Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Marto, J A; White, F M; Seldomridge, S; Marshall, A G

1995-11-01

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode.

Assessing medication adherence in inflammatory bowel diseases. A comparison between a self-administered scale and a pharmacy refill index.

PubMed

de Castro, María Luisa; Sanromán, Luciano; Martín, Alicia; Figueira, Montserrat; Martínez, Noemi; Hernández, Vicent; Del Campo, Victor; Pineda, Juan R; Martínez-Cadilla, Jesús; Pereira, Santos; Rodríguez Prada, José Ignacio

2017-08-01

Medication non-adherence in inflammatory bowel disease (IBD) has a negative impact on disease outcome. Different tools have been proposed to assess non-adherence. We aimed to compare a self-administered scale and a pharmacy refill index as a reliable measure of medication adherence and to determine what factors are related to adherence. Consecutive non-active IBD outpatients were asked to fill in the self-reported Morisky Medication Adherence Scale (MMAS-8) and the Beliefs about Medication Questionnaire (BMQ). Pharmacy refill data were reviewed from the previous three or six months and the medication possession ratio (MPR) was calculated. Non-adherence was defined as MMAS-8 scores < 6 or MPR < 0.8. Two-hundred and three patients were enrolled (60% ulcerative colitis, 40% Crohn's disease); 51% were men, and the mean age was 46.3 (14) years. Seventy-four per cent of patients were on monotherapy and 26% on combination therapy; altogether, 65% received mesalazine, 46% thiopurines and 16% anti-tumor necrosis factor alfa. Non-adherence rate assessed by MPR was 37% and 22.4% by MMAS-8. Receiver operator curve analysis using a MMAS-8 cut-off of six gave an area under the curve of 0.6 (95% CI 0.5-0.7), p = 0.001. This score had an 85% sensitivity and 34% specificity to predict medication non-adherence, with negative and positive predictive values of 57% and 70% respectively. High scores in the BMQ potential for harm of medication were significantly associated with MPR non-adherence (p = 0.01). The accuracy of MMAS-8 to identify medication non-adherence in inactive IBD outpatients in our setting is poor due to a low specificity and a negative predictive value. Psychosocial factors such as beliefs about medication seem to be related to IBD non-adherence.

T/T homozygosity of the tenascin-C gene polymorphism rs2104772 negatively influences exercise-induced angiogenesis.

PubMed

Valdivieso, Paola; Toigo, Marco; Hoppeler, Hans; Flück, Martin

2017-01-01

Mechanical stress, including blood pressure related factors, up-regulate expression of the pro-angiogenic extracellular matrix protein tenascin-C in skeletal muscle. We hypothesized that increased capillarization of skeletal muscle with the repeated augmentation in perfusion during endurance training is associated with blood vessel-related expression of tenascin-C and would be affected by the single-nucleotide polymorphism (SNP) rs2104772, which characterizes the non-synonymous exchange of thymidine (T)-to-adenosine (A) in the amino acid codon 1677 of tenascin-C. Sixty-one healthy, untrained, male white participants of Swiss descent performed thirty 30-min bouts of endurance exercise on consecutive weekdays using a cycling ergometer. Genotype and training interactions were called significant at Bonferroni-corrected p-value of 5% (repeated measures ANOVA). Endurance training increased capillary-to-fiber-ratio (+11%), capillary density (+7%), and mitochondrial volume density (+30%) in m. vastus lateralis. Tenascin-C protein expression in this muscle was confined to arterioles and venules (80% of cases) and increased after training in A-allele carriers. Prior to training, volume densities of subsarcolemmal and myofibrillar mitochondria in m. vastus lateralis muscle were 49% and 18%, respectively, higher in A/A homozygotes relative to T-nucleotide carriers (A/T and T/T). Training specifically increased capillary-to-fiber ratio in A-nucleotide carriers but not in T/T homozygotes. Genotype specific regulation of angiogenesis was reflected by the expression response of 8 angiogenesis-associated transcripts after exercise, and confirmed by training-induced alterations of the shear stress related factors, vimentin and VEGF A. Our findings provide evidence for a negative influence of T/T homozygosity in rs2104772 on capillary remodeling with endurance exercise.

T/T homozygosity of the tenascin-C gene polymorphism rs2104772 negatively influences exercise-induced angiogenesis

PubMed Central

Toigo, Marco; Hoppeler, Hans

2017-01-01

Background Mechanical stress, including blood pressure related factors, up-regulate expression of the pro-angiogenic extracellular matrix protein tenascin-C in skeletal muscle. We hypothesized that increased capillarization of skeletal muscle with the repeated augmentation in perfusion during endurance training is associated with blood vessel-related expression of tenascin-C and would be affected by the single-nucleotide polymorphism (SNP) rs2104772, which characterizes the non-synonymous exchange of thymidine (T)-to-adenosine (A) in the amino acid codon 1677 of tenascin-C. Methods Sixty-one healthy, untrained, male white participants of Swiss descent performed thirty 30-min bouts of endurance exercise on consecutive weekdays using a cycling ergometer. Genotype and training interactions were called significant at Bonferroni-corrected p-value of 5% (repeated measures ANOVA). Results Endurance training increased capillary-to-fiber-ratio (+11%), capillary density (+7%), and mitochondrial volume density (+30%) in m. vastus lateralis. Tenascin-C protein expression in this muscle was confined to arterioles and venules (80% of cases) and increased after training in A-allele carriers. Prior to training, volume densities of subsarcolemmal and myofibrillar mitochondria in m. vastus lateralis muscle were 49% and 18%, respectively, higher in A/A homozygotes relative to T-nucleotide carriers (A/T and T/T). Training specifically increased capillary-to-fiber ratio in A-nucleotide carriers but not in T/T homozygotes. Genotype specific regulation of angiogenesis was reflected by the expression response of 8 angiogenesis-associated transcripts after exercise, and confirmed by training-induced alterations of the shear stress related factors, vimentin and VEGF A. Conclusion Our findings provide evidence for a negative influence of T/T homozygosity in rs2104772 on capillary remodeling with endurance exercise. PMID:28384286

Increase in local protein concentration by field-inversion gel electrophoresis.

PubMed

Tsai, Henghang; Low, Teck Yew; Freeby, Steve; Paulus, Aran; Ramnarayanan, Kalpana; Cheng, Chung-Pui Paul; Leung, Hon-Chiu Eastwood

2007-09-26

Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE). Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE) in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE) showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS), which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein separation tool.

An engineered transforming growth factor β (TGF-β) monomer that functions as a dominant negative to block TGF-β signaling

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

Kim, Sun Kyung; Barron, Lindsey; Hinck, Cynthia S.

The transforming growth factor β isoforms, TGF-β1, -β2, and -β3, are small secreted homodimeric signaling proteins with essential roles in regulating the adaptive immune system and maintaining the extracellular matrix. However, dysregulation of the TGF-β pathway is responsible for promoting the progression of several human diseases, including cancer and fibrosis. Despite the known importance of TGF-βs in promoting disease progression, no inhibitors have been approved for use in humans. Herein, we describe an engineered TGF-β monomer, lacking the heel helix, a structural motif essential for binding the TGF-β type I receptor (TβRI) but dispensable for binding the other receptor requiredmore » for TGF-β signaling, the TGF-β type II receptor (TβRII), as an alternative therapeutic modality for blocking TGF-β signaling in humans. As shown through binding studies and crystallography, the engineered monomer retained the same overall structure of native TGF-β monomers and bound TβRII in an identical manner. Cell-based luciferase assays showed that the engineered monomer functioned as a dominant negative to inhibit TGF-β signaling with a Ki of 20–70 nM. Investigation of the mechanism showed that the high affinity of the engineered monomer for TβRII, coupled with its reduced ability to non-covalently dimerize and its inability to bind and recruit TβRI, enabled it to bind endogenous TβRII but prevented it from binding and recruiting TβRI to form a signaling complex. Such engineered monomers provide a new avenue to probe and manipulate TGF-β signaling and may inform similar modifications of other TGF-β family members.« less

A DEIM Induced CUR Factorization

DTIC Science & Technology

2015-09-18

CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given matrix A, such a factorization provides a...CUR approximations based on leverage scores. 1 Introduction This work presents a new CUR matrix factorization based upon the Discrete Empirical...SUPPLEMENTARY NOTES 14. ABSTRACT We derive a CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given

TM4SF5 promotes metastatic behavior of cells in 3D extracellular matrix gels by reducing dependency on environmental cues

PubMed Central

Nam, Seo Hee; Cheong, Jin-Gyu; Jeong, Doyoung; Lee, Seo-Jin; Pan, Cheol-Ho; Jung, Jae Woo; Kim, Hye-Jin; Ryu, Jihye; Kim, Ji Eon; Kim, Somi; Cho, Chang Yun; Kang, Min-Kyung; Lee, Kyung-Min; Lee, Jung Weon

2017-01-01

Transmembrane 4 L six family member 5 (TM4SF5) is highly expressed in hepatocellular carcinoma tissues and enhances migration in two-dimensional environments. Here, we investigated how TM4SF5 is involved in diverse pro-metastatic phenotypes in in vivo-like three-dimensional (3D) extracellular matrix gels. TM4SF5-positive cells aggressively formed invasive foci in 3D Matrigel, depending on TM4SF5-mediated signaling activity, cytoskeletal organization, and matrix metallopeptidase (MMP) 2-mediated extracellular remodeling, whereas TM4SF5-null cells did not. The TM4SF5-null cells did, however, form invasive foci in 3D Matrigel following inhibition of Rho-associated protein kinase or addition of collagen I, suggesting that collagen I compensated for TM4SF5 expression. Similarly, TM4SF5-positive cells expressing vascular endothelial-cadherin formed network-like vasculogenic mimicry in 3D Matrigel and collagen I mixture gels, whereas TM4SF5-negative cells in the mixture gels displayed the network structures only upon further treatment with epidermal growth factor. The foci formation also required MMP2-mediated remodeling of the extracellular matrix. Co-cultures exhibited TM4SF5-positive or cancer-associated fibroblasts at the outward edges of TM4SF5-null cell clusters. Compared with TM4SF5-null cells, TM4SF5-positive cells in 3D collagen gels showed a more invasive outgrowth with dramatic invadopodia. These observations suggest that TM4SF5 plays roles in the promotion of diverse metastatic properties with fewer environmental requirements than TM4SF5-negative cells. PMID:29137358

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains.

PubMed

Onken, Arno; Liu, Jian K; Karunasekara, P P Chamanthi R; Delis, Ioannis; Gollisch, Tim; Panzeri, Stefano

2016-11-01

Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

PubMed Central

Onken, Arno; Liu, Jian K.; Karunasekara, P. P. Chamanthi R.; Delis, Ioannis; Gollisch, Tim; Panzeri, Stefano

2016-01-01

Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding. PMID:27814363

Surface display of roGFP for monitoring redox status of extracellular microenvironments in Shewanella oneidensis biofilms.

PubMed

Sivakumar, Krishnakumar; Mukherjee, Manisha; Cheng, Hsin-I; Zhang, Yingdan; Ji, Lianghui; Cao, Bin

2015-03-01

Biofilms are the most ubiquitous and resilient form of microbial life on earth. One most important feature of a biofilm is the presence of a self-produced matrix, which creates highly heterogeneous and dynamic microenvironments within biofilms. Redox status in biofilm microenvironments plays a critical role in biofilm development and function. However, there is a lack of non-intrusive tools to quantify extracellular redox status of microenvironments within a biofilm matrix. In this study, using Shewanella oneidensis as a model organism, we demonstrated a novel approach to monitor extracellular redox status in biofilm microenvironments. Specifically, we displayed a redox sensitive fluorescence protein roGFP onto the cell surface of S. oneidensis by fusing it to the C-terminus of BpfA, a large surface protein, and used the surface displayed roGFP as a sensor to quantify the extracellular redox status in the matrix of S. oneidensis biofilms. The fusion of roGFP into BpfA has no negative impacts on cell growth and biofilm formation. Upon exposure to oxidizing agents such as H2 O2 , Ag(+) , and SeO3 (2-) , S. oneidensis BpfA-roGFP cells exhibited a characteristic fluorescence of roGFP. Proteinase treatment assay and super-resolution structured illumination microscopy confirmed the surface localization of BpfA-roGFP. We further used the surface displayed roGFP monitored the extracellular redox status in the matrix at different depths of a biofilm exposed to H2 O2 . This study provides a novel approach to non-invasively monitor extracellular redox status in microenvironments within biofilms, which can be used to understand redox responses of biofilms to environmental perturbations. © 2014 Wiley Periodicals, Inc.

Carbon nanodots as a matrix for the analysis of low-molecular-weight molecules in both positive- and negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantification of glucose and uric acid in real samples.

PubMed

Chen, Suming; Zheng, Huzhi; Wang, Jianing; Hou, Jian; He, Qing; Liu, Huihui; Xiong, Caiqiao; Kong, Xianglei; Nie, Zongxiu

2013-07-16

Carbon nanodots were applied for the first time as a new matrix for the analysis of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in both positive- and negative-ion modes. A wide range of small molecules including amino acids, peptides, fatty acids, as well as β-agonists and neutral oligosaccharides were analyzed by MALDI MS with carbon nanodots as the matrix, and the lowest 0.2 fmol limits-of-detection were obtained for octadecanoic acid. Clear sodium and potassium adducts and deprotonated signals were produced in positive- and negative-ion modes. Furthermore, the glucose and uric acid in real samples were quantitatively determined by the internal standard method with the linear range of 0.5-9 mM and 0.1-1.8 mM (R(2) > 0.999), respectively. This work gives new insight into the application of carbon nanodots and provides a general approach for rapid analysis of low-molecular-weight compounds.

Structural Characterization of Neutral Saccharides by Negative Ion MALDI Mass Spectrometry Using a Superbasic Proton Sponge as Deprotonating Matrix

NASA Astrophysics Data System (ADS)

Calvano, Cosima Damiana; Cataldi, Tommaso R. I.; Kögel, Julius F.; Monopoli, Antonio; Palmisano, Francesco; Sundermeyer, Jorge

2017-08-01

The superbasic proton sponge 1,8-bis(tripyrrolidinylphosphazenyl)naphthalene (TPPN) has been successfully employed for the structural characterization of neutral saccharides, cyclodextrins, and saccharide alditols by matrix assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS). Owing to its inherently high basicity, TPPN is capable of deprotonating neutral carbohydrates (M) providing an efficient and simple way to produce gas-phase [M - H]- ions. Highly informative negative ions MS/MS spectra showing several diagnostic fragment ions were obtained, mainly A-type cross-ring and C-type glycosidic cleavages. Indeed, cross-ring cleavages of monosaccharides with formation of 0,2A, 0,3A, 2,4A, 2,5A, 3,5A, and 0,3X product ions dominate the MS/MS spectra. A significant difference between reducing (e.g., lactose, maltose) and non-reducing disaccharides (e.g., sucrose, trehalose) was observed. Though disaccharides with the anomeric positions blocked give rise to deprotonated molecules, [M - H]-, at m/ z 341.1, reducing ones exhibited a peak at m/ z 340.1, most likely as radical anion, [M - H•- H]-•. The superiority of TPPN was clearly demonstrated by comparison with well recognized matrices, such as 2,5-dihydroxybenzoic acid and 2',4',6'-trihydroxyacetophenone (positive ion mode) and nor-harman (negative ion mode). MALDI MS/MS experiments on isotopically labeled sugars have greatly supported the interpretation of plausible fragmentation pathways.

Source identification of PM10 pollution in subway passenger cabins using positive matrix factorization

NASA Astrophysics Data System (ADS)

Park, Duckshin; Oh, Miseok; Yoon, Younghun; Park, Eunyoung; Lee, Kiyoung

2012-03-01

Monitoring the air quality in subway passenger cabins is important because of the large number of passengers and potentially high levels of air pollution. This report characterized PM10 levels in subway cabins in Seoul, Korea, and identified PM10 sources using elemental analysis and receptor modeling. PM10 levels in subway cabins were continuously measured using a light scattering monitor during rush and non-rush hours. A total of 41 measurements were taken during rush and non-rush hours, and the measurements were repeated in all four seasons. Filter samples were also collected for elemental composition analysis. Major PM10 sources were identified using positive matrix factorization (PMF). The in-cabin PM10 concentrations were the highest in the winter at 152.8 μg m-3 during rush hours and 90.2 μg m-3 during non-rush hours. While PM10 levels were higher during rush hours than during non-rush hours in three seasons (excluding summer), these levels were not associated with number of passenger. Elemental analysis showed that the PM10 was composed of 52.5% inorganic elements, 10.2% anions, and 37.3% other. Fe was the most abundant element and significantly correlated (p < 0.01) with Mn (r = 0.97), Ti (r = 0.91), Cr (r = 0.88), Ni (r = 0.89), and Cu (r = 0.88). Fe, Mn, Cr, and Cu are indicators of railroad-related PM10 sources. The PM10 sources characterized by PMF were soil and road dust sources (27.2%), railroad-related sources (47.6%), secondary nitrate sources (16.2%), and a chlorine factor mixed with a secondary sulfate source (9.1%). Overall, railroad-related sources contributed the most PM10 to subway cabin air.

New intracellular activities of matrix metalloproteinases shine in the moonlight.

PubMed

Jobin, Parker G; Butler, Georgina S; Overall, Christopher M

2017-11-01

Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders. However, growing evidence has convincingly identified select MMPs in intracellular compartments with unexpected physiological and pathological roles. Intracellular MMPs have both proteolytic and non-proteolytic functions, including signal transduction and transcription factor activity thereby challenging their traditional designation as extracellular proteases. This review highlights current knowledge of subcellular location and activity of these "moonlighting" MMPs. Intracellular roles herald a new era of MMP research, rejuvenating interest in targeting these proteases in therapeutic strategies. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman. Copyright © 2017 Elsevier B.V. All rights reserved.

Extracellular matrix metalloproteinase inducer (EMMPRIN) is a potential biomarker of angiogenesis in proliferative diabetic retinopathy.

PubMed

Abu El-Asrar, Ahmed M; Ahmad, Ajmal; Alam, Kaiser; Siddiquei, Mohammad Mairaj; Mohammad, Ghulam; Hertogh, Gert De; Mousa, Ahmed; Opdenakker, Ghislain

2017-11-01

Extracellular matrix metalloproteinase inducer (EMMPRIN) promotes angiogenesis through matrix metalloproteinases (MMPs) and vascular endothelial growth factor (VEGF) production. We investigated the expression levels of EMMPRIN and correlated these levels with VEGF, MMP-1 and MMP-9 in proliferative diabetic retinopathy (PDR). In addition, we examined the expression of EMMPRIN in the retinas of diabetic rats and the effect of EMMPRIN on the induction of angiogenesis regulatory factors in human retinal microvascular endothelial cells (HRMECs). Vitreous samples from 40 PDR and 19 non-diabetic patients, epiretinal membranes from 12 patients with PDR, retinas of rats and HRMECs were studied by enzyme-linked immunosorbent assay (ELISA), immunohistochemistry, Western blot analysis, zymography analysis and RT-PCR. We showed a significant increase in the expression of EMMPRIN, VEGF, MMP-1 and MMP-9 in vitreous samples from PDR patients compared with non-diabetic controls (p < 0.0001; p = 0.001; p = 0.009; p < 0.0001, respectively). Significant positive correlations were found between the levels of EMMPRIN and the levels of VEGF (r = 0.38; p = 0.003), MMP-1 (r = 0.36; p = 0.005) and MMP-9 (r = 0.46; p = 0.003). In epiretinal membranes, EMMPRIN was expressed in vascular endothelial cells and stromal cells. Significant increase of EMMPRIN mRNA was detected in rat retinas after induction of diabetes. EMMPRIN induced hypoxia-inducible factor-1α, VEGF and MMP-1 expression in HRMEC. These results suggest that EMMPRIN/MMPs/VEGF pathway is involved in PDR angiogenesis. © 2016 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Factors that lead to changes in sexual behaviours after a negative HIV test: protocol for a prospective cohort study in Kinshasa.

PubMed

Carlos, Silvia; Nzakimuena, Francis; Reina, Gabriel; Lopez-Del Burgo, Cristina; Burgueño, Eduardo; Ndarabu, Adolphe; Osorio, Alfonso; de Irala, Jokin

2016-07-20

Considering the high percentage of couples in which one or both members are HIV negative, the frequency of transmission among non-regular partners and the probabilities of non-disclosure, attention should be paid to people getting a negative HIV test at the Voluntary Counseling and Testing (VCT). Research has shown that a negative HIV test may be followed by a change in sexual behaviours. In Sub-Saharan Africa, where most HIV infections occur, there are few studies that have analysed the factors associated with changes in sexual risk behaviours after a negative HIV test at the VCT clinic. The aim of this project is to evaluate the specific factors associated with changes in sexual behaviours, three months after a negative result in an HIV test, and to analyse the effect of counseling and testing on HIV-related knowledge of participants in an outpatient centre of Kinshasa (Democratic Republic of Congo). Prospective cohort study from December 2014 until March 2016. People 15-60 year old that received VCT at Monkole Hospital (Kinshasa) were followed three months after they got a negative HIV test. In a face-to-face interview, participants replied to a baseline and a follow-up research questionnaire on HIV-related knowledge, attitudes and behaviours. At follow-up respondents were also offered a new HIV test and additional HIV counseling. Four hundred and fifteen participants completed the baseline questionnaire and 363 (87 %) came back for their 3-month follow up. This is the first longitudinal study in the DRC that evaluates the factors associated with changes in sexual behaviours after a negative HIV test at the VCT. Participants attending the VCT services within a clinical setting are a good study population as they can be good transmitters of preventive information for other people with no access to health facilities.

Active counter electrode in a-SiC electrochemical metallization memory

NASA Astrophysics Data System (ADS)

Morgan, K. A.; Fan, J.; Huang, R.; Zhong, L.; Gowers, R.; Ou, J. Y.; Jiang, L.; De Groot, C. H.

2017-08-01

Cu/amorphous-SiC (a-SiC) electrochemical metallization memory cells have been fabricated with two different counter electrode (CE) materials, W and Au, in order to investigate the role of CEs in a non-oxide semiconductor switching matrix. In a positive bipolar regime with Cu filaments forming and rupturing, the CE influences the OFF state resistance and minimum current compliance. Nevertheless, a similarity in SET kinetics is seen for both CEs, which differs from previously published SiO2 memories, confirming that CE effects are dependent on the switching layer material or type. Both a-SiC memories are able to switch in the negative bipolar regime, indicating Au and W filaments. This confirms that CEs can play an active role in a non-oxide semiconducting switching matrix, such as a-SiC. By comparing both Au and W CEs, this work shows that W is superior in terms of a higher R OFF/R ON ratio, along with the ability to switch at lower current compliances making it a favourable material for future low energy applications. With its CMOS compatibility, a-SiC/W is an excellent choice for future resistive memory applications.

Soft hair of dynamical black hole and Hawking radiation

NASA Astrophysics Data System (ADS)

Chu, Chong-Sun; Koyama, Yoji

2018-04-01

Soft hair of black hole has been proposed recently to play an important role in the resolution of the black hole information paradox. Recent work has emphasized that the soft modes cannot affect the black hole S-matrix due to Weinberg soft theorems. However as soft hair is generated by supertranslation of geometry which involves an angular dependent shift of time, it must have non-trivial quantum effects. We consider supertranslation of the Vaidya black hole and construct a non-spherical symmetric dynamical spacetime with soft hair. We show that this spacetime admits a trapping horizon and is a dynamical black hole. We find that Hawking radiation is emitted from the trapping horizon of the dynamical black hole. The Hawking radiation has a spectrum which depends on the soft hair of the black hole and this is consistent with the factorization property of the black hole S-matrix.

Interaction-induced conducting-non-conducting transition of ultra-cold atoms in one-dimensional optical lattices

NASA Astrophysics Data System (ADS)

Chien, Chih-Chun; Gruss, Daniel; Di Ventra, Massimiliano; Zwolak, Michael

2013-06-01

The study of time-dependent, many-body transport phenomena is increasingly within reach of ultra-cold atom experiments. We show that the introduction of spatially inhomogeneous interactions, e.g., generated by optically controlled collisions, induce negative differential conductance in the transport of atoms in one-dimensional optical lattices. Specifically, we simulate the dynamics of interacting fermionic atoms via a micro-canonical transport formalism within both a mean-field and a higher-order approximation, as well as with a time-dependent density-matrix renormalization group (DMRG). For weakly repulsive interactions, a quasi-steady-state atomic current develops that is similar to the situation occurring for electronic systems subject to an external voltage bias. At the mean-field level, we find that this atomic current is robust against the details of how the interaction is switched on. Further, a conducting-non-conducting transition exists when the interaction imbalance exceeds some threshold from both our approximate and time-dependent DMRG simulations. This transition is preceded by the atomic equivalent of negative differential conductivity observed in transport across solid-state structures.

Predictors and outcomes of non-adherence in patients receiving maintenance hemodialysis.

PubMed

Tohme, Fadi; Mor, Maria K; Pena-Polanco, Julio; Green, Jamie A; Fine, Michael J; Palevsky, Paul M; Weisbord, Steven D

2017-08-01

Predictors of and outcomes associated with non-adherent behavior among patients on chronic hemodialysis (HD) have been incompletely elucidated. We conducted a post hoc analysis of data from the SMILE trial to identify patient factors associated with non-adherence to dialysis-related treatments and the associations of non-adherence with clinical outcomes. We defined non-adherence as missed HD and abbreviated HD. We used negative binomial regression to model the associations of demographic and clinical factors with measures of non-adherence, and negative binomial and Cox regression to analyze the associations of non-adherence with hospitalizations and mortality, respectively. We followed 286 patients for up to 24 months. Factors independently associated with missing HD included Tuesday/Thursday/Saturday HD schedule [incident rate ratio (IRR) 1.85, p < 0.01], current smoking (IRR 2.22, p < 0.01), higher pain score (IRR 1.04, p < 0.01), lower healthy literacy (IRR 3.01, p < 0.01), lower baseline quality of life (IRR 0.89, p = 0.01), and younger age (IRR 1.35, p < 0.01). Factors independently associated with abbreviating HD included dialysis vintage (IRR 1.07, p < 0.01), higher pain score (IRR 1.02, p < 0.01), current non-smoking (IRR 1.32, p = 0.03), and younger age (IRR 1.22, p < 0.01). Abbreviating HD was independently associated with an increased number of total (IRR 1.70, p < 0.01) and ESRD-related (IRR 1.66, p < 0.01) hospitalizations, while missing HD was independently associated with mortality (HR 2.36, p = 0.04). We identified several previously described and novel factors independently associated with non-adherence to HD-related treatments, and independent associations of non-adherence with hospitalization and mortality. These findings should inform the development and implementation of interventions to improve adherence and reduce health resource utilization.

The Exopolysaccharide Matrix

PubMed Central

Koo, H.; Falsetta, M.L.; Klein, M.I.

2013-01-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms. PMID:24045647

The exopolysaccharide matrix: a virulence determinant of cariogenic biofilm.

PubMed

Koo, H; Falsetta, M L; Klein, M I

2013-12-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms.

Determination of Flavonol Aglycones in Ginkgo biloba Dietary Supplement Crude Materials and Finished Products by High-Performance Liquid Chromatography: Single Laboratory Validation

PubMed Central

Gray, Dean; LeVanseler, Kerri; Pan, Meide

2008-01-01

A single laboratory validation (SLV) was completed for a method to determine the flavonol aglycones quercetin, kaempferol, and isorhamnetin in Ginkgo biloba products. The method calculates total glycosides based on these aglycones formed following acid hydrolysis. Nine matrixes were chosen for the study, including crude leaf material, standardized dry powder extract, single and multiple entity finished products, and ethanol and glycerol tinctures. For the 9 matrixes evaluated as part of this SLV, the method appeared to be selective and specific, with no observed interferences. The simplified 60 min oven heating hydrolysis procedure was effective for each of the matrixes studied, with no apparent or consistent differences between 60, 75, and 90 min at 90°C. A Youden ruggedness trial testing 7 factors with the potential to affect quantitative results showed that 2 factors (volume hydrolyzed and test sample extraction/hydrolysis weight) were the most important parameters for control during sample preparation. The method performed well in terms of precision, with 4 matrixes tested in triplicate over a 3-day period showing an overall repeatability (relative standard deviation, RSD) of 2.3%. Analysis of variance testing at α = 0.05 showed no significant differences among the within- or between-group sources of variation, although comparisons of within-day (Sw), between-day (Sb), and total (St) precision showed that a majority of the standard deviation came from within-day determinations for all matrixes. Accuracy testing at 2 levels (approximately 30 and 90% of the determined concentrations in standardized dry powder extract) from 2 complex negative control matrixes showed an overall 96% recovery and RSD of 1.0% for the high spike, and 94% recovery and RSD of 2.5% for the low spike. HorRat scores were within the limits for performance acceptability, ranging from 0.4 to 1.3. Based on the performance results presented herein, it is recommended that this method progress to the collaborative laboratory trial. PMID:16001841

Effect of Twice-Daily Blue Light Treatment on Matrix-Rich Biofilm Development.

PubMed

de Sousa, Denise Lins; Lima, Ramille Araújo; Zanin, Iriana Carla; Klein, Marlise I; Janal, Malvin N; Duarte, Simone

2015-01-01

The use of blue light has been proposed as a direct means of affecting local bacterial infections, however the use of blue light without a photosensitizer to prevent the biofilm development has not yet been explored. The aim of this study was to determine how the twice-daily treatment with blue light affects the development and composition of a matrix-rich biofilm. Biofilms of Streptococcus mutans UA159 were formed on saliva-coated hydroxyapatite discs for 5 days. The biofilms were exposed twice-daily to non-coherent blue light (LumaCare; 420 nm) without a photosensitizer. The distance between the light and the sample was 1.0 cm; energy density of 72 J cm-2; and exposure time of 12 min 56 s. Positive and negative controls were twice-daily 0.12% chlorhexidine (CHX) and 0.89% NaCl, respectively. Biofilms were analyzed for bacterial viability, dry-weight, and extra (EPS-insoluble and soluble) and intracellular (IPS) polysaccharides. Variable pressure scanning electron microscopy and confocal scanning laser microscopy were used to check biofilm morphology and bacterial viability, respectively. When biofilms were exposed to twice-daily blue light, EPS-insoluble was reduced significantly more than in either control group (CHX and 0.89% NaCl). Bacterial viability and dry weight were also reduced relative to the negative control (0.89% NaCl) when the biofilms were treated with twice-daily blue light. Different morphology was also visible when the biofilms were treated with blue light. Twice-daily treatment with blue light without a photosensitizer is a promising mechanism for the inhibition of matrix-rich biofilm development.

Biphasic effect of alcohol intake on the development of fatty liver disease.

PubMed

Takahashi, Hirokazu; Ono, Masafumi; Hyogo, Hideyuki; Tsuji, Chika; Kitajima, Yoichiro; Ono, Naofumi; Eguchi, Takahisa; Fujimoto, Kazuma; Chayama, Kazuaki; Saibara, Toshiji; Anzai, Keizo; Eguchi, Yuichiro

2015-11-01

Fatty liver is an important clinical feature not only in alcoholic and non-alcoholic fatty liver diseases, but in other chronic liver diseases as well. Our aim was to elucidate the effect and relationship between habitual alcohol intake and obesity in the development of fatty liver disease. We enrolled 8,029 subjects undergoing abdominal ultrasonography with general medical examinations, and analyzed the factors associated with fatty liver based on daily alcohol intake, body mass index (BMI), and waist circumference. For fatty liver, BMI, waist circumference, total cholesterol, triglycerides, and fasting plasma glucose were significant and independent risk factors. Heavy alcohol intake (50 g/day) was a significant risk factor for fatty liver in women (odds ratio [OR], 3.35). Analysis based on the presence or absence of obesity revealed that moderate alcohol intake was a significant negative risk factor for fatty liver in both male and female obese (BMI ≥25 kg/m(2)) subjects (OR, 0.74 for non-obese and 0.39 for obese patients, respectively). Heavy alcohol intake was also a significant negative risk factor in obese males (0.62). In contrast, heavy alcohol intake was a risk factor in non-obese males (OR, 1.29) and in all females (OR, 2.22 for non-obese and 6.6 for obese patients, respectively). The influence of alcohol intake on fatty liver differed depending on the level of alcohol consumption, gender, and the presence of obesity, and showed biphasic effects.

Loneliness and Schizotypy Are Distinct Constructs, Separate from General Psychopathology.

PubMed

Badcock, Johanna C; Barkus, Emma; Cohen, Alex S; Bucks, Romola; Badcock, David R

2016-01-01

Loneliness is common in youth and associated with a significantly increased risk of psychological disorders. Although loneliness is strongly associated with psychosis, its relationship with psychosis proneness is unclear. Our aim in this paper was to test the hypothesis that loneliness and schizotypal traits, conveying risk for schizophrenia spectrum disorders, are similar but separate constructs. Pooling data from two non-clinical student samples (N = 551) we modeled the structure of the relationship between loneliness and trait schizotypy. Loneliness was assessed with the University of California, Los Angeles Loneliness Scale (UCLA-3), whilst negative (Social Anhedonia) and positive (Perceptual Aberrations) schizotypal traits were assessed with the Wisconsin Schizotypy Scales-Brief (WSS-B). Fit statistics indicated that the best fitting model of UCLA-3 scores comprises three correlated factors (Isolation, Related Connectedness, and Collective Connectedness), consistent with previous reports. Fit statistics for a two factor model of positive and negative schizotypy were excellent. Next, bi-factor analysis was used to model a general psychopatholgy factor (p) across the three loneliness factors and separate negative and positive schizotypy traits. The results showed that all items (except 1) co-loaded on p. However, with the influence of p removed, additional variance remained within separate sub-factors, indicating that loneliness and negative and positive trait schizotypy are distinct and separable constructs. Similarly, once shared variance with p was removed, correlations between sub-factors of loneliness and schizotypal traits were non-significant. These findings have important clinical implications since they suggest that loneliness should not be conflated with the expression of schizotypy. Rather, loneliness needs to be specifically targeted for assessment and treatment in youth at risk for psychosis.

Elastase and matrix metalloproteinase activities are associated with pulmonary vascular disease in the nitrofen rat model of congenital diaphragmatic hernia.

PubMed

Wild, Benjamin; St-Pierre, Marie-Eve; Langlois, Stéphanie; Cowan, Kyle N

2017-05-01

Pulmonary vascular disease (PVD) is a leading cause of congenital diaphragmatic hernia (CDH) mortality. Progression of PVD involves extracellular matrix remodeling by elastases and matrix metalloproteinases (MMP), concomitant with proliferation of smooth muscle cells in a growth factor-enriched environment. Blockade of this pathway reversed primary pulmonary hypertension and improved survival. This study was designed to determine whether a similar pathway is induced in PVD secondary to CDH. Fetal rats exposed to nitrofen at gestational day 9 developed left-sided CDH and were compared at term to their non-CDH littermates by assessing histologic and biochemical features of PVD. Rats with CDH displayed right ventricle hypertrophy, increased pulmonary artery medial wall thickness and muscularization, and decreased lumen size. As revealed by in situ zymography and immunohistochemistry, this was associated with an induction of elastolytic and MMP activities as well as an elevation of epidermal growth factor and osteopontin levels in the diseased lung vasculature. CDH-associated PVD involves an induction of elastase and MMP activities and increased osteopontin deposition in an epidermal growth factor-rich environment. Inhibition of this pathway may thus represent a novel therapeutic approach for the treatment of CDH-associated PVD. Level I (Basic Science Study). Copyright © 2017 Elsevier Inc. All rights reserved.

Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy.

PubMed

Neal, Sharon L

2018-01-01

The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.

Human performance modeling for system of systems analytics: combat performance-shaping factors.

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

Lawton, Craig R.; Miller, Dwight Peter

The US military has identified Human Performance Modeling (HPM) as a significant requirement and challenge of future systems modeling and analysis initiatives. To support this goal, Sandia National Laboratories (SNL) has undertaken a program of HPM as an integral augmentation to its system-of-system (SoS) analytics capabilities. The previous effort, reported in SAND2005-6569, evaluated the effects of soldier cognitive fatigue on SoS performance. The current effort began with a very broad survey of any performance-shaping factors (PSFs) that also might affect soldiers performance in combat situations. The work included consideration of three different approaches to cognition modeling and how appropriate theymore » would be for application to SoS analytics. This bulk of this report categorizes 47 PSFs into three groups (internal, external, and task-related) and provides brief descriptions of how each affects combat performance, according to the literature. The PSFs were then assembled into a matrix with 22 representative military tasks and assigned one of four levels of estimated negative impact on task performance, based on the literature. Blank versions of the matrix were then sent to two ex-military subject-matter experts to be filled out based on their personal experiences. Data analysis was performed to identify the consensus most influential PSFs. Results indicate that combat-related injury, cognitive fatigue, inadequate training, physical fatigue, thirst, stress, poor perceptual processing, and presence of chemical agents are among the PSFs with the most negative impact on combat performance.« less

Epidemiology, susceptibility, and risk factors for acquisition of MDR/XDR Gram-negative bacteria among kidney transplant recipients with urinary tract infections.

PubMed

Yuan, Xiuhong; Liu, Taohua; Wu, Di; Wan, Qiquan

2018-01-01

Multiple drug resistant/extensively drug resistant (MDR/XDR) Gram-negative urinary tract infections (UTIs) represent a growing threat to kidney transplant recipients. This retrospective study aimed to assess the incidence and microbiological profile of MDR/XDR Gram-negative UTIs, to identify drug susceptibility of MDR/XDR bacteria, and to determine the potential risk factors for MDR/XDR UTIs in kidney recipients. During the study period, 1569 patients underwent consecutive kidney transplantation in two transplantation centers. We studied the demographics, clinical characteristics, and urine culture data from kidney recipients with MDR/XDR Gram-negative UTIs, and verified the risk factors associated with MDR/XDR infections. Eighty-one kidney recipients yielded 88 episodes of MDR/XDR Gram-negative UTIs with five patients (6.2%) succumbing to all-cause in-hospital mortality. The most frequently isolated bacterium was Escherichia coli (62.5%). Almost all MDR/XDR Gram-negative bacteria were resistant to first- and second-generation cephalosporin, and monocyclic beta-lactam. They were relatively sensitive to meropenem, amikacin, and tigecycline. As for the 12 XDR bacteria, all of them were resistant to meropenem and 25% of them were resistant to tigecycline. All XDR Acinetobacter baumannii and E. coli were susceptible to tigecycline. Nosocomial infection (odds ratio [OR] = 11.429, 95% CI = 1.311-99.625, P = 0.027) was the only independent predictor of MDR/XDR Gram-negative UTIs. Non-fermenting bacterial infection (OR = 20.161, 95% CI = 3.409-119.240, P = 0.001), polycystic kidney disease (OR = 39.871, 95% CI = 1.979-803.384, P = 0.016), and serum creatinine level > 1.5 mg/dL (OR = 8.688, 95% CI = 1.354-55.747, P = 0.023) were significantly different between XDR and MDR Gram-negative UTIs. Meropenem, amikacin, and/or tigecycline can be prescribed for MDR/XDR Gram-negative infections. Tigecycline can also be prescribed for XDR A. baumannii and E. coli . Nosocomial infection was a risk factor for MDR/XDR Gram-negative UTIs, while XDR UTIs were associated with non-fermenting bacterial infection, polycystic kidney disease, and impaired renal function.

TECHNICAL JUSTIFICATION FOR CHOOSING PROPANE AS A CALIBRATION AGENT FOR TOTAL FLAMMABLE VOLATILE ORGANIC COMPOUND (VOC) DETERMINATIONS

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

DOUGLAS, J.G.

2006-07-06

This document presents the technical justification for choosing and using propane as a calibration standard for estimating total flammable volatile organic compounds (VOCs) in an air matrix. A propane-in-nitrogen standard was selected based on a number of criteria: (1) has an analytical response similar to the VOCs of interest, (2) can be made with known accuracy and traceability, (3) is available with good purity, (4) has a matrix similar to the sample matrix, (5) is stable during storage and use, (6) is relatively non-hazardous, and (7) is a recognized standard for similar analytical applications. The Waste Retrieval Project (WRP) desiresmore » a fast, reliable, and inexpensive method for screening the flammable VOC content in the vapor-phase headspace of waste containers. Table 1 lists the flammable VOCs of interest to the WRP. The current method used to determine the VOC content of a container is to sample the container's headspace and submit the sample for gas chromatography--mass spectrometry (GC-MS) analysis. The driver for the VOC measurement requirement is safety: potentially flammable atmospheres in the waste containers must be allowed to diffuse prior to processing the container. The proposed flammable VOC screening method is to inject an aliquot of the headspace sample into an argon-doped pulsed-discharge helium ionization detector (Ar-PDHID) contained within a gas chromatograph. No actual chromatography is performed; the sample is transferred directly from a sample loop to the detector through a short, inert transfer line. The peak area resulting from the injected sample is proportional to the flammable VOC content of the sample. However, because the Ar-PDHID has different response factors for different flammable VOCs, a fundamental assumption must be made that the agent used to calibrate the detector is representative of the flammable VOCs of interest that may be in the headspace samples. At worst, we desire that calibration with the selected calibrating agent overestimate the value of the VOCs in a sample. By overestimating the VOC content of a sample, we want to minimize false negatives. A false negative is defined as incorrectly estimating the VOC content of the sample to be below programmatic action limits when, in fact, the sample,exceeds the action limits. The disadvantage of overestimating the flammable VOC content of a sample is that additional cost may be incurred because additional sampling and GC-MS analysis may be required to confirm results over programmatic action limits. Therefore, choosing an appropriate calibration standard for the Ar-PDHID is critical to avoid false negatives and to minimize additional analytical costs.« less

EPA Positive Matrix Factorization (PMF) 3.0 Fundamentals & User Guide

EPA Science Inventory

Positive matrix factorization (PMF) is a multivariate factor analysis tool that decomposes a matrix of ambient data into two matrices - factor contributions and factor profiles - which then need to be interpreted by an analyst as to what source types are represented using measure...

Non-conserved magnetization operator and 'fire-and-ice' ground states in the Ising-Heisenberg diamond chain

NASA Astrophysics Data System (ADS)

Torrico, Jordana; Ohanyan, Vadim; Rojas, Onofre

2018-05-01

We consider the diamond chain with S = 1/2 XYZ vertical dimers which interact with the intermediate sites via the interaction of the Ising type. We also suppose all four spins form the diamond-shaped plaquette to have different g-factors. The non-uniform g-factors within the quantum spin dimer as well as the XY-anisotropy of the exchange interaction lead to the non-conserving magnetization for the chain. We analyze the effects of non-conserving magnetization as well as the effects of the appearance of negative g-factors among the spins from the unit cell. A number of unusual frustrated states for ferromagnetic couplings and g-factors with non-uniform signs are found out. These frustrated states generalize the "half-fire-half-ice" state introduced in reference Yin et al. (2015). The corresponding zero-temperature ground state phase diagrams are presented.

Clinical Manifestations of Helicobacter pylori-Negative Gastritis.

PubMed

Shiota, Seiji; Thrift, Aaron P; Green, Linda; Shah, Rajesh; Verstovsek, Gordana; Rugge, Massimo; Graham, David Y; El-Serag, Hashem B

2017-07-01

There are data to suggest the existence of non-Helicobacter pylori gastritis. However, the risk factors and clinical course for H pylori-negative gastritis remain unclear. We aimed to examine the prevalence and determinants of H pylori-negative gastritis in a large multiethnic clinical population. We conducted a cross-sectional study among patents scheduled for an elective esophagastroduodenoscopy or attending selected primary care clinics and eligible for screening colonoscopy at a single Veterans Affairs medical center. We identified cases of H pylor-negative gastritis, H pylori-positive gastritis, and H pylori-negative nongastritis, where gastritis was defined by the presence of neutrophils and/or mononuclear cells. Risk factors for H pylori-negative gastritis were analyzed in logistic regression models. A total of 1240 patients had information from all biopsy sites, of whom 695 (56.0%) had gastritis. H pylori-negative gastritis was present in 123 patients (9.9% of all study subjects and 17.7% of all patients with gastritis). Among all patients with gastritis, African Americans were statistically significantly less likely than non-Hispanic whites to have H pylori-negative gastritis (odds ratio, 0.25; 95% confidence interval, 0.14-0.43). Conversely, PPI users were more likely to have H pylori-negative gastritis than H pylori-positive gastritis compared with nonusers (odds ratio, 2.02; 95% confidence interval, 1.17-3.49). The cumulative incidence of gastric erosions and ulcers were higher in patients with H pylori-negative gastritis than H pylori-negative nongastritis. We found that H pylori-negative gastritis was present in approximately 18% of patients with gastritis. The potential for H pylori-negative gastritis to progress or the risk of gastric cancer of those with gastric mucosal atrophy/intestinal metaplasia remains unclear. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Detection of the CS20 colonization factor antigen in diffuse-adhering E. coli strains

PubMed Central

Ochoa, Theresa J.; Rivera, Fulton P.; Bernal, Maria; Meza, Rina; Ecker, Lucie; Gil, Ana I.; Cepeda, David; Mosquito, Susan; Mercado, Erik; Maves, Ryan C.; Hall, Eric R.; Svennerholm, Ann-Mari; McVeigh, Annette; Savarino, Stephen; Lanata, Claudio F.

2011-01-01

We analyzed a randomly-selected group of 30 diffusely adherent (DAEC), 30 enteropathogenic, 30 enteroaggregative, and 5 shiga toxin-producing E. coli strains isolated from children with diarrhea. Enterotoxigenic E. coli (ETEC) colonization factors (CFs) were evaluated by dot-blot assay using 21 CF-specific monoclonal antibodies. Out of 95 non-ETEC strains, three DAEC were found to express CS20. No other E. coli expressed CFs. We confirmed the 3 CS20-positive strains as ETEC-negative by repeat PCR and as toxin-negative by GM1-ELISA. To our knowledge, this is the first study that has identified currently-recognized CFs in non-ETEC diarrheagenic E. coli strains identified by molecular methods. CFs may be an unrecognized relevant adherence factor in other E. coli, which may then play a role in pathogenesis and the immune response of the host. PMID:21064230

Eyewitness memory: The impact of a negative mood during encoding and/or retrieval upon recall of a non-emotive event.

PubMed

Thorley, Craig; Dewhurst, Stephen A; Abel, Joseph W; Knott, Lauren M

2016-07-01

The police often appeal for eyewitnesses to events that were unlikely to have been emotive when observed. An eyewitness, however, may be in a negative mood whilst encoding or retrieving such events as mood can be influenced by a range of personal, social, and environmental factors. For example, bad weather can induce a negative mood. This experiment compared the impact of negative and neutral moods during encoding and/or retrieval upon eyewitness recall of a non-emotive event. A negative mood during encoding had no impact upon the number of correct details recalled (provided participants were in a neutral mood at retrieval) but a negative mood during retrieval impaired the number of correct details recalled (provided participants were in a neutral mood at encoding). A negative mood at both time points enhanced the number of correct details recalled, demonstrating a mood-dependent memory enhancement. The forensic implications of these findings are discussed.

Temperature effects on ash physical and chemical properties. A laboratory study.

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Úbeda, Xavier; Martin, Deborah

2010-05-01

Fire temperatures have different impacts on ash physical and chemical properties that depend mainly of the specie affected and time of exposition. In a real prescribed or wildland fire, the temperatures produce ash with different characteristics. Know the impacts of a specific temperature or a gradient on a certain element and specie is very difficult in real fires, especially in wildland fires, where temperatures achieve higher values and the burning conditions are not controlled. Hence, laboratory studies revealed to be an excellent methodology to understand the effects of fire temperatures in ash physical and chemical. The aim of this study is study the effects of a temperature gradient (150, 200, 250, 300, 350, 400, 450, 500 and 550°C) on ash physical and chemical properties. For this study we collected litter of Quercus suber, Pinus pinea and Pinus pinaster in a plot located in Portugal. The selected species are the most common in the ecosystem. We submitted samples to the mentioned temperatures throughout a time of two hours and we analysed several parameters, namely, Loss on Ignition (LOI%), ash colour - through the Croma Value (CV) observed in Munsell color chart - CaCO3, Total Nitrogen (TN), Total Carbon (TC), C/N ratio, ash pH, Electrical Conductivity (EC), extractable Calcium (Ca2+), Magnesium (Mg2+), Sodium (Na+), Potassium (K+), Aluminium (Al3+), Manganese (Mn2+), Iron (Fe2+), Zinc (Zn2+), Total Phosphorous (TP), Sulphur (S) and Silica (SiO2). Since we considered many elements, in order to obtain a better explanation of all dataset, we applied a Factorial Analysis (FA), based on the correlation matrix and the Factors were extracted according to the Principle Components method. To obtain a better relation between the variables with a specific Factor we rotated the matrix according to the VARIMAX NORMALIZED method. FA identified 5 Factors that explained a total of 95% of the variance. We retained in each Factor the variables that presented an eigenvalue >0.7. Factor 1 explained the majority of the variance (60.05%). LOI(%), CV, CaCO3, pH, Na+, K+, S (these last tree elements only in both Pinus) and SiO2, showed positive loadings. Inversely, TC, C/N ratio, Al3+, Fe2+ (these last tree elements for Quercus suber and Pinus pinaster ash) and Mn2+ (In the case of Quercus suber) presented negative loadings. Factor 2 explained 19.89% of the variance and showed higher loadings in TN, Ca2+ and Mg2+ (in the case of the ions only in both Pinus). Factor 3 explains only 6.69% of the variance and we identified higher loadings in Mg2+, Na+ and K+ of Quercus suber. Factor 4 explains less then the last Factor, only 4.60% of the variance and presented negative loadings above -0.7 in TP of Quercus suber and Pinus pinea. Factor 5 explained 3.93% of the variance, less than all other Factors and showed in Al3+, Mn2+ and Zn2+ of Pinus pinea and in the case of the last element, also in Pinus pinaster. The observation of the scores matrix allowed us to understand the major concentration of these elements according the temperature of exposition. Hence, the elements that showed higher positive loadings in Factor 1, have a major concentration at 450, 500 and 550°C, and the ones with higher negative loadings presented higher concentration at 200 and 250°C. The nutrients that presented higher positive loadings in Factor 2 have higher concentrations at 400°C. The elements with higher positive loadings in Factor 3 have bigger amounts in the ash slurries produced at 350°C and the ones with higher negative loadings in the Factor 4 showed greater concentrations in the ash produced at 300°C. The elements with higher negative loadings in the Factor 5 showed higher amounts in the ash created at 150°C of exposition. The results obtained showed that nutrients concentration is a function of the burned specie and temperature reached in the considered exposure time. Micronutrients and TC and C/N showed higher values at lower temperatures, TN, Ca2+, Mg2+ and TP at temperatures between 300-400°C. The other variables in study have major concentrations at temperatures higher than 450°C. Some differences between species can be identified and this is a result of the different litter vulnerabilities to the same temperature, producing diverse fire severities. This and other reasons for this behaviour will be discussed in the communication.

Some Factors Underlying Mathematical Performance: The Role of Visuospatial Working Memory and Non-Verbal Intelligence

ERIC Educational Resources Information Center

Kyttala, Minna; Lehto, Juhani E.

2008-01-01

Passive and active visuospatial working memory (VSWM) were investigated in relation to maths performance. The mental rotation task was employed as a measure of active VSWM whereas passive VSWM was investigated using a modified Corsi Blocks task and a matrix pattern task. The Raven Progressive Matrices Test measured fluid intelligence. A total of…

The Social Physique Anxiety Scale: an example of the potential consequence of negatively worded items in factorial validity studies.

PubMed

Motl, R W; Conroy, D E; Horan, P M

2000-01-01

Social physique anxiety (SPA) based on Hart, Leary, and Rejeski's (1989) Social Physique Anxiety Scale (SPAS) was originally conceptualized to be a unidimensional construct. Empirical evidence on the factorial validity of the SPAS has been contradictory, yielding both one- and two-factor models. The two-factor model, which consists of separate factors associated with positively and negatively worded items, has stimulated an ongoing debate about the dimensionality and content of the SPAS. The present study employed confirmatory factor analysis (CFA) to examine whether the two-factor solution to the 12-item SPAS was substantively meaningful or a methodological artifact. Results of the CFAs, which were performed on responses from four different samples (Eklund, Kelley, and Wilson, 1997; Eklund, Mack, and Hart, 1996), supported the existence of a single substantive SPA factor underlying responses to the 12-item SPAS. There were, in addition, method effects associated with the negatively worded items that could be modeled to achieve good fit. Therefore, it was concluded that a single substantive factor and a non-substantive method effect primarily related to the negatively worded items best represented the 12-item SPAS.

The Long Non-Coding RNA MIR503HG Enhances Proliferation of Human ALK-Negative Anaplastic Large-Cell Lymphoma.

PubMed

Huang, Po-Shuan; Chung, I-Hsiao; Lin, Yang-Hsiang; Lin, Tzu-Kang; Chen, Wei-Jan; Lin, Kwang-Huei

2018-05-14

Anaplastic lymphoma kinase (ALK)-negative anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma. Currently, only a few gene rearrangements have been linked to ALK-negative ALCL progression. However, the specific molecular mechanisms underlying the growth of ALK-negative ALCL tumors remain unclear. Here, we investigated aberrantly expressed, long non-coding RNAs (lncRNAs) in ALK-negative ALCL and assessed their potential biological function. MIR503HG ( miR-503 host gene) was highly expressed in ALK-negative cell lines and was significantly upregulated in tumors in mice formed from ALK-negative ALCL cell lines. Depletion of MIR503HG suppressed tumor cell proliferation in vivo and in vitro; conversely, its overexpression enhanced tumor cell growth. MIR503HG -induced proliferation was mediated by the induction of microRNA-503 ( miR - 503 ) and suppression of Smurf2, resulting in stabilization of the tumor growth factor-β receptor (TGFBR) and enhanced tumor cell growth. Collectively, these findings support a potential role for MIR503HG in cancer cell proliferation through the miR-503 /Smurf2/TGFBR axis and indicate that MIR503HG is a potential marker in ALK-negative ALCL.

Interphase for ceramic matrix composites reinforced by non-oxide ceramic fibers

NASA Technical Reports Server (NTRS)

DiCarlo, James A. (Inventor); Bhatt, Ramakrishna (Inventor); Morscher, Gregory N. (Inventor); Yun, Hee-Mann (Inventor)

2008-01-01

A ceramic matrix composite material is disclosed having non-oxide ceramic fibers, which are formed in a complex fiber architecture by conventional textile processes; a thin mechanically weak interphase material, which is coated on the fibers; and a non-oxide or oxide ceramic matrix, which is formed within the interstices of the interphase-coated fiber architecture. During composite fabrication or post treatment, the interphase is allowed to debond from the matrix while still adhering to the fibers, thereby providing enhanced oxidative durability and damage tolerance to the fibers and the composite material.

Invited review: mesenchymal progenitor cells in intramuscular connective tissue development.

PubMed

Miao, Z G; Zhang, L P; Fu, X; Yang, Q Y; Zhu, M J; Dodson, M V; Du, M

2016-01-01

The abundance and cross-linking of intramuscular connective tissue contributes to the background toughness of meat, and is thus undesirable. Connective tissue is mainly synthesized by intramuscular fibroblasts. Myocytes, adipocytes and fibroblasts are derived from a common pool of progenitor cells during the early embryonic development. It appears that multipotent mesenchymal stem cells first diverge into either myogenic or non-myogenic lineages; non-myogenic mesenchymal progenitors then develop into the stromal-vascular fraction of skeletal muscle wherein adipocytes, fibroblasts and derived mesenchymal progenitors reside. Because non-myogenic mesenchymal progenitors mainly undergo adipogenic or fibrogenic differentiation during muscle development, strengthening progenitor proliferation enhances the potential for both intramuscular adipogenesis and fibrogenesis, leading to the elevation of both marbling and connective tissue content in the resulting meat product. Furthermore, given the bipotent developmental potential of progenitor cells, enhancing their conversion to adipogenesis reduces fibrogenesis, which likely results in the overall improvement of marbling (more intramuscular adipocytes) and tenderness (less connective tissue) of meat. Fibrogenesis is mainly regulated by the transforming growth factor (TGF) β signaling pathway and its regulatory cascade. In addition, extracellular matrix, a part of the intramuscular connective tissue, provides a niche environment for regulating myogenic differentiation of satellite cells and muscle growth. Despite rapid progress, many questions remain in the role of extracellular matrix on muscle development, and factors determining the early differentiation of myogenic, adipogenic and fibrogenic cells, which warrant further studies.

Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression.

PubMed

Wang, Lixin; Brugge, Joan S; Janes, Kevin A

2011-10-04

Gene expression networks are complicated by the assortment of regulatory factors that bind DNA and modulate transcription combinatorially. Single-cell measurements can reveal biological mechanisms hidden by population averages, but their value has not been fully explored in the context of mRNA regulation. Here, we adapted a single-cell expression profiling technique to examine the gene expression program downstream of Forkhead box O (FOXO) transcription factors during 3D breast epithelial acinar morphogenesis. By analyzing patterns of mRNA fluctuations among individual matrix-attached epithelial cells, we found that a subset of FOXO target genes was jointly regulated by the transcription factor Runt-related transcription factor 1 (RUNX1). Knockdown of RUNX1 causes hyperproliferation and abnormal morphogenesis, both of which require normal FOXO function. Down-regulating RUNX1 and FOXOs simultaneously causes widespread oxidative stress, which arrests proliferation and restores normal acinar morphology. In hormone-negative breast cancers lacking human epidermal growth factor receptor 2 (HER2) amplification, we find that RUNX1 down-regulation is strongly associated with up-regulation of FOXO1, which may be required to support growth of RUNX1-negative tumors. The coordinate function of these two tumor suppressors may provide a failsafe mechanism that inhibits cancer progression.

Effect of inclusions on heterogeneous crack nucleation in nanocomposites

NASA Astrophysics Data System (ADS)

Gutkin, M. Yu.; Ovid'Ko, I. A.; Skiba, N. V.

2007-02-01

A two-dimensional theoretical model is proposed for the heterogeneous nucleation of a grain-boundary nanocrack in a nanocomposite consisting of a nanocrystalline matrix and nanoinclusions whose elastic moduli are identical to those of the matrix. The inclusions have the form of rods with a rectangular cross section and undergo dilatation eigenstrain induced by the differences in the lattice parameters and thermal expansion coefficients of the matrix and inclusions. In terms of the model, a mode-I-II nanocrack nucleates at the negative disclination of a biaxial dipole consisting of wedge grain-boundary (or junction) disclinations; then, the nanocrack opens along a grain boundary and reaches an inclusion boundary. Depending on the relative positions and orientations of the initial segment of the nanocrack and the inclusion, the nanocrack can either penetrate into the inclusion or bypass it along the matrix-inclusion interface. The nanocrack nucleation probability increases near an inclusion with negative (compressive) dilatation eigenstrain. A decrease in the inclusion size decreases (increases) the probability of a crack opening along the interface if the dilatation eigenstrain is negative (positive).

Fast iterative image reconstruction using sparse matrix factorization with GPU acceleration

NASA Astrophysics Data System (ADS)

Zhou, Jian; Qi, Jinyi

2011-03-01

Statistically based iterative approaches for image reconstruction have gained much attention in medical imaging. An accurate system matrix that defines the mapping from the image space to the data space is the key to high-resolution image reconstruction. However, an accurate system matrix is often associated with high computational cost and huge storage requirement. Here we present a method to address this problem by using sparse matrix factorization and parallel computing on a graphic processing unit (GPU).We factor the accurate system matrix into three sparse matrices: a sinogram blurring matrix, a geometric projection matrix, and an image blurring matrix. The sinogram blurring matrix models the detector response. The geometric projection matrix is based on a simple line integral model. The image blurring matrix is to compensate for the line-of-response (LOR) degradation due to the simplified geometric projection matrix. The geometric projection matrix is precomputed, while the sinogram and image blurring matrices are estimated by minimizing the difference between the factored system matrix and the original system matrix. The resulting factored system matrix has much less number of nonzero elements than the original system matrix and thus substantially reduces the storage and computation cost. The smaller size also allows an efficient implement of the forward and back projectors on GPUs, which have limited amount of memory. Our simulation studies show that the proposed method can dramatically reduce the computation cost of high-resolution iterative image reconstruction. The proposed technique is applicable to image reconstruction for different imaging modalities, including x-ray CT, PET, and SPECT.

Adsorbing/dissolving Lyoprotectant Matrix Technology for Non-cryogenic Storage of Archival Human Sera

NASA Astrophysics Data System (ADS)

Solivio, Morwena J.; Less, Rebekah; Rynes, Mathew L.; Kramer, Marcus; Aksan, Alptekin

2016-04-01

Despite abundant research conducted on cancer biomarker discovery and validation, to date, less than two-dozen biomarkers have been approved by the FDA for clinical use. One main reason is attributed to inadvertent use of low quality biospecimens in biomarker research. Most proteinaceous biomarkers are extremely susceptible to pre-analytical factors such as collection, processing, and storage. For example, cryogenic storage imposes very harsh chemical, physical, and mechanical stresses on biospecimens, significantly compromising sample quality. In this communication, we report the development of an electrospun lyoprotectant matrix and isothermal vitrification methodology for non-cryogenic stabilization and storage of liquid biospecimens. The lyoprotectant matrix was mainly composed of trehalose and dextran (and various low concentration excipients targeting different mechanisms of damage), and it was engineered to minimize heterogeneity during vitrification. The technology was validated using five biomarkers; LDH, CRP, PSA, MMP-7, and C3a. Complete recovery of LDH, CRP, and PSA levels was achieved post-rehydration while more than 90% recovery was accomplished for MMP-7 and C3a, showing promise for isothermal vitrification as a safe, efficient, and low-cost alternative to cryogenic storage.

HIV-Negative Partnered Men's Willingness to Use Pre-Exposure Prophylaxis and Associated Factors Among an Internet Sample of U.S. HIV-Negative and HIV-Discordant Male Couples

PubMed Central

Stephenson, Rob

2015-01-01

Abstract Purpose: Research on male couples' willingness to use pre-exposure prophylaxis (PrEP) is critically lacking. Methods: A cross-sectional 2011 Internet survey collected dyadic data from 275 HIV-negative and 58 HIV-discordant male couples to describe 631 HIV-negative partnered mens' willingness to use PrEP and associated couple-level demographic and behavioral factors with multivariate multilevel modeling. Results: Fifty-three percent were very to extremely likely to use PrEP. Willingness was positively associated with being in a mixed race and behaviorally non-monogamous relationship, and with amyl nitrate use with sex outside the relationship. Willingness was negatively associated with having a college education. Conclusion: Prevention efforts should educate male couples about the potential benefits of PrEP. PMID:26790016

Radiation-Induced Dedifferentiation of Head and Neck Cancer Cells Into Cancer Stem Cells Depends on Human Papillomavirus Status

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

Vlashi, Erina, E-mail: evlashi@mednet.ucla.edu; Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California; Chen, Allen M.

Purpose: To test the hypothesis that the radiation response of cancer stem cells (CSCs) in human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) differs and is not reflected in the radiation response of the bulk tumor populations, that radiation therapy (RT) can dedifferentiate non-stem HNSCC cells into CSCs, and that radiation-induced dedifferentiation depends on the HPV status. Methods and Materials: Records of a cohort of 162 HNSCC patients were reviewed, and their outcomes were correlated with their HPV status. Using a panel of HPV-positive and HPV-negative HNSCC cell lines expressing a reporter for CSCs, we characterized HPV-positivemore » and HPV-negative lines via flow cytometry, sphere-forming capacity assays in vitro, and limiting dilution assays in vivo. Non-CSCs were treated with different doses of radiation, and the dedifferentiation of non-CSCs into CSCs was investigated via flow cytometry and quantitative reverse transcription–polymerase chain reaction for re-expression of reprogramming factors. Results: Patients with HPV-positive tumors have superior overall survival and local–regional control. Human papillomavirus–positive HNSCC cell lines have lower numbers of CSCs, which inversely correlates with radiosensitivity. Human papillomavirus–negative HNSCC cell lines lack hierarchy owing to enhanced spontaneous dedifferentiation. Non-CSCs from HPV-negative lines show enhanced radiation-induced dedifferentiation compared with HPV-positive lines, and RT induced re-expression of Yamanaka reprogramming factors. Conclusions: Supporting the favorable prognosis of HPV-positive HNSCCs, we show that (1) HPV-positive HNSCCs have a lower frequency of CSCs; (2) RT can dedifferentiate HNSCC cells into CSCs; and (3) radiation-induced dedifferentiation depends on the HPV status of the tumor.« less

Radiation-Induced Dedifferentiation of Head and Neck Cancer Cells Into Cancer Stem Cells Depends on Human Papillomavirus Status.

PubMed

Vlashi, Erina; Chen, Allen M; Boyrie, Sabrina; Yu, Garrett; Nguyen, Andrea; Brower, Philip A; Hess, Clayton B; Pajonk, Frank

2016-04-01

To test the hypothesis that the radiation response of cancer stem cells (CSCs) in human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) differs and is not reflected in the radiation response of the bulk tumor populations, that radiation therapy (RT) can dedifferentiate non-stem HNSCC cells into CSCs, and that radiation-induced dedifferentiation depends on the HPV status. Records of a cohort of 162 HNSCC patients were reviewed, and their outcomes were correlated with their HPV status. Using a panel of HPV-positive and HPV-negative HNSCC cell lines expressing a reporter for CSCs, we characterized HPV-positive and HPV-negative lines via flow cytometry, sphere-forming capacity assays in vitro, and limiting dilution assays in vivo. Non-CSCs were treated with different doses of radiation, and the dedifferentiation of non-CSCs into CSCs was investigated via flow cytometry and quantitative reverse transcription-polymerase chain reaction for re-expression of reprogramming factors. Patients with HPV-positive tumors have superior overall survival and local-regional control. Human papillomavirus-positive HNSCC cell lines have lower numbers of CSCs, which inversely correlates with radiosensitivity. Human papillomavirus-negative HNSCC cell lines lack hierarchy owing to enhanced spontaneous dedifferentiation. Non-CSCs from HPV-negative lines show enhanced radiation-induced dedifferentiation compared with HPV-positive lines, and RT induced re-expression of Yamanaka reprogramming factors. Supporting the favorable prognosis of HPV-positive HNSCCs, we show that (1) HPV-positive HNSCCs have a lower frequency of CSCs; (2) RT can dedifferentiate HNSCC cells into CSCs; and (3) radiation-induced dedifferentiation depends on the HPV status of the tumor. Copyright © 2016 Elsevier Inc. All rights reserved.

Non-resident fathers' relationships with their secondary school age children: determinants and children's mental health outcomes.

PubMed

Flouri, Eirini

2006-08-01

Data from 520 British secondary school age children were used to explore determinants of and mental health outcomes (measured with the Strengths and Difficulties Questionnaire) from their non-resident fathers' relationships (child-reported father's involvement and frequency of contact) with them. Frequency of contact was negatively related to time elapsed since parents separated, and was higher if fathers were single than partnered. Compared to White, non-White adolescents reported lower frequency of father's contact but not lower father's involvement. Father's involvement was related positively to mother's involvement and negatively to interparental conflict. As a whole, non-resident father's involvement and frequency of contact did not improve the regression models predicting children's total difficulties or pro-social behaviour. Even after controlling for other factors non-resident father's involvement did not predict child's difficulties or pro-social behaviour, although frequency of contact was negatively associated with child's emotional symptoms. Neither child's ethnicity or gender nor mother's partner status moderated the link between child's mental health outcomes and non-resident father's involvement or frequency of contact.

Self-Injurious Behavior and Suicide Attempts among Indonesian College Students

ERIC Educational Resources Information Center

Tresno, Fiona; Ito, Yoshimi; Mearns, Jack

2012-01-01

This study reports the prevalence of self-injurious behavior and suicide attempts among college students in Indonesia and examines risk factors distinguishing between 3 groups: self-injury with suicide attempt, non-suicidal self-injury, and non-self-injury. Self-report questionnaires measuring self-injury and suicide attempts, negative mood…

Can positive matrix factorization help to understand patterns of organic trace gases at the continental Global Atmosphere Watch site Hohenpeissenberg?

NASA Astrophysics Data System (ADS)

Leuchner, M.; Gubo, S.; Schunk, C.; Wastl, C.; Kirchner, M.; Menzel, A.; Plass-Dülmer, C.

2015-02-01

From the rural Global Atmosphere Watch (GAW) site Hohenpeissenberg in the pre-alpine area of southern Germany, a data set of 24 C2-C8 non-methane hydrocarbons over a period of 7 years was analyzed. Receptor modeling was performed by positive matrix factorization (PMF) and the resulting factors were interpreted with respect to source profiles and photochemical aging. Differing from other studies, no direct source attribution was intended because, due to chemistry along transport, mass conservation from source to receptor is not given. However, at remote sites such as Hohenpeissenberg, the observed patterns of non-methane hydrocarbons can be derived from combinations of factors determined by PMF. A six-factor solution showed high stability and the most plausible results. In addition to a biogenic and a background factor of very stable compounds, four additional anthropogenic factors were resolved that could be divided into two short- and two long-lived patterns from evaporative sources/natural gas leakage and incomplete combustion processes. The volume or mass contribution at the site over the entire period was, in decreasing order, from the following factor categories: background, gas leakage and long-lived evaporative, residential heating and long-lived combustion, short-lived evaporative, short-lived combustion, and biogenic. The importance with respect to reactivity contribution was generally in reverse order, with the biogenic and the short-lived combustion factors contributing most. The seasonality of the factors was analyzed and compared to results of a simple box model using constant emissions and the photochemical decay calculated from the measured annual cycles of OH radicals and ozone. Two of the factors, short-lived combustion and gas leakage/long-lived evaporative, showed winter/summer ratios of about 9 and 7, respectively, as expected from constant source estimations. Contrarily, the short-lived evaporative emissions were about 3 times higher in summer than in winter, while residential heating/long-lived combustion emissions were about 2 times higher in winter than in summer.

Integration of living cells into nanostructures using non-conventional self-assembly

NASA Astrophysics Data System (ADS)

Carnes, Eric C.

Patternable cell immobilization is an essential feature of any solid-state device designed for interrogating or exploiting living cells. Immobilized cells must remain viable in a robust matrix that promotes fluidic connectivity between the cells and their environment while retaining the ability to establish and maintain necessary chemical gradients. A suitable inorganic matrix can be constructed via evaporation-induced self-assembly of nanostructured silica, in which phospholipids are used in place of traditional surfactant structure-directing agents in order to enhance cell viability and to create a coherent interface between the cell and the surrounding three-dimensional nanostructure. We have used this technique to develop two distinct cell encapsulation processes: cell-directed assembly and cell-directed integration. Cell-directed assembly is a one-step procedure that provides superior viability of immobilized cells by encouraging cells to interact with the developing host matrix. Limitations of this system include low viability for some cell types due to exposure to solvents and stresses, as well as a lack of control over the developing host nanostructure. Cell-directed integration addresses these shortcomings by introducing a two-step process in which cells become encapsulated in a pre-formed silica matrix. The validity of each encapsulation method has been demonstrated with Gram-positive and Gram-negative bacteria, yeast, and mammalian cells. The ability of the immobilized cells to establish relevant gradients of ions or signaling molecules, a key feature of these systems, has been characterized. Additionally, extension of cell encapsulation to address lingering questions in cell biology is addressed. We have also adapted these immobilization processes to be compatible with a variety of patterning strategies having tailorable properties. Widely available photolithography techniques, as well as direct aerosol deposition, have been adapted to provide methods for obtaining both positive and negative transfer of desired cell patterns. Multi-step lithography is also used to create a highly functional system allowing spatial control of not only cells but also media and other molecules of interest.

Identifying Dust Sources by Positive Matrix Factorization (PMF)

NASA Astrophysics Data System (ADS)

Engelbrecht, Johann P.

2010-05-01

This presentation is on the source attribution by Positive Matrix Factorization (PMF) of aerosol samples collected in Iraq, a major source of mineral dust in the Middle East. Globally transported mineral dust from North Africa, the Middle East, China, and elsewhere are routinely being sampled at high elevation monitoring sites such as those on the Canary Islands and Hawaii, and many ambient monitoring sites worldwide. Chemical results of these filter samples reflect differences in sources impacting at each site, further complicated by the regional geomorphology and meteorology. Trace elements, isotopes, elemental ratios, and mineralogy are generally being used to pinpoint geological source regions of natural and anthropogenic dusts. A receptor site is seldom impacted by only one source at a time. Dust palls are continually being modified by added dust from soils across which they migrate, also by particle segregation in the dust plume, and precipitation of the coarser particles. The result is that dust is a mixture, with contributions from different sources, each with a different chemical and mineralogical signature. PMF is a non-negative factorization procedure that produces only positive factor scores and loadings, in contrast to classical factor analysis (FA) and Principal Components Analysis (PCA). PMF enables us to resolve factors (chemical signatures) for source types contributing to the ambient chemical data set, and also models the source-type contributions to individual ambient samples. The latter can often be related to specific source regions. PMF was applied separately to two ambient data sets collected in Iraq in 2006, the one on Teflon membrane filters and the other on quartz fiber. Each of the filter types were previously analyzed for different chemical species: Teflon membrane for elements, by XRF and ICP-MS, while quartz fiber filters were analyzed for ions and carbon. [Engelbrecht et al. 2009] A set of 392 Teflon filter samples analyzed for 25 elemental species was modeled by PMF. A five factor solution identified three soil factors, a silicate soil, limestone soil, and a gypsum soil, as well as a salt factor and an anthropogenic metal factor. Similarly, a set of 362 quartz filter samples analyzed for 10 selected chemical species was modeled by PMF. A five factor solution provided a limestone-gypsum soil, diesel combustion, secondary ammonium sulfate, salt and agricultural-burnpit combustion source type. Examples of time series plots of PMF factor contributions for each of six sampling sites (Balad, Baghdad, Tallil, Tikrit, Taji, and Al Asad) will be discussed. Engelbrecht , J. P., McDonald, E. V., Gillies, J. A., Jayanty, R. K. M., Casuccio, G., and Gertler, A. W., 2009, Characterizing mineral dusts and other aerosols from the Middle East - Part 1: Ambient sampling: Inhalation Toxicology, v. 21, p. 297-326.

Factor structure of the Positive and Negative Affect Schedule (PANAS) in adult women with fibromyalgia from Southern Spain: the al-Ándalus project.

PubMed

Estévez-López, Fernando; Pulido-Martos, Manuel; Armitage, Christopher J; Wearden, Alison; Álvarez-Gallardo, Inmaculada C; Arrayás-Grajera, Manuel Javier; Girela-Rejón, María J; Carbonell-Baeza, Ana; Aparicio, Virginia A; Geenen, Rinie; Delgado-Fernández, Manuel; Segura-Jiménez, Víctor

2016-01-01

Fibromyalgia is a syndrome characterized by the presence of widespread chronic pain. People with fibromyalgia report lower levels of Positive Affect and higher levels of Negative Affect than non-fibromyalgia peers. The Positive and Negative Affect Schedule (PANAS)-a widely used questionnaire to assess two core domains of affect; namely 'Positive Affect' and 'Negative Affect' -has a controversial factor structure varying across studies. The internal structure of a measurement instrument has an impact on the meaning and validity of its score. Therefore, the aim of the present study was to assess the structural construct validity of the PANAS in adult women with fibromyalgia. This population-based cross-sectional study included 442 adult women with fibromyalgia (age: 51.3 ± 7.4 years old) from Andalusia (Southern Spain). Confirmatory factor analyses were conducted to test the factor structure of the PANAS. A structure with two correlated factors (Positive Affect and Negative Affect) obtained the best fit; S-B χ(2) = 288.49, df = 155, p < .001; RMSEA = .04; 90% CI of RMSEA = (.036, .052); the best fit SRMR = .05; CFI = .96; CAIC = -810.66, respectively. The present study demonstrates that both Positive Affect and Negative Affect are core dimensions of affect in adult women with fibromyalgia. A structure with two correlated factors of the PANAS emerged from our sample of women with fibromyalgia from Andalusia (Southern Spain). In this model, the amount of variance shared by Positive Affect and Negative Affect was small. Therefore, our findings support to use and interpret the Positive Affect and Negative Affect subscales of the PANAS as separate factors that are associated but distinctive as well.

Generalized sidelobe canceller beamforming method for ultrasound imaging.

PubMed

Wang, Ping; Li, Na; Luo, Han-Wu; Zhu, Yong-Kun; Cui, Shi-Gang

2017-03-01

A modified generalized sidelobe canceller (IGSC) algorithm is proposed to enhance the resolution and robustness against the noise of the traditional generalized sidelobe canceller (GSC) and coherence factor combined method (GSC-CF). In the GSC algorithm, weighting vector is divided into adaptive and non-adaptive parts, while the non-adaptive part does not block all the desired signal. A modified steer vector of the IGSC algorithm is generated by the projection of the non-adaptive vector on the signal space constructed by the covariance matrix of received data. The blocking matrix is generated based on the orthogonal complementary space of the modified steer vector and the weighting vector is updated subsequently. The performance of IGSC was investigated by simulations and experiments. Through simulations, IGSC outperformed GSC-CF in terms of spatial resolution by 0.1 mm regardless there is noise or not, as well as the contrast ratio respect. The proposed IGSC can be further improved by combining with CF. The experimental results also validated the effectiveness of the proposed algorithm with dataset provided by the University of Michigan.

The role of BRCA1-IRIS in the development and progression of triple negative breast cancers in Egypt: possible link to disease early lesion.

PubMed

Bogan, Danielle; Meile, Lucio; El Bastawisy, Ahmed; Yousef, Hend F; Zekri, Abdel-Rahman N; Bahnassy, Abeer A; ElShamy, Wael M

2017-05-12

Breast cancer is the most globally diagnosed female cancer, with the triple negative breast cancer (TNBC) being the most aggressive subtype of the disease. In this study we aimed at comparing the effect of BRCA1-IRIS overexpression on the clinico-pathological characteristics in breast cancer patients with TNBC or non-TNBC in the largest comprehensive cancer center in Egypt. To reach this goal, we conducted an observational study at the National Cancer Institute (NCI), Cairo University (Cairo, Egypt). The data on all diagnosed breast cancer patients, between 2009 and 2012, were reviewed. BRCA1-IRIS expression measured using real time RT/PCR in these patients' tumor samples was correlated to tumor characteristics, such as to clinico-pathological features, therapeutic responses, and survival outcomes. 96 patients were enrolled and of these 45% were TNBC, and 55% were of other subtypes (hereafter, non-TNBC). All patients presented with invasive ductal carcinomas. No significant difference was observed for risk factors, such as age and menopausal status between the TNBC and the non-TNBC groups except after BRCA1-IRIS expression was factored in. The majority of the tumors in both groups were ≤5 cm at surgery (p = 0.013). However, in the TNBC group, ≤5 cm tumors were BRCA1-IRIS-overexpressing, whereas in the non-TNBC group they were BRCA1-IRIS-negative (p = 0.00007). Most of the TNBC patients diagnosed with grade 1 or 2 were BRCA1-IRIS-overexpressing, whereas non-TNBCs were IRIS-negative (p = 0.00035). No statistical significance was measured in patients diagnosed with grade 3 tumors. Statistically significant difference between TNBCs and non-TNBCs and tumor stage with regard to BRCA1-IRIS-overexpression was observed. Presence of axillary lymph node metastases was positively associated with BRCA1-IRIS overexpression in TNBC group, and with BRCA1-IRIS-negative status in the non-TNBC group (p = 0.00009). Relapse after chemotherapy (p < 0.00001), and local recurrence/distant metastasis after surgery (p = 0.0028) were more pronounced in TNBC patients with BRCA1-IRIS-overexpressing tumors compared to non-TNBC patients. Finally, decreased disease-free survival in TNBC/BRCA1-IRIS-overexpressing patients compared to TNBC/BRCA1-IRIS-negative patients, and decreased overall survival in TNBC as well as non-TNBC patients was driven by BRCA1-IRIS overexpression. TNBC/BRCA1-IRIS-overexpressing tumors are more aggressive than TNBC/BRCA1-IRIS-negative or non-TNBC/BRCA1-IRIS-overexpressing or both negative tumors. Further studies are warranted to define whether BRCA1-IRIS drives the early TNBC lesions growth and dissemination and whether it could be used as a diagnostic biomarker and/or therapeutic target for these lesions at an early stage setting.

Heart rate reactivity associated to positive and negative food and non-food visual stimuli.

PubMed

Kuoppa, Pekka; Tarvainen, Mika P; Karhunen, Leila; Narvainen, Johanna

2016-08-01

Using food as a stimuli is known to cause multiple psychophysiological reactions. Heart rate variability (HRV) is common tool for assessing physiological reactions in autonomic nervous system. However, the findings in HRV related to food stimuli have not been consistent. In this paper the quick changes in HRV related to positive and negative food and non-food visual stimuli are investigated. Electrocardiogram (ECG) was measured from 18 healthy females while being stimulated with the pictures. Subjects also filled Three-Factor Eating Questionnaire to determine their eating behavior. The inter-beat-interval time series and the HRV parameters were extracted from the ECG. The quick change in HRV parameters were studied by calculating the change from baseline value (10 s window before stimulus) to value after the onset of the stimulus (10 s window during stimulus). The paired t-test showed significant difference between positive and negative food pictures but not between positive and negative non-food pictures. All the HRV parameters decreased for positive food pictures while they stayed the same or increased a little for negative food pictures. The eating behavior characteristic cognitive restraint was negatively correlated with HRV parameters that describe decreasing of heart rate.

A novel highly charged exopolysaccharide produced by two strains of Stenotrophomonas maltophilia recovered from patients with cystic fibrosis.

PubMed

Cescutti, Paola; Cuzzi, Bruno; Liut, Gianfranco; Segonds, Christine; Di Bonaventura, Giovanni; Rizzo, Roberto

2011-09-27

Stenotrophomonas maltophilia is a non-fermenting Gram-negative microorganism capable of causing chronic pulmonary infection in cystic fibrosis patients and its ability to form biofilms on polystyrene and glass surfaces, as well as on cystic fibrosis-derived bronchial epithelial IB3-I cells was recently demonstrated. The latter evidence might explain the power of S. maltophilia to produce persistent lung infections, despite intensive antibiotic treatment. In addition to being important components of the extracellular biofilm matrix, polysaccharides are involved in virulence, as they contribute to bacterial survival in a hostile environment. With the aim of contributing to the elucidation of S. maltophilia virulence factors, the exopolysaccharides produced by two mucoid clinical isolates of S. maltophilia obtained from two cystic fibrosis patients were completely characterised, mainly by means of ESI-MS and NMR spectroscopy. The results showed that, although the two isolates were recovered from two different patients living in different countries (Italy and France), the exopolysaccharides produced have an identical primary structure, with the following repeating unit: The exopolysaccharide is highly negatively charged for the presence of three uronic acids on four residues in the repeating unit. Moreover, an ether-linked d-lactate substituent is located on C-3 and one O-acetyl group on C-4 of the galacturonic acid side chain. Another O-acetyl group substitutes C-2 of the galacturonic acid in the backbone, making this primary structure unique. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Sorption properties of various polysaccharide matrixes to Lactobacillus plantarum 8RA-3 bacteria].

PubMed

Bondarenko, V M; Larionov, I V; Rybal'chenko, O V; Potokin, I L; Ryzhankova, A V

2011-01-01

Study of sorption properties of various spherical polysaccharide matrixes designated as Spherocell to probiotic Lactobacillus plantarum 8RA-3 bacteria. Industrial strain of L. plantarum 8PA-3 was used. The process of immobilization of lactobacilli on 3 variants of spherical sorbents was studied. The first sorbent - neutral, composed of nonpolar cellulose matrix with ("0") charge, the second--DEAE obtained by modification of cellulose by diethylaminoethyl groups with positive ("+") charge and the third--CM (carboxymethyl) with negative ("-") charge. Cellulose matrixes were designated by us by the term Spherocell. Immobilization of bacterial cells on Spherocell was performed by addition of suspension containing 1.0 x 10(9) CFU/ml. The effect of bacterial immobilization was evaluated by CFU/ ml titration and by electron microscopy. The dependence on matrix charge of adsorption immobilization on sorbent granules of lactobacilli cells was shown. At certain equal parameters (granule size, surface characteristics, charge value) the positively charged matrix sorbed 3-10 times more cells than neutral and 20-25 times more than negatively charged matrix. Each 100-180 microm Spherocell DEAE particle could sorb more than 1000 viable bacterial cells. Positively charged polysaccharide matrix Spherocell DEAE obtained by modification of cellulose by diethylaminoethyl groups is promising for creation of immobilized probiotic preparations.

Damage to the anterior arcuate fasciculus predicts non-fluent speech production in aphasia.

PubMed

Fridriksson, Julius; Guo, Dazhou; Fillmore, Paul; Holland, Audrey; Rorden, Chris

2013-11-01

Non-fluent aphasia implies a relatively straightforward neurological condition characterized by limited speech output. However, it is an umbrella term for different underlying impairments affecting speech production. Several studies have sought the critical lesion location that gives rise to non-fluent aphasia. The results have been mixed but typically implicate anterior cortical regions such as Broca's area, the left anterior insula, and deep white matter regions. To provide a clearer picture of cortical damage in non-fluent aphasia, the current study examined brain damage that negatively influences speech fluency in patients with aphasia. It controlled for some basic speech and language comprehension factors in order to better isolate the contribution of different mechanisms to fluency, or its lack. Cortical damage was related to overall speech fluency, as estimated by clinical judgements using the Western Aphasia Battery speech fluency scale, diadochokinetic rate, rudimentary auditory language comprehension, and executive functioning (scores on a matrix reasoning test) in 64 patients with chronic left hemisphere stroke. A region of interest analysis that included brain regions typically implicated in speech and language processing revealed that non-fluency in aphasia is primarily predicted by damage to the anterior segment of the left arcuate fasciculus. An improved prediction model also included the left uncinate fasciculus, a white matter tract connecting the middle and anterior temporal lobe with frontal lobe regions, including the pars triangularis. Models that controlled for diadochokinetic rate, picture-word recognition, or executive functioning also revealed a strong relationship between anterior segment involvement and speech fluency. Whole brain analyses corroborated the findings from the region of interest analyses. An additional exploratory analysis revealed that involvement of the uncinate fasciculus adjudicated between Broca's and global aphasia, the two most common kinds of non-fluent aphasia. In summary, the current results suggest that the anterior segment of the left arcuate fasciculus, a white matter tract that lies deep to posterior portions of Broca's area and the sensory-motor cortex, is a robust predictor of impaired speech fluency in aphasic patients, even when motor speech, lexical processing, and executive functioning are included as co-factors. Simply put, damage to those regions results in non-fluent aphasic speech; when they are undamaged, fluent aphasias result.

Damage to the anterior arcuate fasciculus predicts non-fluent speech production in aphasia

PubMed Central

Guo, Dazhou; Fillmore, Paul; Holland, Audrey; Rorden, Chris

2013-01-01

Non-fluent aphasia implies a relatively straightforward neurological condition characterized by limited speech output. However, it is an umbrella term for different underlying impairments affecting speech production. Several studies have sought the critical lesion location that gives rise to non-fluent aphasia. The results have been mixed but typically implicate anterior cortical regions such as Broca’s area, the left anterior insula, and deep white matter regions. To provide a clearer picture of cortical damage in non-fluent aphasia, the current study examined brain damage that negatively influences speech fluency in patients with aphasia. It controlled for some basic speech and language comprehension factors in order to better isolate the contribution of different mechanisms to fluency, or its lack. Cortical damage was related to overall speech fluency, as estimated by clinical judgements using the Western Aphasia Battery speech fluency scale, diadochokinetic rate, rudimentary auditory language comprehension, and executive functioning (scores on a matrix reasoning test) in 64 patients with chronic left hemisphere stroke. A region of interest analysis that included brain regions typically implicated in speech and language processing revealed that non-fluency in aphasia is primarily predicted by damage to the anterior segment of the left arcuate fasciculus. An improved prediction model also included the left uncinate fasciculus, a white matter tract connecting the middle and anterior temporal lobe with frontal lobe regions, including the pars triangularis. Models that controlled for diadochokinetic rate, picture-word recognition, or executive functioning also revealed a strong relationship between anterior segment involvement and speech fluency. Whole brain analyses corroborated the findings from the region of interest analyses. An additional exploratory analysis revealed that involvement of the uncinate fasciculus adjudicated between Broca’s and global aphasia, the two most common kinds of non-fluent aphasia. In summary, the current results suggest that the anterior segment of the left arcuate fasciculus, a white matter tract that lies deep to posterior portions of Broca’s area and the sensory-motor cortex, is a robust predictor of impaired speech fluency in aphasic patients, even when motor speech, lexical processing, and executive functioning are included as co-factors. Simply put, damage to those regions results in non-fluent aphasic speech; when they are undamaged, fluent aphasias result. PMID:24131592

Desire thinking: A risk factor for binge eating?

PubMed

Spada, Marcantonio M; Caselli, Gabriele; Fernie, Bruce A; Manfredi, Chiara; Boccaletti, Fabio; Dallari, Giulia; Gandini, Federica; Pinna, Eleonora; Ruggiero, Giovanni M; Sassaroli, Sandra

2015-08-01

In the current study we explored the role of desire thinking in predicting binge eating independently of Body Mass Index, negative affect and irrational food beliefs. A sample of binge eaters (n=77) and a sample of non-binge eaters (n=185) completed the following self-report instruments: Hospital Anxiety and Depression Scale, Irrational Food Beliefs Scale, Desire Thinking Questionnaire, and Binge Eating Scale. Mann-Whitney U tests revealed that all variable scores were significantly higher for binge eaters than non-binge eaters. A logistic regression analysis indicated that verbal perseveration was a predictor of classification as a binge eater over and above Body Mass Index, negative affect and irrational food beliefs. A hierarchical regression analysis, on the combined sample, indicated that verbal perseveration predicted levels of binge eating independently of Body Mass Index, negative affect and irrational food beliefs. These results highlight the possible role of desire thinking as a risk factor for binge eating. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computing row and column counts for sparse QR and LU factorization

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

Gilbert, John R.; Li, Xiaoye S.; Ng, Esmond G.

2001-01-01

We present algorithms to determine the number of nonzeros in each row and column of the factors of a sparse matrix, for both the QR factorization and the LU factorization with partial pivoting. The algorithms use only the nonzero structure of the input matrix, and run in time nearly linear in the number of nonzeros in that matrix. They may be used to set up data structures or schedule parallel operations in advance of the numerical factorization. The row and column counts we compute are upper bounds on the actual counts. If the input matrix is strong Hall and theremore » is no coincidental numerical cancellation, the counts are exact for QR factorization and are the tightest bounds possible for LU factorization. These algorithms are based on our earlier work on computing row and column counts for sparse Cholesky factorization, plus an efficient method to compute the column elimination tree of a sparse matrix without explicitly forming the product of the matrix and its transpose.« less

Cell Proliferation and Epidermal Growth Factor Signaling in Non-small Cell Lung Adenocarcinoma Cell Lines Are Dependent on Rin1

PubMed Central

Tomshine, Jin C.; Severson, Sandra R.; Wigle, Dennis A.; Sun, Zhifu; Beleford, Daniah A. T.; Shridhar, Vijayalakshmi; Horazdovsky, Bruce F.

2009-01-01

Rin1 is a Rab5 guanine nucleotide exchange factor that plays an important role in Ras-activated endocytosis and growth factor receptor trafficking in fibroblasts. In this study, we show that Rin1 is expressed at high levels in a large number of non-small cell lung adenocarcinoma cell lines, including Hop62, H650, HCC4006, HCC827, EKVX, HCC2935, and A549. Rin1 depletion from A549 cells resulted in a decrease in cell proliferation that was correlated to a decrease in epidermal growth factor receptor (EGFR) signaling. Expression of wild type Rin1 but not the Rab5 guanine nucleotide exchange factor-deficient Rin1 (Rin1Δ) complemented the Rin1 depletion effects, and overexpression of Rin1Δ had a dominant negative effect on cell proliferation. Rin1 depletion stabilized the cell surface levels of EGFR, suggesting that internalization was necessary for robust signaling in A549 cells. In support of this conclusion, introduction of either dominant negative Rab5 or dominant negative dynamin decreased A549 proliferation and EGFR signaling. These data demonstrate that proper internalization and endocytic trafficking are critical for EGFR-mediated signaling in A549 cells and suggest that up-regulation of Rin1 in A549 cell lines may contribute to their proliferative nature. PMID:19570984

Motor modules in robot-aided walking

PubMed Central

2012-01-01

Background It is hypothesized that locomotion is achieved by means of rhythm generating networks (central pattern generators) and muscle activation generating networks. This modular organization can be partly identified from the analysis of the muscular activity by means of factorization algorithms. The activity of rhythm generating networks is described by activation signals whilst the muscle intervention generating network is represented by motor modules (muscle synergies). In this study, we extend the analysis of modular organization of walking to the case of robot-aided locomotion, at varying speed and body weight support level. Methods Non Negative Matrix Factorization was applied on surface electromyographic signals of 8 lower limb muscles of healthy subjects walking in gait robotic trainer at different walking velocities (1 to 3km/h) and levels of body weight support (0 to 30%). Results The muscular activity of volunteers could be described by low dimensionality (4 modules), as for overground walking. Moreover, the activation signals during robot-aided walking were bursts of activation timed at specific phases of the gait cycle, underlying an impulsive controller, as also observed in overground walking. This modular organization was consistent across the investigated speeds, body weight support level, and subjects. Conclusions These results indicate that walking in a Lokomat robotic trainer is achieved by similar motor modules and activation signals as overground walking and thus supports the use of robotic training for re-establishing natural walking patterns. PMID:23043818

A Green's function method for two-dimensional reactive solute transport in a parallel fracture-matrix system

NASA Astrophysics Data System (ADS)

Chen, Kewei; Zhan, Hongbin

2018-06-01

The reactive solute transport in a single fracture bounded by upper and lower matrixes is a classical problem that captures the dominant factors affecting transport behavior beyond pore scale. A parallel fracture-matrix system which considers the interaction among multiple paralleled fractures is an extension to a single fracture-matrix system. The existing analytical or semi-analytical solution for solute transport in a parallel fracture-matrix simplifies the problem to various degrees, such as neglecting the transverse dispersion in the fracture and/or the longitudinal diffusion in the matrix. The difficulty of solving the full two-dimensional (2-D) problem lies in the calculation of the mass exchange between the fracture and matrix. In this study, we propose an innovative Green's function approach to address the 2-D reactive solute transport in a parallel fracture-matrix system. The flux at the interface is calculated numerically. It is found that the transverse dispersion in the fracture can be safely neglected due to the small scale of fracture aperture. However, neglecting the longitudinal matrix diffusion would overestimate the concentration profile near the solute entrance face and underestimate the concentration profile at the far side. The error caused by neglecting the longitudinal matrix diffusion decreases with increasing Peclet number. The longitudinal matrix diffusion does not have obvious influence on the concentration profile in long-term. The developed model is applied to a non-aqueous-phase-liquid (DNAPL) contamination field case in New Haven Arkose of Connecticut in USA to estimate the Trichloroethylene (TCE) behavior over 40 years. The ratio of TCE mass stored in the matrix and the injected TCE mass increases above 90% in less than 10 years.

Non-uniformity calibration for MWIR polarization imagery obtained with integrated microgrid polarimeters

NASA Astrophysics Data System (ADS)

Liu, Hai-Zheng; Shi, Ze-Lin; Feng, Bin; Hui, Bin; Zhao, Yao-Hong

2016-03-01

Integrating microgrid polarimeters on focal plane array (FPA) of an infrared detector causes non-uniformity of polarization response. In order to reduce the effect of polarization non-uniformity, this paper constructs an experimental setup for capturing raw flat-field images and proposes a procedure for acquiring non-uniform calibration (NUC) matrix and calibrating raw polarization images. The proposed procedure takes the incident radiation as a polarization vector and offers a calibration matrix for each pixel. Both our matrix calibration and two-point calibration are applied to our mid-wavelength infrared (MWIR) polarization imaging system with integrated microgrid polarimeters. Compared with two point calibration, our matrix calibration reduces non-uniformity by 30 40% under condition of flat-field data test with polarization. The ourdoor scene observation experiment indicates that our calibration can effectively reduce polarization non-uniformity and improve the image quality of our MWIR polarization imaging system.

Rectified factor networks for biclustering of omics data.

PubMed

Clevert, Djork-Arné; Unterthiner, Thomas; Povysil, Gundula; Hochreiter, Sepp

2017-07-15

Biclustering has become a major tool for analyzing large datasets given as matrix of samples times features and has been successfully applied in life sciences and e-commerce for drug design and recommender systems, respectively. actor nalysis for cluster cquisition (FABIA), one of the most successful biclustering methods, is a generative model that represents each bicluster by two sparse membership vectors: one for the samples and one for the features. However, FABIA is restricted to about 20 code units because of the high computational complexity of computing the posterior. Furthermore, code units are sometimes insufficiently decorrelated and sample membership is difficult to determine. We propose to use the recently introduced unsupervised Deep Learning approach Rectified Factor Networks (RFNs) to overcome the drawbacks of existing biclustering methods. RFNs efficiently construct very sparse, non-linear, high-dimensional representations of the input via their posterior means. RFN learning is a generalized alternating minimization algorithm based on the posterior regularization method which enforces non-negative and normalized posterior means. Each code unit represents a bicluster, where samples for which the code unit is active belong to the bicluster and features that have activating weights to the code unit belong to the bicluster. On 400 benchmark datasets and on three gene expression datasets with known clusters, RFN outperformed 13 other biclustering methods including FABIA. On data of the 1000 Genomes Project, RFN could identify DNA segments which indicate, that interbreeding with other hominins starting already before ancestors of modern humans left Africa. https://github.com/bioinf-jku/librfn. djork-arne.clevert@bayer.com or hochreit@bioinf.jku.at. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Identification of Logic Relationships between Genes and Subtypes of Non-Small Cell Lung Cancer

PubMed Central

Su, Yansen; Pan, Linqiang

2014-01-01

Non-small cell lung cancer (NSCLC) has two major subtypes: adenocarcinoma (AC) and squamous cell carcinoma (SCC). The diagnosis and treatment of NSCLC are hindered by the limited knowledge about the pathogenesis mechanisms of subtypes of NSCLC. It is necessary to research the molecular mechanisms related with AC and SCC. In this work, we improved the logic analysis algorithm to mine the sufficient and necessary conditions for the presence states (presence or absence) of phenotypes. We applied our method to AC and SCC specimens, and identified lower and higher logic relationships between genes and two subtypes of NSCLC. The discovered relationships were independent of specimens selected, and their significance was validated by statistic test. Compared with the two earlier methods (the non-negative matrix factorization method and the relevance analysis method), the current method outperformed these methods in the recall rate and classification accuracy on NSCLC and normal specimens. We obtained biomarkers. Among biomarkers, genes have been used to distinguish AC from SCC in practice, and other six genes were newly discovered biomarkers for distinguishing subtypes. Furthermore, NKX2-1 has been considered as a molecular target for the targeted therapy of AC, and other genes may be novel molecular targets. By gene ontology analysis, we found that two biological processes (‘epidermis development’ and ‘cell adhesion’) were closely related with the tumorigenesis of subtypes of NSCLC. More generally, the current method could be extended to other complex diseases for distinguishing subtypes and detecting the molecular targets for targeted therapy. PMID:24743794

Temporal growth factor release from platelet-rich plasma, trehalose lyophilized platelets, and bone marrow aspirate and their effect on tendon and ligament gene expression.

PubMed

McCarrel, Taralyn; Fortier, Lisa

2009-08-01

Platelet-rich plasma (PRP) has generated substantial interest for tendon and ligament regeneration because of the high concentrations of growth factors in platelet alpha-granules. This study compared the temporal release of growth factors from bone marrow aspirate (BMA), PRP, and lyophilized platelet product (PP), and measured their effects on tendon and ligament gene expression. Blood and BMA were collected and processed to yield PRP and plasma. Flexor digitorum superficialis tendon (FDS) and suspensory ligament (SL) explants were cultured in 10% plasma in DMEM (control), BMA, PRP, or PP. TGF-beta1 and PDGF-BB concentrations were determined at 0, 24, and 96 h of culture using ELISA. Quantitative RT-PCR for collagen types I and III (COL1A1, COL3A1), cartilage oligomeric matrix protein (COMP), decorin, and matrix metalloproteinases-3 and 13 (MMP-3, MMP-13) was performed. TGF-beta1 and PDGF-BB concentrations were highest in PRP and PP. Growth factor quantity was unchanged in BMA, increased in PRP, and decreased in PP over 4 days. TGF-beta1 and platelet concentrations were positively correlated. Lyophilized PP and PRP resulted in increased COL1A1:COL3A1 ratio, increased COMP, and decreased MMP-13 expression. BMA resulted in decreased COMP and increased MMP-3 and MMP-13 gene expression. Platelet concentration was positively correlated with COL1A1, ratio of COL1A1:COL3A1, and COMP, and negatively correlated with COL3A1, MMP-13, and MMP-3. White blood cell concentration was positively correlated with COL3A1, MMP3, and MMP13, and negatively correlated with a ratio of COL1A1:COL3A1, COMP, and decorin. These findings support further in vivo investigation of PRP and PP for treatment of tendonitis and desmitis. Copyright 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Laplace-domain waveform modeling and inversion for the 3D acoustic-elastic coupled media

NASA Astrophysics Data System (ADS)

Shin, Jungkyun; Shin, Changsoo; Calandra, Henri

2016-06-01

Laplace-domain waveform inversion reconstructs long-wavelength subsurface models by using the zero-frequency component of damped seismic signals. Despite the computational advantages of Laplace-domain waveform inversion over conventional frequency-domain waveform inversion, an acoustic assumption and an iterative matrix solver have been used to invert 3D marine datasets to mitigate the intensive computing cost. In this study, we develop a Laplace-domain waveform modeling and inversion algorithm for 3D acoustic-elastic coupled media by using a parallel sparse direct solver library (MUltifrontal Massively Parallel Solver, MUMPS). We precisely simulate a real marine environment by coupling the 3D acoustic and elastic wave equations with the proper boundary condition at the fluid-solid interface. In addition, we can extract the elastic properties of the Earth below the sea bottom from the recorded acoustic pressure datasets. As a matrix solver, the parallel sparse direct solver is used to factorize the non-symmetric impedance matrix in a distributed memory architecture and rapidly solve the wave field for a number of shots by using the lower and upper matrix factors. Using both synthetic datasets and real datasets obtained by a 3D wide azimuth survey, the long-wavelength component of the P-wave and S-wave velocity models is reconstructed and the proposed modeling and inversion algorithm are verified. A cluster of 80 CPU cores is used for this study.

Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts

PubMed Central

Roy, Sujoy; Yun, Daqing; Madahian, Behrouz; Berry, Michael W.; Deng, Lih-Yuan; Goldowitz, Daniel; Homayouni, Ramin

2017-01-01

In this study, we developed and evaluated a novel text-mining approach, using non-negative tensor factorization (NTF), to simultaneously extract and functionally annotate transcriptional modules consisting of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts. A sparse 3-mode term × gene × TF tensor was constructed that contained weighted frequencies of 106,895 terms in 26,781 abstracts shared among 7,695 genes and 994 TFs. The tensor was decomposed into sub-tensors using non-negative tensor factorization (NTF) across 16 different approximation ranks. Dominant entries of each of 2,861 sub-tensors were extracted to form term–gene–TF annotated transcriptional modules (ATMs). More than 94% of the ATMs were found to be enriched in at least one KEGG pathway or GO category, suggesting that the ATMs are functionally relevant. One advantage of this method is that it can discover potentially new gene–TF associations from the literature. Using a set of microarray and ChIP-Seq datasets as gold standard, we show that the precision of our method for predicting gene–TF associations is significantly higher than chance. In addition, we demonstrate that the terms in each ATM can be used to suggest new GO classifications to genes and TFs. Taken together, our results indicate that NTF is useful for simultaneous extraction and functional annotation of transcriptional regulatory networks from unstructured text, as well as for literature based discovery. A web tool called Transcriptional Regulatory Modules Extracted from Literature (TREMEL), available at http://binf1.memphis.edu/tremel, was built to enable browsing and searching of ATMs. PMID:28894735

Influence of misfit stresses on dislocation glide in single crystal superalloys: A three-dimensional discrete dislocation dynamics study

NASA Astrophysics Data System (ADS)

Gao, Siwen; Fivel, Marc; Ma, Anxin; Hartmaier, Alexander

2015-03-01

In the characteristic γ / γ ‧ microstructure of single crystal superalloys, misfit stresses occur due to a significant lattice mismatch of those two phases. The magnitude of this lattice mismatch depends on the chemical composition of both phases as well as on temperature. Furthermore, the lattice mismatch of γ and γ ‧ phases can be either positive or negative in sign. The internal stresses caused by such lattice mismatch play a decisive role for the micromechanical processes that lead to the observed macroscopic athermal deformation behavior of these high-temperature alloys. Three-dimensional discrete dislocation dynamics (DDD) simulations are applied to investigate dislocation glide in γ matrix channels and shearing of γ ‧ precipitates by superdislocations under externally applied uniaxial stresses, by fully taking into account internal misfit stresses. Misfit stress fields are calculated by the fast Fourier transformation (FFT) method and hybridized with DDD simulations. For external loading along the crystallographic [001] direction of the single crystal, it was found that the different internal stress states for negative and positive lattice mismatch result in non-uniform dislocation movement and different dislocation patterns in horizontal and vertical γ matrix channels. Furthermore, positive lattice mismatch produces a lower deformation rate than negative lattice mismatch under the same tensile loading, but for an increasing magnitude of lattice mismatch, the deformation resistance always diminishes. Hence, the best deformation performance is expected to result from alloys with either small positive, or even better, vanishing lattice mismatch between γ and γ ‧ phase.

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

DOE PAGES

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.; ...

2016-08-30

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

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

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

Therapeutic Strategies for Modulating the Extracellular Matrix to Improve Pancreatic Islet Function and Survival After Transplantation.

PubMed

Smink, Alexandra M; de Vos, Paul

2018-05-19

Extracellular matrix (ECM) components modulate the interaction between pancreatic islet cells. During the islet isolation prior to transplantation as treatment for type 1 diabetes, the ECM is disrupted impacting functional graft survival. Recently, strategies for restoring ECM have shown to improve transplantation outcomes. This review discusses the current therapeutic strategies to modulate ECM components to improve islet engraftment. Approaches applied are seeding islets in ECM of decellularized organs, supplementation of specific ECM components in polymeric scaffolds or immunoisolating capsules, and stimulating islet ECM production with specific growth factors or ECM-producing cells. These strategies have shown success in improving functional islet survival. However, the same experiments show that caution should be taken as some ECM components may negatively impact islet function and engraftment. ECM restoration resulted in improved transplantation outcomes, but careful selection of beneficial ECM components and strategies is warranted.

Efficient system modeling for a small animal PET scanner with tapered DOI detectors.

PubMed

Zhang, Mengxi; Zhou, Jian; Yang, Yongfeng; Rodríguez-Villafuerte, Mercedes; Qi, Jinyi

2016-01-21

A prototype small animal positron emission tomography (PET) scanner for mouse brain imaging has been developed at UC Davis. The new scanner uses tapered detector arrays with depth of interaction (DOI) measurement. In this paper, we present an efficient system model for the tapered PET scanner using matrix factorization and a virtual scanner geometry. The factored system matrix mainly consists of two components: a sinogram blurring matrix and a geometrical matrix. The geometric matrix is based on a virtual scanner geometry. The sinogram blurring matrix is estimated by matrix factorization. We investigate the performance of different virtual scanner geometries. Both simulation study and real data experiments are performed in the fully 3D mode to study the image quality under different system models. The results indicate that the proposed matrix factorization can maintain image quality while substantially reduce the image reconstruction time and system matrix storage cost. The proposed method can be also applied to other PET scanners with DOI measurement.

How electronic dynamics with Pauli exclusion produces Fermi-Dirac statistics.

PubMed

Nguyen, Triet S; Nanguneri, Ravindra; Parkhill, John

2015-04-07

It is important that any dynamics method approaches the correct population distribution at long times. In this paper, we derive a one-body reduced density matrix dynamics for electrons in energetic contact with a bath. We obtain a remarkable equation of motion which shows that in order to reach equilibrium properly, rates of electron transitions depend on the density matrix. Even though the bath drives the electrons towards a Boltzmann distribution, hole blocking factors in our equation of motion cause the electronic populations to relax to a Fermi-Dirac distribution. These factors are an old concept, but we show how they can be derived with a combination of time-dependent perturbation theory and the extended normal ordering of Mukherjee and Kutzelnigg for a general electronic state. The resulting non-equilibrium kinetic equations generalize the usual Redfield theory to many-electron systems, while ensuring that the orbital occupations remain between zero and one. In numerical applications of our equations, we show that relaxation rates of molecules are not constant because of the blocking effect. Other applications to model atomic chains are also presented which highlight the importance of treating both dephasing and relaxation. Finally, we show how the bath localizes the electron density matrix.

Analytic tools for investigating the structure of network reliability measures with regard to observation correlations

NASA Astrophysics Data System (ADS)

Prószyński, W.; Kwaśniak, M.

2018-03-01

A global measure of observation correlations in a network is proposed, together with the auxiliary indices related to non-diagonal elements of the correlation matrix. Based on the above global measure, a specific representation of the correlation matrix is presented, being the result of rigorously proven theorem formulated within the present research. According to the theorem, each positive definite correlation matrix can be expressed by a scale factor and a so-called internal weight matrix. Such a representation made it possible to investigate the structure of the basic reliability measures with regard to observation correlations. Numerical examples carried out for two test networks illustrate the structure of those measures that proved to be dependent on global correlation index. Also, the levels of global correlation are proposed. It is shown that one can readily find an approximate value of the global correlation index, and hence the correlation level, for the expected values of auxiliary indices being the only knowledge about a correlation matrix of interest. The paper is an extended continuation of the previous study of authors that was confined to the elementary case termed uniform correlation. The extension covers arbitrary correlation matrices and a structure of correlation effect.

Recurrence quantity analysis based on matrix eigenvalues

NASA Astrophysics Data System (ADS)

Yang, Pengbo; Shang, Pengjian

2018-06-01

Recurrence plots is a powerful tool for visualization and analysis of dynamical systems. Recurrence quantification analysis (RQA), based on point density and diagonal and vertical line structures in the recurrence plots, is considered to be alternative measures to quantify the complexity of dynamical systems. In this paper, we present a new measure based on recurrence matrix to quantify the dynamical properties of a given system. Matrix eigenvalues can reflect the basic characteristics of the complex systems, so we show the properties of the system by exploring the eigenvalues of the recurrence matrix. Considering that Shannon entropy has been defined as a complexity measure, we propose the definition of entropy of matrix eigenvalues (EOME) as a new RQA measure. We confirm that EOME can be used as a metric to quantify the behavior changes of the system. As a given dynamical system changes from a non-chaotic to a chaotic regime, the EOME will increase as well. The bigger EOME values imply higher complexity and lower predictability. We also study the effect of some factors on EOME,including data length, recurrence threshold, the embedding dimension, and additional noise. Finally, we demonstrate an application in physiology. The advantage of this measure lies in a high sensitivity and simple computation.

Neanderthal and Denisova tooth protein variants in present-day humans

PubMed Central

Zanolli, Clément; Hourset, Mathilde; Esclassan, Rémi

2017-01-01

Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein). Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes) and one is the derived enamelin major variant, T648I (rs7671281), associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or disease susceptibility in these populations. This modern regional distribution of archaic dental polymorphisms may reflect persistence of archaic variants in some populations and may contribute in part to the geographic dental variations described in modern humans. PMID:28902892

Emotion-Bracelet: A Web Service for Expressing Emotions through an Electronic Interface.

PubMed

Martinez, Alicia; Estrada, Hugo; Molina, Alejandra; Mejia, Manuel; Perez, Joaquin

2016-11-24

The mechanisms to communicate emotions have dramatically changed in the last 10 years with social networks, where users massively communicate their emotional states by using the Internet. However, people with socialization problems have difficulty expressing their emotions verbally or interpreting the environment and providing an appropriate emotional response. In this paper, a novel solution called the Emotion-Bracelet is presented that combines a hardware device and a software system. The proposed approach identifies the polarity and emotional intensity of texts published on a social network site by performing real-time processing using a web service. It also shows emotions with a LED matrix using five emoticons that represent positive, very positive, negative, very negative, and neutral states. The Emotion-Bracelet is designed to help people express their emotions in a non-intrusive way, thereby expanding the social aspect of human emotions.

Emotion-Bracelet: A Web Service for Expressing Emotions through an Electronic Interface

PubMed Central

Martinez, Alicia; Estrada, Hugo; Molina, Alejandra; Mejia, Manuel; Perez, Joaquin

2016-01-01

The mechanisms to communicate emotions have dramatically changed in the last 10 years with social networks, where users massively communicate their emotional states by using the Internet. However, people with socialization problems have difficulty expressing their emotions verbally or interpreting the environment and providing an appropriate emotional response. In this paper, a novel solution called the Emotion-Bracelet is presented that combines a hardware device and a software system. The proposed approach identifies the polarity and emotional intensity of texts published on a social network site by performing real-time processing using a web service. It also shows emotions with a LED matrix using five emoticons that represent positive, very positive, negative, very negative, and neutral states. The Emotion-Bracelet is designed to help people express their emotions in a non-intrusive way, thereby expanding the social aspect of human emotions. PMID:27886130

Osteoblastic differentiation of human stem cells derived from bone marrow and periodontal ligament under the effect of enamel matrix derivative and transforming growth factor-beta.

PubMed

Houshmand, Behzad; Behnia, Hossein; Khoshzaban, Ahad; Morad, Golnaz; Behrouzi, Gholamreza; Dashti, Seyedeh Ghazaleh; Khojasteh, Arash

2013-01-01

To increase the understanding of the applicability of biomaterials and growth factors in enhancing stem cell-based bone regeneration modalities, this study evaluated the effects of enamel matrix derivative (EMD) and recombinant human transforming growth factor-beta (rhTGF-β) on osteoblastic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) as well as human periodontal ligament stem cells (hPDLSCs). hBMSCs and hPDLSCs were obtained, and identification of stem cell surface markers was performed according to the criteria of the International Society for Cellular Therapy. Each group of stem cells was separately treated with a serial dilution of EMD (10, 50, and 100 μg/mL) or rhTGF-β (10 ng/mL). Osteoblastic differentiation was examined through in vitro matrix mineralization by alizarin red staining, and mRNA expression of osteopontin and osteonectin was determined by quantitative reverse-transcriptase polymerase chain reaction. hPDLSCs were further assessed for osteocalcin mRNA expression. Stem cells cultured in osteogenic medium were employed as a standard positive control group. In none of the experimental groups were bone-related mRNAs detected subsequent to treatment with EMD for 5, 10, and 15 days. Alizarin red staining on day 21 was negative in EMD-treated BMSC and PDLSC cultures. In rhTGF-β-supplemented BMSC culture, expression of osteonectin mRNA was demonstrated on day 15, which was statistically comparable to the positive control group. Nevertheless, extracellular matrix mineralization was inhibited in both groups of stem cells. Within the limitations of this study, it could be concluded that EMD with a concentration of 10, 50, or 100 μg/mL has no appreciable effect on osteoblastic differentiation of BMSCs and PDLSCs. Application of rhTGF-β increased osteonectin mRNA expression in BMSCs. This finding corroborates the hypothesis that TGF-β might be involved in early osteoblastic maturation.

[Pregnancy-Associated Breast Cancer: An analytical observational study].

PubMed

Baulies, Sonia; Cusidó, Maite; Tresserra, Francisco; Rodríguez, Ignacio; Ubeda, Belén; Ara, Carmen; Fábregas, Rafael

2014-03-04

Pregnancy-associated breast cancer is defined as breast cancer diagnosed during pregnancy and up to one year postpartum. A retrospective, analytical, observational study comparing 56 cases of breast cancer and pregnancy (PABC) diagnosed 1976-2008 with 73 patients with breast cancer not associated with pregnancy (non-PABC) was performed. Demographic data, prognostic factors, treatment and survival were reviewed and compared. The prevalence of PABC in our center is 8.3/10,000. The highest frequency (62%) appeared during the postpartum period. The stages are higher in PABC, being 31.3% advanced (EIII and EIV) in PABC versus 13.3% in non-PABC (P < .05). Regarding prognostic factors, 27.3% in PABC had a tumoral grade 3 versus 15.8% of non-PABC. Among women with PABC, 33.3% had negative estrogen receptors, 48.7% negative progesterone receptors and 34.5% positive Her2Neu compared with 22.2, 24.1 and 31%, respectively of non-PABC patients. Finally, positive lymph nodes were found in 52.8% of PABC, versus 33.8% non-PABC (P < .05). Overall and disease-free survival rate at 5 years for PABC was 63.7 and 74.2%, respectively. The poorer survival observed is possibly due to the presence of adverse prognostic features such as lymph node metastases, negative hormone receptors, tumoral grade iii, as well as a delay in diagnosis with a higher rate of advanced stages. Copyright © 2012 Elsevier España, S.L. All rights reserved.

Functional connectivity experiments reflect routine movement behavior of a tropical hummingbird species.

PubMed

Volpe, Noelia L; Hadley, Adam S; Robinson, W Douglas; Betts, Matthew G

Translocation experiments, in which researchers displace animals and then monitor their movements to return home, are commonly used as tools to assess functional connectivity of fragmented landscapes. Such experiments are purported to have important advantages of being time efficient and of standardizing “motivation” to move across individuals. Yet, we lack tests of whether movement behavior of translocated birds reflects natural behavior of unmanipulated birds. We compared the routine movement behavior of a tropical hummingbird, the Green Hermit (Phaethornis guy), to that of experimentally translocated individuals. We tested for differences in site selection patterns during movement at two spatial scales (point and path levels). We also compared movement rates between treatments. Behaviors documented during translocation experiments reflected those observed during routine movements. At the point level, both translocated and non-translocated birds showed similar levels of preference for mature tropical forest. At the path level, step selection functions showed both translocated and non-translocated hummingbirds avoiding movement across non-forested matrix and selecting streams as movement corridors. Movement rates were generally higher during translocation experiments. However, the negative influence of forest cover on movement rates was proportionately similar in translocation and routine movement treatments. We report the first evidence showing that movement behavior of birds during translocation experiments is similar to their natural movement behavior. Therefore, translocation experiments may be reliable tools to address effects of landscape structure on animal movement. We observed consistent selection of landscape elements between translocated and non-translocated birds, indicating that both routine and translocation movement studies lead to similar conclusions regarding the effect of landscape structure and forest composition on functional connectivity. Our observation that hummingbirds avoid non-forest matrix and select riparian corridors also provides a potential mechanism for pollen limitation in fragmented tropical forest.

Perceptions of work and family assistance and the prevalence of lower back problems in a South African manganese factory.

PubMed

van Vuuren, Bernard; van Heerden, Hendrik Johannes; Zinzen, Evert; Becker, Piet; Meeusen, Romain

2006-10-01

An analytical cross-sectional epidemiological study was carried out among 109 manganese plant workers to examine the prevalence and association between lower back problems (LBP) and family and workplace related psychosocial risk factors. Outcome (LBP) was defined using a guided questionnaire and a functional rating index. Exposure to family and workplace related psychosocial risk was determined using the Occupational Risk Factor (ORFQ) and APGAR questionnaires for work and family support. Using inclusive and stringent definitions for perceived LBP, point prevalence was 37.6% and 29.4%, respectively. Only 8 cases of LBP were, however recorded officially over a 7-yr period (1996-2003). Multivariate analyses indicated a high, but non-significant odds ratio (OR) for negative perceptions of workplace support OR 3.29 (CI 0.95-11.30). A positive, non-significant, association for negative perceptions of family support (2.56; CI 0.69-9.52) and a protective, but non-significant, association for control over the order and pace of working tasks (OR 0.40; CI 0.12-1.35) was found. These findings together with the under-reporting, leads one to conclude that work hardening and a cultural ethos of non-complaining among manual labourers, moderates the association between LBP and the aetiological factors studied.

A Note on the Factor Analysis of Partial Covariance Matrices

ERIC Educational Resources Information Center

McDonald, Roderick P.

1978-01-01

The relationship between the factor structure of a convariance matrix and the factor structure of a partial convariance matrix when one or more variables are partialled out of the original matrix is given in this brief note. (JKS)

Wedge disclination dipole in an embedded nanowire within the surface/interface elasticity

NASA Astrophysics Data System (ADS)

Shodja, Hossein M.; Rezazadeh-Kalehbasti, Shaghayegh; Gutkin, Mikhail Yu

2013-12-01

The elastic behavior of an arbitrary oriented wedge disclination dipole located inside a nanowire, which in turn is embedded in an infinite matrix, is studied within the surface/interface theory of elasticity. The corresponding boundary value problem is provided using complex potential functions. The potential functions are defined through modeling the wedge disclination in terms of an equivalent distribution of edge dislocations. The interface effects on the stress field and strain energy of the disclination dipole and image forces acting on it, the influence of relative shear moduli of the nanowire and the matrix, as well as the different characteristics of the interface are studied thoroughly. It is shown that the positive interface modulus leads to increased strain energy and extra repulsive forces on the disclination dipole. The noticeable effect of the negative interface modulus is the non-classical oscillations in the stress field of the disclination dipole and an extra attractive image force on it.

Matrix elements and duality for type 2 unitary representations of the Lie superalgebra gl(m|n)

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

Werry, Jason L.; Gould, Mark D.; Isaac, Phillip S.

The characteristic identity formalism discussed in our recent articles is further utilized to derive matrix elements of type 2 unitary irreducible gl(m|n) modules. In particular, we give matrix element formulae for all gl(m|n) generators, including the non-elementary generators, together with their phases on finite dimensional type 2 unitary irreducible representations which include the contravariant tensor representations and an additional class of essentially typical representations. Remarkably, we find that the type 2 unitary matrix element equations coincide with the type 1 unitary matrix element equations for non-vanishing matrix elements up to a phase.

Application of micromechanics to the characterization of mortar by ultrasound.

PubMed

Hernández, M G; Anaya, J J; Izquierdo, M A G; Ullate, L G

2002-05-01

Mechanical properties of concrete and mortar structures can be estimated by ultrasonic non-destructive testing. When the ultrasonic velocity is known, there are standardized methods based on considering the concrete a homogeneous material. Cement composites, however, are heterogeneous and porous, and have a negative effect on the mechanical properties of structures. This work studies the impact of porosity on mechanical properties by considering concrete a multiphase material. A micromechanical model is applied in which the material is considered to consist of two phases: a solid matrix and pores. From this method, a set of expressions is obtained that relates the acoustic velocity and Young's modulus of mortar. Experimental work is based on non-destructive and destructive procedures over mortar samples whose porosity is varied. A comparison is drawn between micromechanical and standard methods, showing positive results for the method here proposed.

Airborne agent concentration analysis

DOEpatents

Gelbard, Fred

2004-02-03

A method and system for inferring airborne contaminant concentrations in rooms without contaminant sensors, based on data collected by contaminant sensors in other rooms of a building, using known airflow interconnectivity data. The method solves a least squares problem that minimizes the difference between measured and predicted contaminant sensor concentrations with respect to an unknown contaminant release time. Solutions are constrained to providing non-negative initial contaminant concentrations in all rooms. The method can be used to identify a near-optimal distribution of sensors within the building, when then number of available sensors is less than the total number of rooms. This is achieved by having a system-sensor matrix that is non-singular, and by selecting that distribution which yields the lowest condition number of all the distributions considered. The method can predict one or more contaminant initial release points from the collected data.

Prognostication in Philadelphia Chromosome Negative Myeloproliferative Neoplasms: a Review of the Recent Literature.

PubMed

Zhou, Amy; Afzal, Amber; Oh, Stephen T

2017-10-01

The prognosis for patients with Philadelphia chromosome (Ph)-negative myeloproliferative neoplasms (MPNs) is highly variable. All Ph-negative MPNs carry an increased risk for thrombotic complications, bleeding, and leukemic transformation. Several clinical, biological, and molecular prognostic factors have been identified in recent years, which provide important information in guiding management of patients with Ph-negative MPNs. In this review, we critically evaluate the recent published literature and discuss important new developments in clinical and molecular factors that impact survival, disease transformation, and thrombosis in patients with polycythemia vera, essential thrombocythemia, and primary myelofibrosis. Recent studies have identified several clinical factors and non-driver mutations to have prognostic impact on Ph-negative MPNs independent of conventional risk stratification and prognostic models. In polycythemia vera (PV), leukocytosis, abnormal karyotype, phlebotomy requirement on hydroxyurea, increased bone marrow fibrosis, and mutations in ASXL1, SRSF2, and IDH2 were identified as additional adverse prognostic factors. In essential thrombocythemia (ET), JAK2 V617F mutation, splenomegaly, and mutations in SH2B3, SF3B1, U2AF1, TP53, IDH2, and EZH2 were found to be additional negative prognostic factors. Bone marrow fibrosis and mutations in ASXL1, SRSF2, EZH2, and IDH1/2 have been found to be additional prognostic factors in primary myelofibrosis (PMF). CALR mutations appear to be a favorable prognostic factor in PMF, which has not been clearly demonstrated in ET. The prognosis for patients with PV, ET, and PMF is dependent upon the presence or absence of several clinical, biological, and molecular risk factors. The significance of additional risk factors identified in these recent studies will need further validation in prospective studies to determine how they may be best utilized in the management of these disorders.

Lactoferricin Enhances BMP7-Stimulated Anabolic Pathways in Intervertebral Disc Cells

PubMed Central

Ellman, Michael B; Kim, Jaesung; An, Howard S; Chen, Di; Kc, Ranjan; Li, Xin; Xiao, Guozhi; Yan, Dongyao; Suh, Joon; van Wijnen, Andre J.; Wang, James H-C; Kim, Su-Gwan; Im, Hee-Jeong

2013-01-01

Bone-morphogenetic protein-7 (BMP7) is a well-known anabolic and anti-catabolic growth factor on intervertebral (IVD) matrix and cell homeostasis. Similarly, lactoferricin B (LfcinB) has recently been shown to have pro-anabolic, anti-catabolic, anti-oxidative and/or anti-inflammatory effects in bovine disc cells in vitro. In this study, we investigated the potential benefits of using combined peptide therapy with LfcinB and BMP7 for intervertebral disc (IVD) matrix repair and to understand cellular and signaling mechanisms controlled by these factors. We studied the effects of BMP7 and LfcinB as individual treatments and combined therapy on bovine nucleus pulposus (NP) cells by assessing proteoglycan (PG) accumulation and synthesis, and the expression of matrix protein aggrecan and transcription factor SOX-9. We also analyzed the role of noggin, a BMP antagonist, in IVD tissue and examined its effect after stimulation with LfcinB. To understand the molecular mechanisms by which LfcinB synergizes with BMP7, we investigated the ERK-SP1 axis as a downstream intracellular signaling regulator involved in BMP7 and LfcinB-mediated activities. Treatment of bovine NP cells cultured in alginate with LfcinB plus BMP7 synergistically stimulates PG synthesis and accumulation in part by upregulation of aggrecan gene expression. The synergism results from LfcinB-mediated activation of Sp1 and SMAD signaling pathways by (i) phosphorylation of SMAD 1/5/8; (ii) downregulation of SMAD inhibitory factors [i.e., noggin (BMP receptor antagonist) and SMAD6 (inhibitory SMAD)]; and (iii) upregulation of SMAD4 (universal co-SMAD). These data indicate that LfcinB-suppression of noggin may eliminate the negative feedback of BMP7, thereby maximizing biological activity of BMP7 and ultimately shifting homeostasis to a pro-anabolic state in disc cells. We propose that combination growth factor therapy using BMP7 and LfcinB may be beneficial for treatment of disc degeneration. PMID:23644135

Lactoferricin enhances BMP7-stimulated anabolic pathways in intervertebral disc cells.

PubMed

Ellman, Michael B; Kim, Jaesung; An, Howard S; Chen, Di; Kc, Ranjan; Li, Xin; Xiao, Guozhi; Yan, Dongyao; Suh, Joon; van Wjnen, Andre J; Wang, James H-C; Kim, Su-Gwan; Im, Hee-Jeong

2013-07-25

Bone-morphogenetic protein-7 (BMP7) is a well-known anabolic and anti-catabolic growth factor on intervertebral disc (IVD) matrix and cell homeostasis. Similarly, Lactoferricin B (LfcinB) has recently been shown to have pro-anabolic, anti-catabolic, anti-oxidative and/or anti-inflammatory effects in bovine disc cells in vitro. In this study, we investigated the potential benefits of using combined peptide therapy with LfcinB and BMP7 for intervertebral disc matrix repair and to understand cellular and signaling mechanisms controlled by these factors. We studied the effects of BMP7 and LfcinB as individual treatments and combined therapy on bovine nucleus pulposus (NP) cells by assessing proteoglycan (PG) accumulation and synthesis, and the gene expression of matrix protein aggrecan and transcription factor SOX-9. We also analyzed the role of Noggin, a BMP antagonist, in IVD tissue and examined its effect after stimulation with LfcinB. To understand the molecular mechanisms by which LfcinB synergizes with BMP7, we investigated the ERK-SP1 axis as a downstream intracellular signaling regulator involved in BMP7 and LfcinB-mediated activities. Treatment of bovine NP cells cultured in alginate with LfcinB plus BMP7 synergistically stimulates PG synthesis and accumulation in part by upregulation of aggrecan gene expression. The synergism results from LfcinB-mediated activation of Sp1 and SMAD signaling pathways by (i) phosphorylation of SMAD 1/5/8; (ii) downregulation of SMAD inhibitory factors [i.e., noggin and SMAD6 (inhibitory SMAD)]; and (iii) upregulation of SMAD4 (universal co-SMAD). These data indicate that LfcinB-suppression of Noggin may eliminate the negative feedback of BMP7, thereby maximizing biological activity of BMP7 and ultimately shifting homeostasis to a pro-anabolic state in disc cells. We propose that combination growth factor therapy using BMP7 and LfcinB may be beneficial for treatment of disc degeneration. Copyright © 2013 Elsevier B.V. All rights reserved.

Risk factors for non-alcoholic fatty liver disease are common in patients with non-B non-C hepatocellular carcinoma in India.

PubMed

David, Deepu; Raghavendran, Anantharam; Goel, Ashish; Bharath Kumar, C; Kodiatte, Thomas Alex; Burad, Deepak; Abraham, Priya; Ramakrishna, Banumathi; Joseph, Philip; Ramachandran, Jeyamani; Eapen, C E

2017-09-01

The aim of the study was to analyze the prevalence of risk factors for non-alcoholic fatty liver disease (NAFLD) in patients with non-B non-C hepatocellular carcinoma (HCC). Between June 2012 and November 2014, patients with HCC, negative for hepatitis B surface antigen and hepatitis C virus antibody, were included in this study. All patients were assessed for risk factors for NAFLD such as diabetes mellitus (DM), hypertension, dyslipidemia, metabolic syndrome, and obesity. Forty-seven patients with non-B non-C HCC (males, 37; age, 60±10 years; mean±SD) were studied. Model for end-stage liver disease score was 11±4. Twenty-five patients were in Child's class A. History of significant alcohol intake was noted in 11 (23%) patients. Prevalence of risk factors for NAFLD were obesity 24 (51%), DM 22 (47%), metabolic syndrome 21 (45%), hypertension 16 (34%), and dyslipidemia 13 (28%). Forty (85%) patients had at least one risk factor for NAFLD. The mean duration of at least one NAFLD risk factor was 7.5 years, prior to diagnosis of HCC. Thirteen (28%) patients were positive for anti-HBc; however, none of the study patients had detectable HBV DNA in blood. Eighty-five percent of the patients with non-B non-C HCC had at least one risk factor for NAFLD. None of the study patients had occult hepatitis B infection. NAFLD is emerging as the major etiological contributing factor for non-B non-C HCC in India.

Collective Human Mobility Pattern from Taxi Trips in Urban Area

PubMed Central

Peng, Chengbin; Jin, Xiaogang; Wong, Ka-Chun; Shi, Meixia; Liò, Pietro

2012-01-01

We analyze the passengers' traffic pattern for 1.58 million taxi trips of Shanghai, China. By employing the non-negative matrix factorization and optimization methods, we find that, people travel on workdays mainly for three purposes: commuting between home and workplace, traveling from workplace to workplace, and others such as leisure activities. Therefore, traffic flow in one area or between any pair of locations can be approximated by a linear combination of three basis flows, corresponding to the three purposes respectively. We name the coefficients in the linear combination as traffic powers, each of which indicates the strength of each basis flow. The traffic powers on different days are typically different even for the same location, due to the uncertainty of the human motion. Therefore, we provide a probability distribution function for the relative deviation of the traffic power. This distribution function is in terms of a series of functions for normalized binomial distributions. It can be well explained by statistical theories and is verified by empirical data. These findings are applicable in predicting the road traffic, tracing the traffic pattern and diagnosing the traffic related abnormal events. These results can also be used to infer land uses of urban area quite parsimoniously. PMID:22529917

Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI.

PubMed

Sauwen, N; Acou, M; Van Cauter, S; Sima, D M; Veraart, J; Maes, F; Himmelreich, U; Achten, E; Van Huffel, S

2016-01-01

Tumor segmentation is a particularly challenging task in high-grade gliomas (HGGs), as they are among the most heterogeneous tumors in oncology. An accurate delineation of the lesion and its main subcomponents contributes to optimal treatment planning, prognosis and follow-up. Conventional MRI (cMRI) is the imaging modality of choice for manual segmentation, and is also considered in the vast majority of automated segmentation studies. Advanced MRI modalities such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have already shown their added value in tumor tissue characterization, hence there have been recent suggestions of combining different MRI modalities into a multi-parametric MRI (MP-MRI) approach for brain tumor segmentation. In this paper, we compare the performance of several unsupervised classification methods for HGG segmentation based on MP-MRI data including cMRI, DWI, MRSI and PWI. Two independent MP-MRI datasets with a different acquisition protocol were available from different hospitals. We demonstrate that a hierarchical non-negative matrix factorization variant which was previously introduced for MP-MRI tumor segmentation gives the best performance in terms of mean Dice-scores for the pathologic tissue classes on both datasets.

Graphical Methods for Quantifying Macromolecules through Bright Field Imaging

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

Chang, Hang; DeFilippis, Rosa Anna; Tlsty, Thea D.

Bright ?eld imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition, and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to Flbroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color imagesmore » into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quanti?ed by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of samplepreparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions, and (iv) has a superior computing performance« less

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

Hyperspectral cytometry.

PubMed

Grégori, Gérald; Rajwa, Bartek; Patsekin, Valery; Jones, James; Furuki, Motohiro; Yamamoto, Masanobu; Paul Robinson, J

2014-01-01

Hyperspectral cytometry is an emerging technology for single-cell analysis that combines ultrafast optical spectroscopy and flow cytometry. Spectral cytometry systems utilize diffraction gratings or prism-based monochromators to disperse fluorescence signals from multiple labels (organic dyes, nanoparticles, or fluorescent proteins) present in each analyzed bioparticle onto linear detector arrays such as multianode photomultipliers or charge-coupled device sensors. The resultant data, consisting of a series of characterizing every analyzed cell, are not compensated by employing the traditional cytometry approach, but rather are spectrally unmixed utilizing algorithms such as constrained Poisson regression or non-negative matrix factorization. Although implementations of spectral cytometry were envisioned as early as the 1980s, only recently has the development of highly sensitive photomultiplier tube arrays led to design and construction of functional prototypes and subsequently to introduction of commercially available systems. This chapter summarizes the historical efforts and work in the field of spectral cytometry performed at Purdue University Cytometry Laboratories and describes the technology developed by Sony Corporation that resulted in release of the first commercial spectral cytometry system-the Sony SP6800. A brief introduction to spectral data analysis is also provided, with emphasis on the differences between traditional polychromatic and spectral cytometry approaches.

NMF-Based Image Quality Assessment Using Extreme Learning Machine.

PubMed

Wang, Shuigen; Deng, Chenwei; Lin, Weisi; Huang, Guang-Bin; Zhao, Baojun

2017-01-01

Numerous state-of-the-art perceptual image quality assessment (IQA) algorithms share a common two-stage process: distortion description followed by distortion effects pooling. As for the first stage, the distortion descriptors or measurements are expected to be effective representatives of human visual variations, while the second stage should well express the relationship among quality descriptors and the perceptual visual quality. However, most of the existing quality descriptors (e.g., luminance, contrast, and gradient) do not seem to be consistent with human perception, and the effects pooling is often done in ad-hoc ways. In this paper, we propose a novel full-reference IQA metric. It applies non-negative matrix factorization (NMF) to measure image degradations by making use of the parts-based representation of NMF. On the other hand, a new machine learning technique [extreme learning machine (ELM)] is employed to address the limitations of the existing pooling techniques. Compared with neural networks and support vector regression, ELM can achieve higher learning accuracy with faster learning speed. Extensive experimental results demonstrate that the proposed metric has better performance and lower computational complexity in comparison with the relevant state-of-the-art approaches.

Muscle synergies and complexity of neuromuscular control during gait in cerebral palsy.

PubMed

Steele, Katherine M; Rozumalski, Adam; Schwartz, Michael H

2015-12-01

Individuals with cerebral palsy (CP) have impaired movement due to a brain injury near birth. Understanding how neuromuscular control is altered in CP can provide insight into pathological movement. We sought to determine if individuals with CP demonstrate reduced complexity of neuromuscular control during gait compared with unimpaired individuals and if changes in control are related to functional ability. Muscle synergies during gait were retrospectively analyzed for 633 individuals (age range 3.9-70y): 549 with CP (hemiplegia, n=122; diplegia, n=266; triplegia, n=73; quadriplegia, n=88) and 84 unimpaired individuals. Synergies were calculated using non-negative matrix factorization from surface electromyography collected during previous clinical gait analyses. Synergy complexity during gait was compared with diagnosis subtype, functional ability, and clinical examination measures. Fewer synergies were required to describe muscle activity during gait in individuals with CP compared with unimpaired individuals. Changes in synergies were related to functional impairment and clinical examination measures including selective motor control, strength, and spasticity. Individuals with CP use a simplified control strategy during gait compared with unimpaired individuals. These results were similar to synergies during walking among adult stroke survivors, suggesting similar neuromuscular control strategies between these clinical populations. © 2015 Mac Keith Press.

Fault detection, isolation, and diagnosis of self-validating multifunctional sensors.

PubMed

Yang, Jing-Li; Chen, Yin-Sheng; Zhang, Li-Li; Sun, Zhen

2016-06-01

A novel fault detection, isolation, and diagnosis (FDID) strategy for self-validating multifunctional sensors is presented in this paper. The sparse non-negative matrix factorization-based method can effectively detect faults by using the squared prediction error (SPE) statistic, and the variables contribution plots based on SPE statistic can help to locate and isolate the faulty sensitive units. The complete ensemble empirical mode decomposition is employed to decompose the fault signals to a series of intrinsic mode functions (IMFs) and a residual. The sample entropy (SampEn)-weighted energy values of each IMFs and the residual are estimated to represent the characteristics of the fault signals. Multi-class support vector machine is introduced to identify the fault mode with the purpose of diagnosing status of the faulty sensitive units. The performance of the proposed strategy is compared with other fault detection strategies such as principal component analysis, independent component analysis, and fault diagnosis strategies such as empirical mode decomposition coupled with support vector machine. The proposed strategy is fully evaluated in a real self-validating multifunctional sensors experimental system, and the experimental results demonstrate that the proposed strategy provides an excellent solution to the FDID research topic of self-validating multifunctional sensors.

The Sox2 high mobility group transcription factor inhibits mature osteoblast function in transgenic mice

PubMed Central

Holmes, Greg; Bromage, Timothy G.; Basilico, Claudio

2011-01-01

We have previously shown that in osteoblasts Sox2 expression can be induced by Fgfs, and can inhibit Wnt signaling and differentiation. Furthermore, in mice in which Sox2 is conditionally deleted in the osteoblastic lineage, bones are osteopenic, and Sox2 inactivation in cultured osteoblasts leads to a loss of proliferative ability with a senescent phenotype. To help understand the role of Sox2 in osteoblast development we have specifically expressed Sox2 in bone from a Col1α1 promoter, which extended Sox2 expression into more mature osteoblasts. In long bones, trabecular cartilage remodeling was delayed and the transition from endochondral to cortical bone was disrupted, resulting in porous and undermineralized cortical bone. Collagen deposition was disorganized, and patterns of osteoclast activity were altered. Calvarial bones were thinner and parietal bones failed to develop the diploic space. Microarray analysis showed significant up- or downregulation of a variety of genes coding for non-collagenous extracellular matrix proteins, with a number of genes typical of mature osteoblasts being downregulated. Our results position Sox2 as a negative regulator of osteoblast maturation in vivo. PMID:21703370

Age-related differences in muscle control of the lower extremity for support and propulsion during walking

PubMed Central

Toda, Haruki; Nagano, Akinori; Luo, Zhiwei

2016-01-01

[Purpose] This study examined age-related differences in muscle control for support and propulsion during walking in both males and females in order to develop optimal exercise regimens for muscle control. [Subjects and Methods] Twenty elderly people and 20 young people participated in this study. Coordinates of anatomical landmarks and ground reaction force during walking were obtained using a 3D motion analysis system and force plates. Muscle forces during walking were estimated using OpenSim. Muscle modules were obtained by using non-negative matrix factorization analysis. A two-way analysis of covariance was performed to examine the difference between the elderly and the young in muscle weightings using walking speed as a covariate. The similarities in activation timing profiles between the elderly and the young were analyzed by cross-correlation analysis in males and females. [Results] In the elderly, there was a change in the coordination of muscles around the ankle, and muscles of the lower extremity exhibited co-contraction in late stance. Timing and shape of these modules were similar between elderly and young people. [Conclusion] Our results suggested that age-related alteration of muscle control was associated with support and propulsion during walking. PMID:27134360

Topic Modeling Reveals Distinct Interests within an Online Conspiracy Forum

PubMed Central

Klein, Colin; Clutton, Peter; Polito, Vince

2018-01-01

Conspiracy theories play a troubling role in political discourse. Online forums provide a valuable window into everyday conspiracy theorizing, and can give a clue to the motivations and interests of those who post in such forums. Yet this online activity can be difficult to quantify and study. We describe a unique approach to studying online conspiracy theorists which used non-negative matrix factorization to create a topic model of authors' contributions to the main conspiracy forum on Reddit.com. This subreddit provides a large corpus of comments which spans many years and numerous authors. We show that within the forum, there are multiple sub-populations distinguishable by their loadings on different topics in the model. Further, we argue, these differences are interpretable as differences in background beliefs and motivations. The diversity of the distinct subgroups places constraints on theories of what generates conspiracy theorizing. We argue that traditional “monological” believers are only the tip of an iceberg of commenters. Neither simple irrationality nor common preoccupations can account for the observed diversity. Instead, we suggest, those who endorse conspiracies seem to be primarily brought together by epistemological concerns, and that these central concerns link an otherwise heterogenous group of individuals. PMID:29515501

Effect of flaw size and temperature on the matrix cracking behavior of a brittle ceramic matrix composite

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

Anandakumar, U.; Webb, J.E.; Singh, R.N.

The matrix cracking behavior of a zircon matrix - uniaxial SCS 6 fiber composite was studied as a function of initial flaw size and temperature. The composites were fabricated by a tape casting and hot pressing technique. Surface flaws of controlled size were introduced using a vicker`s indenter. The composite samples were tested in three point flexure at three different temperatures to study the non steady state and steady state matrix cracking behavior. The composite samples exhibited steady state and non steady matrix cracking behavior at all temperatures. The steady state matrix cracking stress and steady state crack size increasedmore » with increasing temperature. The results of the study correlated well with the results predicted by the matrix cracking models.« less

Associations between cognitive biases and domains of schizotypy in a non-clinical sample.

PubMed

Aldebot Sacks, Stephanie; Weisman de Mamani, Amy Gina; Garcia, Cristina Phoenix

2012-03-30

Schizotypy is a non-clinical manifestation of the same underlying biological factors that give rise to psychotic disorders (Claridge and Beech, 1995). Research on normative populations scoring high on schizotypy is valuable because it may help elucidate the predisposition to schizophrenia (Jahshan and Sergi, 2007) and because performance is not confounded by issues present in schizophrenia samples. In the current study, a Confirmatory Factor Analysis was conducted using several comprehensive measures of schizotypy. As expected and replicating prior research, a four-factor model of schizotypy emerged including a positive, a negative, a cognitive disorganization, and an impulsive nonconformity factor. We also evaluated how each factor related to distinct cognitive biases. In support of hypotheses, increased self-certainty, decreased theory of mind, and decreased source memory were associated with higher scores on the positive factor; decreased theory of mind was associated with higher scores on the negative factor; and increased self-certainty was associated with greater impulsive nonconformity. Unexpectedly, decreased self-certainty and increased theory of mind were associated with greater cognitive disorganization, and decreased source memory was associated with greater impulsive nonconformity. These findings offer new insights by highlighting cognitive biases that may be risk factors for psychosis. Published by Elsevier Ireland Ltd.

Transformed PANSS Factors Intended to Reduce Pseudospecificity Among Symptom Domains and Enhance Understanding of Symptom Change in Antipsychotic-Treated Patients With Schizophrenia

PubMed Central

Hopkins, Seth C; Ogirala, Ajay; Loebel, Antony; Koblan, Kenneth S

2018-01-01

Abstract Positive and Negative Syndrome Scale (PANSS) total score is the standard primary efficacy measure in acute treatment studies of schizophrenia. However, PANSS factors that have been derived from factor analytic approaches over the past several decades have uncertain clinical and regulatory status as they are, to varying degrees, intercorrelated. As a consequence of cross-factor correlations, the apparent improvement in key clinical domains (eg, negative symptoms, disorganized thinking/behavior) may largely be attributable to improvement in a related clinical domain, such as positive symptoms, a problem often referred to as pseudospecificity. Here, we analyzed correlations among PANSS items, at baseline and change post-baseline, in a pooled sample of 5 placebo-controlled clinical trials (N = 1710 patients), using clustering and factor analysis to identify an uncorrelated PANSS score matrix (UPSM) that minimized the degree of correlation between each resulting transformed PANSS factor. The transformed PANSS factors corresponded well with discrete symptom domains described by prior factor analyses, but between-factor change-scores correlations were markedly lower. We then used the UPSM to transform PANSS in data from 4657 unique schizophrenia patients included in 12 additional lurasidone clinical trials. The results confirmed that transformed PANSS factors retained a high degree of specificity, thus validating that low between-factor correlations are a reliable property of the USPM when transforming PANSS data from a variety of clinical trial data sets. These results provide a more robust understanding of the structure of symptom change in schizophrenia and suggest a means to evaluate the specificity of antipsychotic treatment effects. PMID:28981857

Online assessment of risk factors for dementia and cognitive function in healthy adults.

PubMed

Huntley, J; Corbett, A; Wesnes, K; Brooker, H; Stenton, R; Hampshire, A; Ballard, C

2018-02-01

Several potentially modifiable risk factors for cognitive decline and dementia have been identified, including low educational attainment, smoking, diabetes, physical inactivity, hypertension, midlife obesity, depression, and perceived social isolation. Managing these risk factors in late midlife and older age may help reduce the risk of dementia; however, it is unclear whether these factors also relate to cognitive performance in older individuals without dementia. Data from 14 201 non-demented individuals aged >50 years who enrolled in the online PROTECT study were used to examine the relationship between cognitive function and known modifiable risk factors for dementia. Multivariate regression analyses were conducted on 4 cognitive outcomes assessing verbal and spatial working memory, visual episodic memory, and verbal reasoning. Increasing age was associated with reduced performance across all tasks. Higher educational achievement, the presence of a close confiding relationship, and moderate alcohol intake were associated with benefits across all 4 cognitive tasks, and exercise was associated with better performance on verbal reasoning and verbal working memory tasks. A diagnosis of depression was negatively associated with performance on visual episodic memory and working memory tasks, whereas being underweight negatively affected performance on all tasks apart from verbal working memory. A history of stroke was negatively associated with verbal reasoning and working memory performance. Known modifiable risk factors for dementia are associated with cognitive performance in non-demented individuals in late midlife and older age. This provides further support for public health interventions that seek to manage these risk factors across the lifespan. Copyright © 2017 John Wiley & Sons, Ltd.

High efficient optical remote sensing images acquisition for nano-satellite: reconstruction algorithms

NASA Astrophysics Data System (ADS)

Liu, Yang; Li, Feng; Xin, Lei; Fu, Jie; Huang, Puming

2017-10-01

Large amount of data is one of the most obvious features in satellite based remote sensing systems, which is also a burden for data processing and transmission. The theory of compressive sensing(CS) has been proposed for almost a decade, and massive experiments show that CS has favorable performance in data compression and recovery, so we apply CS theory to remote sensing images acquisition. In CS, the construction of classical sensing matrix for all sparse signals has to satisfy the Restricted Isometry Property (RIP) strictly, which limits applying CS in practical in image compression. While for remote sensing images, we know some inherent characteristics such as non-negative, smoothness and etc.. Therefore, the goal of this paper is to present a novel measurement matrix that breaks RIP. The new sensing matrix consists of two parts: the standard Nyquist sampling matrix for thumbnails and the conventional CS sampling matrix. Since most of sun-synchronous based satellites fly around the earth 90 minutes and the revisit cycle is also short, lots of previously captured remote sensing images of the same place are available in advance. This drives us to reconstruct remote sensing images through a deep learning approach with those measurements from the new framework. Therefore, we propose a novel deep convolutional neural network (CNN) architecture which takes in undersampsing measurements as input and outputs an intermediate reconstruction image. It is well known that the training procedure to the network costs long time, luckily, the training step can be done only once, which makes the approach attractive for a host of sparse recovery problems.

Mechanics of a fiber network within a non-fibrillar matrix: model and comparison with collagen-agarose co-gels

PubMed Central

Lake, Spencer P.; Hadi, Mohammad F.; Lai, Victor K.; Barocas, Victor H.

2013-01-01

While collagen is recognized as the predominant mechanical component of soft connective tissues, the role of the non-fibrillar matrix (NFM) is less well understood. Even model systems, such as the collagen-agarose co-gel, can exhibit complex behavior, making it difficult to identify relative contributions of specific tissue constituents. In the present study, we developed a two-component microscale model of collagen-agarose tissue analogs and used it to elucidate the interaction between collagen and NFM in uniaxial tension. Collagen fibers were represented with Voronoi networks, and the NFM was modeled as a neo-Hookean solid. Model predictions of total normal stress and Poisson’s ratio matched experimental observations well (including high Poisson’s values of ~3), and the addition of NFM led to composition-dependent decreases in volume change and increases in fiber stretch. Because the NFM was more resistant to volume change than the fiber network, extension of the composite led to pressurization of the NFM. Within a specific range of parameter values (low shear modulus and moderate Poisson’s ratio), the magnitude of the reaction force decreased relative to this pressurization component resulting in a negative (compressive) NFM stress in the loading direction, even though the composite tissue was in tension. PMID:22565816

Comparative proteomics of matrix fractions between pimpled and normal chicken eggshells.

PubMed

Liu, Zhangguo; Song, Lingzi; Lu, Lizhi; Zhang, Xianfu; Zhang, Fuming; Wang, Kehua; Linhardt, Robert J

2017-09-07

Eggshell matrix can be dissociated into three matrix fractions: acid-insoluble matrix (M1), water-insoluble matrix (M2) and acid-water facultative-soluble matrix (M3). Matrix fractions from pimpled and normal eggshells were compared using label-free proteomic method to understand the differences among three matrix fractions and the proteins involved with eggshell quality. A total of 738 and 600 proteins were identified in the pimpled and normal calcified eggshells, respectively. Both eggshells showed a combined proteomic inventory of 769 proteins. In the same type of eggshell, a high similarity was present in the proteomes of three matrix fractions. These triply overlapped common proteins formed the predominant contributor to proteomic abundance in the matrix fractions. In each matrix fraction and between both eggshell models, normal and pimpled eggshells, a majority of the proteomes of the fractions were commonly observed. Forty-two common major proteins (iBAQ-derived abundance ≥0.095% of proteomic abundance) were identified throughout the three matrix fractions and these proteins might act as backbone constituents in chicken eggshell matrix. Finally, using 1.75-fold as up-regulated and using 0.57-fold as down-regulated cutoff values, twenty-five differential major proteins were screened and they all negatively influence and none showed any effect on eggshell quality. Overall, we uncovered the characteristics of proteomics of three eggshell matrix fractions and identified candidate proteins influencing eggshell quality. The next research on differential proteins will uncover the potential mechanisms underlying how proteins affect eggshell quality. It was reported that the proteins in an eggshell can be divided into insoluble and soluble proteins. The insoluble proteins are thought to be an inter-mineral matrix and acts as a structural framework, while the soluble proteins are thought as intra-mineral matrix that are embedded within the crystal during calcification. However, the difference between matrix fractions is unknown. Cross-analysis of proteomic data of three matrix fractions from the same type of eggshell, uncovered triply overlapped common proteins formed the predominant contributor to proteomic abundance of any matrix fraction, and we suggested that abundance variance of some common proteins between the three matrix fractions might be an important cause of their solubility differences. Moreover, eggshell is formed in hen's uterus, and uterus tend to be considered as unique organ determining eggshell quality. By cross-analysis on proteomic data of three matrix fractions between two eggshell models, normal and pimpled eggshells, the differential proteins were screened as candidates influencing eggshell quality. And we suggested that the liver and spleen or lymphocytes might be the major organs influencing eggshell quality, because the most promising candidates are almost blood and non-collagenous proteins, and originated from above organs. Copyright © 2017 Elsevier B.V. All rights reserved.

Risk of non-fatal suicide ideation and behaviour in recent onset schizophrenia--the influence of clinical, social, self-esteem and demographic factors.

PubMed

Tarrier, Nicholas; Barrowclough, Christine; Andrews, Bernice; Gregg, Lynsey

2004-11-01

Suicide rates amongst schizophrenic patients are high. There are disadvantages in investigating successfully completed suicides which make suicidal ideation and previous attempts important proxy measures of suicidal risk. The aim of this study was to investigate factors associated with these risk measures. Fifty-nine patients suffering recent onset schizophrenia were assessed for suicidal ideation and history, and a range of demographic, clinical, social (including relatives' Expressed Emotion) and self-esteem measures. Univariate comparisons were made between those with and without suicide ideation and previous attempts. Path analysis was conducted to identify factors directly or indirectly associated with a composite scale of risk (low, medium or high). Approximately 25% of the sample reported a current desire to kill themselves and 47% had made one or more previous attempts. There were numerous significant univariate differences between those with or without ideation or history. Path analysis indicated that greater hopelessness (OR 1.22) and longer duration of illness (OR 1.13) increased risk. Hopelessness was associated with higher negative self-evaluation and social isolation. Negative self-evaluation was associated with more relatives' criticism which was associated with more negative symptoms. Being a male, unmarried and unemployed were all significantly associated with an increase in negative symptoms. Social isolation was associated with being unemployed, older, more positive symptoms and longer illness duration. Duration of illness was not itself predicted by any other variables. Non-fatal suicide ideation and behaviour are significantly associated with an array of demographic, clinical, interpersonal and psychological factors. To reduce risk of suicide, these factors need to be assessed and methods developed to reduce their influence.

Is Valuing Happiness Associated With Lower Well-Being? A Factor-Level Analysis using the Valuing Happiness Scale

PubMed Central

Luhmann, Maike; Necka, Elizabeth A.; Schönbrodt, Felix D.; Hawkley, Louise C.

2015-01-01

Recent studies suggest that valuing happiness is negatively associated with well-being. Most of these studies used the Valuing Happiness Scale (Mauss, Tamir, et al., 2011). In the present paper, we examined the factor structure of this scale using data pooled from six independent samples (Ntotal = 938). Exploratory and confirmatory factor analysis showed that the Valuing Happiness Scale is not unidimensional and that only one of its three factors correlates negatively with various indicators of well-being, whereas non-significant or positive correlations were found for the other factors. These findings indicate that valuing happiness may not necessarily be bad for one’s well-being, and call for a better definition, theoretical foundation, and operationalization of this construct. PMID:26778865

Negative regulators in homeostasis of naïve peripheral T cells.

PubMed

Modiano, Jaime F; Johnson, Lisa D S; Bellgrau, Donald

2008-01-01

It is now apparent that naïve peripheral T cells are a dynamic population where active processes prevent inappropriate activation while supporting survival. The process of thymic education makes naïve peripheral T cells dependent on interactions with self-MHC for survival. However, as these signals can potentially result in inappropriate activation, various non-redundant, intrinsic negative regulatory molecules including Tob, Nfatc2, and Smad3 actively enforce T cell quiescence. Interactions among these pathways are only now coming to light and may include positive or negative crosstalk. In the case of positive crosstalk, self-MHC initiated signals and intrinsic negative regulatory factors may cooperate to dampen T cell activation and sustain peripheral tolerance in a binary fashion (on-off). In the case of negative crosstalk, self-MHC signals may promote survival through partial activation while intrinsic negative regulatory factors act as rheostats to restrain cell cycle entry and prevent T cells from crossing a threshold that would break tolerance.

Data in support of the negative influence of divalent cations on (−)-epigallocatechin-3-gallate (EGCG)-mediated inhibition of matrix metalloproteinase-2 (MMP-2)

PubMed Central

Deb, Gauri; Batra, Sahil; Limaye, Anil M.

2015-01-01

In this data article we have provided evidence for the negative influence of divalent cations on (−)‐epigallocatechin-3-gallate (EGCG)-mediated inhibition of matrix metalloproteinase-2 (MMP-2) activity in cell-free experiments. Chelating agents, such as EDTA and sodium citrate alone, did not affect MMP-2 activity. While EDTA enhanced, excess of divalent cations interfered with EGCG-mediated inhibition of MMP-2. PMID:26977427

Mechanisms of Normal and Abnormal Endometrial Bleeding

PubMed Central

Lockwood, Charles J.

2011-01-01

Expression of tissue factor (TF), the primary initiator of coagulation, is enhanced in decidualized human endometrial stromal cells (HESC) during the progesterone-dominated luteal phase. Progesterone also augments a second HESC hemostatic factor, plasminogen activator inhibitor-1 (PAI-1). In contrast, progestins inhibit HESC matrix metalloproteinase (MMP)-1, 3 and 9 expression to stabilize endometrial stromal and vascular extracellular matrix. Through these mechanisms decidualized endometrium is rendered both hemostatic and resistant to excess trophoblast invasion in the mid-luteal phase and throughout gestation to prevent hemorrhage and accreta. In non-fertile cycles, progesterone withdrawal results in decreased HESC TF and PAI-expression and increased MMP activity and inflammatory cytokine production promoting the controlled hemorrhage of menstruation and related tissue sloughing. In contrast to these well ordered biochemical processes, unpredictable endometrial bleeding associated with anovulation reflects absence of progestational effects on TF, PAI-1 and MMP activity as well as unrestrained angiogenesis rendering the endometrium non-hemostatic, proteolytic and highly vascular. Abnormal bleeding associated with long-term progestin-only contraceptives results not from impaired hemostasis but from unrestrained angiogenesis leading to large fragile endometrial vessels. This abnormal angiogenesis reflects progestational inhibition of endometrial blood flow promoting local hypoxia and generation of reactive oxygen species that increase production of angiogenic factors such as vascular endothelial growth factor (VEGF) in HESCs and Angiopoietin-2 (Ang-2) in endometrial endothelial cells while decreasing HESC expression of angiostatic, Ang-1. The resulting vessel fragility promotes bleeding. Aberrant angiogenesis also underlies abnormal bleeding associated with myomas and endometrial polyps however there are gaps in our understanding of this pathology. PMID:21499503

Failure of Non-Circular Composite Cylinders

NASA Technical Reports Server (NTRS)

Hyer, M. W.

2004-01-01

In this study, a progressive failure analysis is used to investigate leakage in internally pressurized non-circular composite cylinders. This type of approach accounts for the localized loss of stiffness when material failure occurs at some location in a structure by degrading the local material elastic properties by a certain factor. The manner in which this degradation of material properties takes place depends on the failure modes, which are determined by the application of a failure criterion. The finite-element code STAGS, which has the capability to perform progressive failure analysis using different degradation schemes and failure criteria, is utilized to analyze laboratory scale, graphite-epoxy, elliptical cylinders with quasi-isotropic, circumferentially-stiff, and axially-stiff material orthotropies. The results are divided into two parts. The first part shows that leakage, which is assumed to develop if there is material failure in every layer at some axial and circumferential location within the cylinder, does not occur without failure of fibers. Moreover before fibers begin to fail, only matrix tensile failures, or matrix cracking, takes place, and at least one layer in all three cylinders studied remain uncracked, preventing the formation of a leakage path. That determination is corroborated by the use of different degradation schemes and various failure criteria. Among the degradation schemes investigated are the degradation of different engineering properties, the use of various degradation factors, the recursive or non-recursive degradation of the engineering properties, and the degradation of material properties using different computational approaches. The failure criteria used in the analysis include the noninteractive maximum stress criterion and the interactive Hashin and Tsai-Wu criteria. The second part of the results shows that leakage occurs due to a combination of matrix tensile and compressive, fiber tensile and compressive, and inplane shear failure modes in all three cylinders. Leakage develops after a relatively low amount of fiber damage, at about the same pressure for three material orthotropies, and at approximately the same location.

Bayesian Factor Analysis When Only a Sample Covariance Matrix Is Available

ERIC Educational Resources Information Center

Hayashi, Kentaro; Arav, Marina

2006-01-01

In traditional factor analysis, the variance-covariance matrix or the correlation matrix has often been a form of inputting data. In contrast, in Bayesian factor analysis, the entire data set is typically required to compute the posterior estimates, such as Bayes factor loadings and Bayes unique variances. We propose a simple method for computing…

Prevalence and functions of non-suicidal self-injury in Spanish adolescents.

PubMed

Calvete, Esther; Orue, Izaskun; Aizpuru, Leire; Brotherton, Hardin

2015-01-01

This study examined the prevalence, characteristics and functions of Non-suicidal Self-injury (NSSI) among Spanish adolescents. The sample consisted of 1,864 adolescents aged between 12 and 19 years (Mean Age = 15.32, SD = 1.97, 51.45% girls). The participants completed a modified version of the self-report scale Functional Assessment of Self-Mutilation (FASM; Lloyd, Kelley, & Hope, 1997) to assess rates and methods of NSSI used during the last 12 months. They also indicated the functions of NSSI. NSSI behaviors are common among Spanish adolescents. More than half of the sample showed such behavior in the past year, and 32.2% had carried out severe NSSI behaviors. The functions of NSSI were examined by using confirmatory factor analyses. Results supported a hierarchical model consisting of two second-order factors: automatic reinforcement, which explained both positive and negative automatic reinforcement, and social reinforcement, which explained both positive and negative social reinforcement. These dimensions are critical to understand the factors that maintain NSSI behavior and have implications for treatments.

Algorithms for Solvents and Spectral Factors of Matrix Polynomials

DTIC Science & Technology

1981-01-01

spectral factors of matrix polynomials LEANG S. SHIEHt, YIH T. TSAYt and NORMAN P. COLEMANt A generalized Newton method , based on the contracted gradient...of a matrix poly- nomial, is derived for solving the right (left) solvents and spectral factors of matrix polynomials. Two methods of selecting initial...estimates for rapid convergence of the newly developed numerical method are proposed. Also, new algorithms for solving complete sets of the right

Composition and sources of fine particulate matter across urban and rural sites in the Midwestern United States

PubMed Central

Kundu, Shuvashish; Stone, Elizabeth. A.

2014-01-01

The composition and sources of fine particulate matter (PM2.5) were investigated in rural and urban locations in Iowa, located in the agricultural and industrial Midwestern United States from April 2009 to December 2012. Major chemical contributors to PM2.5 mass were sulfate, nitrate, ammonium, and organic carbon. Non-parametric statistical analyses demonstrated that the two rural sites had significantly enhanced levels of crustal materials (Si, Al) driven by agricultural activities and unpaved roads. Meanwhile, the three urban areas had enhanced levels of secondary aerosol (nitrate, sulfate, and ammonium) and combustion (organic and elemental carbon). The heavily industrialized Davenport site had significantly higher levels of PM2.5 and trace metals (Fe, Pb, Zn), demonstrating the important local impact of industrial point sources on air quality. Sources of PM2.5 were evaluated by the multi-variant positive matrix factorization (PMF) source apportionment model. For each individual site, seven to nine factors were identified: secondary sulfate (accounting for 29–30% of PM2.5), secondary nitrate (17–24%), biomass burning (9–21%), gasoline combustion (6–16), diesel combustion (3–9%), dust (6–11%), industry (0.4–5%) and winter salt (2–6%). Source contributions demonstrated a clear urban enhancement in PM2.5 from gasoline engines (by a factor of 1.14) and diesel engines (by a factor of 2.3), which is significant due to the well-documented negative health impacts of vehicular emissions. This study presents the first source apportionment results from the state of Iowa and is broadly applicable to understanding the differences in anthropogenic and natural sources in the urban-rural continuum of particle air pollution. PMID:24736797

Matrix-directed differentiation of human adipose-derived mesenchymal stem cells to dermal-like fibroblasts that produce extracellular matrix.

PubMed

Sivan, Unnikrishnan; Jayakumar, K; Krishnan, Lissy K

2016-10-01

Commercially available skin substitutes lack essential non-immune cells for adequate tissue regeneration of non-healing wounds. A tissue-engineered, patient-specific, dermal substitute could be an attractive option for regenerating chronic wounds, for which adipose-derived mesenchymal stem cells (ADMSCs) could become an autologous source. However, ADMSCs are multipotent in nature and may differentiate into adipocytes, osteocytes and chondrocytes in vitro, and may develop into undesirable tissues upon transplantation. Therefore, ADMSCs committed to the fibroblast lineage could be a better option for in vitro or in vivo skin tissue engineering. The objective of this study was to standardize in vitro culture conditions for ADMSCs differentiation into dermal-like fibroblasts which can synthesize extracellular matrix (ECM) proteins. Biomimetic matrix composite, deposited on tissue culture polystyrene (TCPS), and differentiation medium (DM), supplemented with fibroblast-conditioned medium and growth factors, were used as a fibroblast-specific niche (FSN) for cell culture. For controls, ADMSCs were cultured on bare TCPS with either DM or basal medium (BM). Culture of ADMSCs on FSN upregulated the expression of differentiation markers such as fibroblast-specific protein-1 (FSP-1) and a panel of ECM molecules specific to the dermis, such as fibrillin-1, collagen I, collagen IV and elastin. Immunostaining showed the deposition of dermal-specific ECM, which was significantly higher in FSN compared to control. Fibroblasts derived from ADMSCs can synthesize elastin, which is an added advantage for successful skin tissue engineering as compared to fibroblasts from skin biopsy. To obtain rapid differentiation of ADMSCs to dermal-like fibroblasts for regenerative medicine, a matrix-directed differentiation strategy may be employed. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

Testing the Perey effect

DOE PAGES

Titus, L. J.; Nunes, Filomena M.

2014-03-12

Here, the effects of non-local potentials have historically been approximately included by applying a correction factor to the solution of the corresponding equation for the local equivalent interaction. This is usually referred to as the Perey correction factor. In this work we investigate the validity of the Perey correction factor for single-channel bound and scattering states, as well as in transfer (p, d) cross sections. Method: We solve the scattering and bound state equations for non-local interactions of the Perey-Buck type, through an iterative method. Using the distorted wave Born approximation, we construct the T-matrix for (p,d) on 17O, 41Ca,more » 49Ca, 127Sn, 133Sn, and 209Pb at 20 and 50 MeV. As a result, we found that for bound states, the Perey corrected wave function resulting from the local equation agreed well with that from the non-local equation in the interior region, but discrepancies were found in the surface and peripheral regions. Overall, the Perey correction factor was adequate for scattering states, with the exception of a few partial waves corresponding to the grazing impact parameters. These differences proved to be important for transfer reactions. In conclusion, the Perey correction factor does offer an improvement over taking a direct local equivalent solution. However, if the desired accuracy is to be better than 10%, the exact solution of the non-local equation should be pursued.« less

Cell plasticity in wound healing: paracrine factors of M1/ M2 polarized macrophages influence the phenotypical state of dermal fibroblasts

PubMed Central

2013-01-01

Background Macrophages and fibroblasts are two major players in tissue repair and fibrosis. Despite the relevance of macrophages and fibroblasts in tissue homeostasis, remarkably little is known whether macrophages are able to influence the properties of fibroblasts. Here we investigated the role of paracrine factors secreted by classically activated (M1) and alternatively activated (M2) human macrophages on human dermal fibroblasts (HDFs). Results HDFs stimulated with paracrine factors from M1 macrophages showed a 10 to > 100-fold increase in the expression of the inflammatory cytokines IL6, CCL2 and CCL7 and the matrix metalloproteinases MMP1 and MMP3. This indicates that factors produced by M1 macrophages induce a fibroblast phenotype with pro-inflammatory and extracellular matrix (ECM) degrading properties. HDFs stimulated with paracrine factors secreted by M2 macrophages displayed an increased proliferation rate. Interestingly, the M1-activated pro-inflammatory fibroblasts downregulated, after exposure to paracrine factors produced by M2 macrophages or non-conditioned media, the inflammatory markers as well as MMPs and upregulated their collagen production. Conclusions Paracrine factors of M1 or M2 polarized macrophages induced different phenotypes of HDFs and the HDF phenotypes can in turn be reversed, pointing to a high dynamic plasticity of fibroblasts in the different phases of tissue repair. PMID:23601247

Body Image as a Mediator of Non-Suicidal Self-Injury in Adolescents

ERIC Educational Resources Information Center

Muehlenkamp, Jennifer J.; Brausch, Amy M.

2012-01-01

Attitudes towards the body have been largely overlooked as a potential risk factor for adolescent non-suicidal self-injury (NSSI) despite theorizing that a negative body image may play a critical role in the development of this behavior. The current study used structural equation modeling to evaluate the fit of a theoretical model specifying body…

Estimates of 2012/13 influenza vaccine effectiveness using the case test-negative control design with different influenza negative control groups.

PubMed

Nunes, Baltazar; Machado, Ausenda; Guiomar, Raquel; Pechirra, Pedro; Conde, Patrícia; Cristovão, Paula; Falcão, Isabel

2014-07-31

In recent years several reports of influenza vaccine effectiveness (VE) have been made early for public health decision. The majority of these studies use the case test-negative control design (TND), which has been showed to provide, under certain conditions, unbiased estimates of influenza VE. Nevertheless, discussions have been taken on the best influenza negative control group to use. The present study aims to contribute to the knowledge on this field by comparing influenza VE estimates using three test-negative controls: all influenza negative, non-influenza respiratory virus and pan-negative. Incident ILI patients were prospectively selected and swabbed by a sample of general practitioners. Cases were ILI patients tested positive for influenza and controls ILI patients tested negative for influenza. The influenza negative control group was divided into non-influenza virus control group and pan-negative control group. Data were collected on vaccination status and confounding factors. Influenza VE was estimated as one minus the odds ratio of been vaccinated in cases versus controls adjusted for confounding effect by logistic regression. Confounder adjusted influenza VE against medically attended laboratory-confirmed influenza was 68.4% (95% CI: 20.7-87.4%) using all influenza negatives controls, 82.1% (95% CI: 47.6-93.9%) using non-influenza controls and 49.4% (95% CI: -44.7% to 82.3%) using pan-negative controls. Influenza VE estimates differed according to the influenza negative control group used. These results are in accordance with the expected under the hypothesis of differential viral interference between influenza vaccinated and unvaccinated individuals. Given the wide importance of TND study further studies should be conducted in order to clarify the observed differences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Quantum correlations of helicity entangled states in non-inertial frames beyond single mode approximation

NASA Astrophysics Data System (ADS)

Harsij, Zeynab; Mirza, Behrouz

2014-12-01

A helicity entangled tripartite state is considered in which the degree of entanglement is preserved in non-inertial frames. It is shown that Quantum Entanglement remains observer independent. As another measure of quantum correlation, Quantum Discord has been investigated. It is explicitly shown that acceleration has no effect on the degree of quantum correlation for the bipartite and tripartite helicity entangled states. Geometric Quantum Discord as a Hilbert-Schmidt distance is computed for helicity entangled states. It is shown that living in non-inertial frames does not make any influence on this distance, either. In addition, the analysis has been extended beyond single mode approximation to show that acceleration does not have any impact on the quantum features in the limit beyond the single mode. As an interesting result, while the density matrix depends on the right and left Unruh modes, the Negativity as a measure of Quantum Entanglement remains constant. Also, Quantum Discord does not change beyond single mode approximation.

The General Factor of Personality: A General Critique.

PubMed

Revelle, William; Wilt, Joshua

2013-10-01

Recently, it has been proposed that all non-cognitive measures of personality share a general factor of personality. A problem with many of these studies is a lack of clarity in defining a general factor. In this paper we address the multiple ways in which a general factor has been identified and argue that many of these approaches find factors that are not in fact general. Through the use of artificial examples, we show that a general factor is not: The first factor or component of a correlation or covariance matrix.The first factor resulting from a bifactor rotation or biquartimin transformationNecessarily the result of a confirmatory factor analysis forcing a bifactor solution We consider how the definition of what constitutes a general factor can lead to confusion, and we will demonstrate alternative ways of estimating the general factor saturation that are more appropriate.

The General Factor of Personality: A General Critique

PubMed Central

Revelle, William; Wilt, Joshua

2013-01-01

Recently, it has been proposed that all non-cognitive measures of personality share a general factor of personality. A problem with many of these studies is a lack of clarity in defining a general factor. In this paper we address the multiple ways in which a general factor has been identified and argue that many of these approaches find factors that are not in fact general. Through the use of artificial examples, we show that a general factor is not: The first factor or component of a correlation or covariance matrix.The first factor resulting from a bifactor rotation or biquartimin transformationNecessarily the result of a confirmatory factor analysis forcing a bifactor solution We consider how the definition of what constitutes a general factor can lead to confusion, and we will demonstrate alternative ways of estimating the general factor saturation that are more appropriate. PMID:23956474

Assessing the Straightforwardly-Worded Brief Fear of Negative Evaluation Scale for Differential Item Functioning Across Gender and Ethnicity.

PubMed

Harpole, Jared K; Levinson, Cheri A; Woods, Carol M; Rodebaugh, Thomas L; Weeks, Justin W; Brown, Patrick J; Heimberg, Richard G; Menatti, Andrew R; Blanco, Carlos; Schneier, Franklin; Liebowitz, Michael

2015-06-01

The Brief Fear of Negative Evaluation Scale (BFNE; Leary Personality and Social Psychology Bulletin , 9, 371-375, 1983) assesses fear and worry about receiving negative evaluation from others. Rodebaugh et al. Psychological Assessment, 16 , 169-181, (2004) found that the BFNE is composed of a reverse-worded factor (BFNE-R) and straightforwardly-worded factor (BFNE-S). Further, they found the BFNE-S to have better psychometric properties and provide more information than the BFNE-R. Currently there is a lack of research regarding the measurement invariance of the BFNE-S across gender and ethnicity with respect to item thresholds. The present study uses item response theory (IRT) to test the BFNE-S for differential item functioning (DIF) related to gender and ethnicity (White, Asian, and Black). Six data sets consisting of clinical, community, and undergraduate participants were utilized ( N =2,109). The factor structure of the BFNE-S was confirmed using categorical confirmatory factor analysis, IRT model assumptions were tested, and the BFNE-S was evaluated for DIF. Item nine demonstrated significant non-uniform DIF between White and Black participants. No other items showed significant uniform or non-uniform DIF across gender or ethnicity. Results suggest the BFNE-S can be used reliably with men and women and Asian and White participants. More research is needed to understand the implications of using the BFNE-S with Black participants.

Coupled social and ecological outcomes of land use change and agricultural intensification in Costa Rica and the future of biodiversity conservation in tropical agricultural regions.

NASA Astrophysics Data System (ADS)

Sanfiorenzo, A. R.; Shaver, I.; Chain Guadarrama, A.; Cleary, K.; Santiago-Garcia, R.; Finegan, B.; Hormel, L.; Sibelet, N.; Vierling, L. A.; Bosque-Perez, N.; DeClerck, F.; Fagan, M. E.; Waits, L.

2016-12-01

Tropical ecosystem conversion to agriculture has caused widespread habitat loss and created fragmented landscapes composed of remnant forest patches embedded in a matrix of agricultural land uses. Non- traditional agricultural export (NTAE) crops such as pineapple are rapidly replacing multiuse landscapes characterized by a diverse matrix of pasture and smallholder crops with intensive, large-scale, monoculture plantations. Using an interdisciplinary approach, we conduct a case study to examine the coupled social and ecological implications of LUCC and agricultural intensification in this region, with larger application to regions experiencing similar patterns. Guided by frameworks from both political and landscape ecology, we: (1) describe the social and economic implications of pineapple expansion, specifically the concentration of land, labor and financial resources, (2) quantify pineapple cultivation's spatial characteristics, and (3) assess the effects of pineapple expansion on surrounding forest ecosystems, on the agricultural matrix and on biodiversity conservation. Our results indicate that pineapple production concentrates land, labor, and financial resources, which has a homogenizing effect on the agricultural economy in the study region. This constrains farm-based livelihoods, with larger implications for food security and agricultural diversity. Landscape ecology analyses further reveal how pineapple production simplifies and homogenizes the agricultural matrix between forest patches, which is likely to have a negative effect on biodiversity. To offset the effects of pineapple expansion on social and environmental systems, we recommend developing landscape level land use planning capacity. Furthermore, agricultural and conservation policy reform is needed to promote landscape heterogeneity and economic diversity within the agricultural sector. Our interdisciplinary research provides a detailed examination of the social and ecological impacts of agricultural intensification in a tropical landscape, and offers recommendations for improvement relevant not only to our study region but to the many other tropical landscapes currently undergoing non-traditional agricultural export driven agricultural intensification.

Coupled social and ecological outcomes of land use change and agricultural intensification in Costa Rica and the future of biodiversity conservation in tropical agricultural regions.

NASA Astrophysics Data System (ADS)

Sanfiorenzo, A. R.; Shaver, I.; Chain Guadarrama, A.; Cleary, K.; Santiago-Garcia, R.; Finegan, B.; Hormel, L.; Sibelet, N.; Vierling, L. A.; Bosque-Perez, N.; DeClerck, F.; Fagan, M. E.; Waits, L.

2017-12-01

Tropical ecosystem conversion to agriculture has caused widespread habitat loss and created fragmented landscapes composed of remnant forest patches embedded in a matrix of agricultural land uses. Non- traditional agricultural export (NTAE) crops such as pineapple are rapidly replacing multiuse landscapes characterized by a diverse matrix of pasture and smallholder crops with intensive, large-scale, monoculture plantations. Using an interdisciplinary approach, we conduct a case study to examine the coupled social and ecological implications of LUCC and agricultural intensification in this region, with larger application to regions experiencing similar patterns. Guided by frameworks from both political and landscape ecology, we: (1) describe the social and economic implications of pineapple expansion, specifically the concentration of land, labor and financial resources, (2) quantify pineapple cultivation's spatial characteristics, and (3) assess the effects of pineapple expansion on surrounding forest ecosystems, on the agricultural matrix and on biodiversity conservation. Our results indicate that pineapple production concentrates land, labor, and financial resources, which has a homogenizing effect on the agricultural economy in the study region. This constrains farm-based livelihoods, with larger implications for food security and agricultural diversity. Landscape ecology analyses further reveal how pineapple production simplifies and homogenizes the agricultural matrix between forest patches, which is likely to have a negative effect on biodiversity. To offset the effects of pineapple expansion on social and environmental systems, we recommend developing landscape level land use planning capacity. Furthermore, agricultural and conservation policy reform is needed to promote landscape heterogeneity and economic diversity within the agricultural sector. Our interdisciplinary research provides a detailed examination of the social and ecological impacts of agricultural intensification in a tropical landscape, and offers recommendations for improvement relevant not only to our study region but to the many other tropical landscapes currently undergoing non-traditional agricultural export driven agricultural intensification.

Localization of matrix metalloproteinases, (MMPs) their tissue inhibitors, and vascular endothelial growth factor (VEGF) in growth plates of children and adolescents indicates a role for MMPs in human postnatal growth and skeletal maturation.

PubMed

Haeusler, G; Walter, I; Helmreich, M; Egerbacher, M

2005-05-01

Numerous studies have focused on the expression, regulation, and biological significance of matrix metalloproteinases (MMPs) in the growth plate. Findings in mouse knockout models and in vitro data from various species indicate that MMPs not only degrade extracellular matrix components but may regulate the activity of local growth factors. In this study we investigated the presence, distribution, and activity of various MMPs and inhibitors, tissue transglutaminase (tTG or TG2) and vascular endothelial growth factor (VEGF) in the human child and adolescent growth plates by means of immunohistochemistry and gelatin zymography. Tissue was derived during orthopedic surgery (epiphysiodesis) in two prepubertal and four pubertal patients.MMP-2 and MMP-14 were present in reserve cell chondrocytes. MMP-14 was the most prominent MMP within all zones of the growth plate including proliferating chondrocytes. MMP-1 and MMP-13 (collagenases 1 and 3), MMP-9 (gelatinases B), MMP-10, and MMP-11 (stromelysins) and VEGF were positive in hypertrophic chondrocytes and osteoblasts. MMP-2 showed the same expression pattern but was negative in osteoblasts. Osteoclasts stained positive for MMP-9, MMP-2, and TG2. Tissue inhibitor of MMP (TIMP)-1 was present in all zones of the growth plate, osteoblasts, and osteoclasts; TIMP-2 was found in hypertrophic chondrocytes and osteoblasts. In summary, the presence of MMPs, TIMPs, TG2, and VEGF in our study indicated that the MMPs are relevant in growth plate physiology during the postnatal period in humans. The specific location of MMP expression within the growth plate may be the basis for further studies on the role of MMPs in the local regulation of chondrocyte differentiation, proliferation, and ossification at the chondroosseus junction.

Selective factors governing in vitro β-carotene bioaccessibility: negative influence of low filtration cutoffs and alterations by emulsifiers and food matrices.

PubMed

Corte-Real, Joana; Richling, Elke; Hoffmann, Lucien; Bohn, Torsten

2014-12-01

Because of their putative health benefits, the biological fate of carotenoids after digestion has been met with much interest, and ex vivo methods using carotenoid standards to study their digestion and further metabolism have been developed. In the absence of a complex food matrix, that is, when studying isolated carotenoids, protocol conditions of gastrointestinal digestion models have to be adjusted. In this investigation, we hypothesized that certain selected factors would significantly influence the bioaccessibility of β-carotene in vitro. The factors considered included (i) type of lipid matrix employed (milk, cream, or oil), (ii) presence/absence of emulsifiers (e.g. lecithin and taurocholate), (iii) addition of a gastric lipase, and (iv) final filtration (20 or 200 nm) of the digesta. Adding an emulsifier mixture (10 mg lecithin + 50 mg monoolein + 5 mg oleic acid) enhanced β-carotene bioaccessibility 3 times (P < 0.001), whereas additional taurocholate and the presence/absence of gastric lipase added before intestinal digestion had no significant effect. β-Carotene bioaccessibility was superior with oil than with milk (18.8% ± 0.7% and 6.1% ± 0.7%, respectively; P = 0.03), especially after filtration, thus suggesting incomplete micelle formation after addition of milk. Filtration through 20 nm filters reduced carotenoid concentration in the aqueous fraction (from 7.1% ± 0.2% to 5.5% ± 0.2% in samples digested with canola oil, P < 0.001), indicating that not all formed micelles compared in size with those normally formed in vivo. When studying carotenoid standards during in vitro digestion, care should be taken to separate mixed micelles by filtration, and the choice of emulsifier and matrix should be considered. Copyright © 2014 Elsevier Inc. All rights reserved.

[Cytotonic and cytotoxic effect of cholera toxin on Vero cells and its relation to PCR].

PubMed

Rodríguez-Angeles, M G; Giono-Cerezo, S; Valdespino-Gómez, J L

1994-01-01

We studied 40 Vibrio cholerae strains: 16 from stool, 16 from sewage and 8 from food. The serotypes were Inaba in 21 strains, 8 Ogawa strains and 11 V. cholerae non-O1. PCR was made with ctx2 and ctx3 primers with 25 cycles of temperature: 1 min at 94 degrees C, 1 min at 60 degrees C and 1 min at 72 degrees C. 24 V. cholerae strains were positive: 18/24 Inaba y 6/24 Ogawa. PCR was negative for 16 strains: 3 Inaba serotype, 2 Ogawa y 11 V. cholerae non-O1. In Vero culture cells 18 strains were cytotonic, 21 cytotoxic and 1 strain was negative. ELISA was positive for 11 strains with PCR positive. The PCR sensitivity was 95.83% compared with culture cells. V. cholerae O1 produced cytotoxic effect on Vero culture cells, maybe related to ACE factor. Colony blot was made with a specific probe labeled with digoxigenin and it could detect 4 Vibrio cholerae toxigenic strains with PCR negative. All V. cholerae Non O1 strains were PCR negative.

Negative pressure wound therapy inhibits inflammation and upregulates activating transcription factor-3 and downregulates nuclear factor-κB in diabetic patients with foot ulcerations.

PubMed

Wang, T; He, R; Zhao, J; Mei, J C; Shao, M Z; Pan, Y; Zhang, J; Wu, H S; Yu, M; Yan, W C; Liu, L M; Liu, F; Jia, W P

2017-05-01

Negative pressure wound therapy (NPWT) is one of the most important treatments for diabetic foot, but the underlying mechanisms of its benefits still remain elusive. This study aims to evaluate the inflammatory signals involved in the effects of negative pressure therapy on diabetic foot ulcers. We enrolled 22 patients with diabetic foot ulceration, 11 treated with NPWT and the other 11 treated with traditional debridement. All patients were treated and observed for 1 week. Granulation tissues were harvested and analyzed in both groups, and then were histologically and immunohistochemically analyzed. Enzyme-linked immunosorbent assay, Western blot analysis, and real-time PCR were performed to evaluate the expression of interleukin-6 (IL-6), tumor necrosis factor α (TNF-α), inducible nitric oxide synthase (iNOS), nuclear factor-κB (NF-κB) p65, I k B-α, and activating transcription factor-3 (ATF-3). After 7 days of treatment, NPWT could obviously promote diabetic wound healing because of the mild inflammation and the dense cell-deposited matrix. Meanwhile, NPWT significantly decreased the expression of TNF-α, IL-6, and iNOS (all P < .05). The result of Western blotting and real-time PCR indicated that NPWT obviously decreased the level of I k B-α and NF-κB p65, and increased the level of ATF-3 (all P < .05). NPWT exerts an anti-inflammatory effect, possibly through the suppression of proinflammatory enzymes and cytokines resulting from I k B-α inhibition and ATF-3 activation, which may prevent the activation of the NF-κB pathway in human diabetic foot wounds. Copyright © 2016 John Wiley & Sons, Ltd.

No influence of supplemental dietary calcium intake on the bioavailability of spinach carotenoids in humans.

PubMed

Corte-Real, Joana; Guignard, Cédric; Gantenbein, Manon; Weber, Bernard; Burgard, Kim; Hoffmann, Lucien; Richling, Elke; Bohn, Torsten

2017-06-01

Dietary carotenoid intake, especially from fruits and vegetables, has been associated with a reduced incidence of several chronic diseases. However, its bioavailability can vary, depending on the food matrix and host factors. Recently, it has been suggested that divalent minerals negatively impinge on carotenoid bioavailability by reducing bile-salt and non-esterified fatty-acid levels in the gut, which normally aid in emulsifying carotenoids. The aim of the present study was to investigate whether supplemental Ca would negatively influence carotenoid absorption in humans. A total of twenty-five healthy, non-obese men (age: 20-46 years, BMI<30 kg/m2) were recruited for this postprandial, randomised, crossover, double-blinded trial. Following a randomised block design, each participant received (after 2-week washout periods), on three occasions separated by 1 week, 270 g of spinach-based meals (8·61 (sd 1·08) mg carotenoids/100 g fresh weight), supplemented with 0, 500 or 1000 mg of Ca (as calcium carbonate), with each participant acting as his or her own control. Blood samples were collected at regular postprandial intervals for up to 10 h following test meal intake, and standardised lunches were served. TAG-rich lipoprotein fractions were separated and carotenoid concentrations determined. AUC for meals without supplemented Ca were 22·72 (sem 2·78) nmol×h/l (lutein), 0·19 (sem 3·90) nmol×h/l (β-carotene) and 2·80 (sem 1·75) nmol×h/l (β-cryptoxanthin). No significant influence of supplementation with either 500 or 1000 mg of supplemental Ca was found. In conclusion, Ca - the most abundant divalent mineral in the diet - given at high but physiological concentrations, does not appear to have repercussions on the bioavailability of carotenoids from a spinach-based meal.

A Cross-Lingual Similarity Measure for Detecting Biomedical Term Translations

PubMed Central

Bollegala, Danushka; Kontonatsios, Georgios; Ananiadou, Sophia

2015-01-01

Bilingual dictionaries for technical terms such as biomedical terms are an important resource for machine translation systems as well as for humans who would like to understand a concept described in a foreign language. Often a biomedical term is first proposed in English and later it is manually translated to other languages. Despite the fact that there are large monolingual lexicons of biomedical terms, only a fraction of those term lexicons are translated to other languages. Manually compiling large-scale bilingual dictionaries for technical domains is a challenging task because it is difficult to find a sufficiently large number of bilingual experts. We propose a cross-lingual similarity measure for detecting most similar translation candidates for a biomedical term specified in one language (source) from another language (target). Specifically, a biomedical term in a language is represented using two types of features: (a) intrinsic features that consist of character n-grams extracted from the term under consideration, and (b) extrinsic features that consist of unigrams and bigrams extracted from the contextual windows surrounding the term under consideration. We propose a cross-lingual similarity measure using each of those feature types. First, to reduce the dimensionality of the feature space in each language, we propose prototype vector projection (PVP)—a non-negative lower-dimensional vector projection method. Second, we propose a method to learn a mapping between the feature spaces in the source and target language using partial least squares regression (PLSR). The proposed method requires only a small number of training instances to learn a cross-lingual similarity measure. The proposed PVP method outperforms popular dimensionality reduction methods such as the singular value decomposition (SVD) and non-negative matrix factorization (NMF) in a nearest neighbor prediction task. Moreover, our experimental results covering several language pairs such as English–French, English–Spanish, English–Greek, and English–Japanese show that the proposed method outperforms several other feature projection methods in biomedical term translation prediction tasks. PMID:26030738

Matrix De Rham Complex and Quantum A-infinity algebras

NASA Astrophysics Data System (ADS)

Barannikov, S.

2014-04-01

I establish the relation of the non-commutative BV-formalism with super-invariant matrix integration. In particular, the non-commutative BV-equation, defining the quantum A ∞-algebras, introduced in Barannikov (Modular operads and non-commutative Batalin-Vilkovisky geometry. IMRN, vol. 2007, rnm075. Max Planck Institute for Mathematics 2006-48, 2007), is represented via de Rham differential acting on the supermatrix spaces related with Bernstein-Leites simple associative algebras with odd trace q( N), and gl( N| N). I also show that the matrix Lagrangians from Barannikov (Noncommutative Batalin-Vilkovisky geometry and matrix integrals. Isaac Newton Institute for Mathematical Sciences, Cambridge University, 2006) are represented by equivariantly closed differential forms.

Polyelectrolyte-assisted preparation of gold nanocluster-doped silica particles with high incorporation efficiency and improved stability

NASA Astrophysics Data System (ADS)

Wang, Haonan; Huang, Zhenzhen; Guo, Zilong; Yang, Wensheng

2017-07-01

In this paper, we reported an approach for efficient incorporation of glutathione-capped gold nanoclusters (GSH-Au NCs) into silica particles with the assistance of a polyelectrolyte, poly-diallyldimethyl-ammoniumchloride (PDDA). In this approach, the negatively charged GSH-Au NCs were firstly mixed with the positively charged PDDA to form PDDA-Au NC complexes. Then, the complexes were added into a pre-hydrolyzed Stöber system to get the Au NCs-doped silica particles. With increased ratio of PDDA in the complexes, the negative charges on surface of the Au NCs were neutralized gradually and finally reversed to positive in presence of excess PDDA, which facilitated the incorporation of the Au NCs into the negatively charged silica matrix. Under the optimal amount of PDDA in the complexes, the incorporation efficiency of Au NCs could be as high as 88%. After being incorporated into the silica matrix, the Au NCs become much robust against pH and heavy metal ions attributed to the protection effect of silica and PDDA. This approach was also extendable to highly efficient incorporation of other negatively charged metal nanoclusters, such as bovine serum albumin-capped Cu nanoclusters, into silica matrix.

INSM1 is a Sensitive and Specific Marker of Neuroendocrine Differentiation in Head and Neck Tumors.

PubMed

Rooper, Lisa M; Bishop, Justin A; Westra, William H

2018-05-01

The head and neck is the site of a wide and sometimes bewildering array of neuroendocrine (NE) tumors. Although recognition of NE differentiation may be necessary for appropriate tumor classification and treatment, traditional NE markers such as synaptophysin, chromogranin, and CD56 are not always sufficiently sensitive or specific to make this distinction. Insulinoma-associated protein 1 (INSM1) is a novel transcription factor that has recently demonstrated excellent sensitivity and specificity for NE differentiation in various anatomic sites, but has not yet been extensively evaluated in tumors of the head and neck. We performed INSM1 immunohistochemistry on NE tumors (n=97) and non-NE tumors (n=626) across all histologic grades and anatomic subsites of the head and neck. INSM1 was positive in all types of head and neck NE tumors evaluated here (99.0% sensitivity), including middle ear adenoma, pituitary adenoma, paraganglioma, medullary thyroid carcinoma, olfactory neuroblastoma, small cell carcinoma, large cell NE carcinoma, and sinonasal teratocarcinosarcoma. Notably, it was positive in the vast majority of high-grade NE malignancies (95.8% sensitivity). INSM1 also was negative in almost all non-NE tumors (97.6% specificity) with the highest rates of reactivity in alveolar rhabdomyosarcoma and SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily B, member 1 (SMARCB1)-deficient sinonasal carcinoma. These findings confirm that INSM1 may be used as a standalone first-line marker of NE differentiation for tumors of the head and neck.

Unphysiologically high magnesium concentrations support chondrocyte proliferation and redifferentiation.

PubMed

Feyerabend, Frank; Witte, Frank; Kammal, Michael; Willumeit, Regine

2006-12-01

The effect of unphysiologically high extracellular magnesium concentrations on chondrocytes, induced by the supplementation of magnesium sulfate, was studied using a 3-phase tissue engineering model. The experiments showed that chondrocyte proliferation and redifferentiation, on the gene and protein expression level, are enhanced. A negative influence was found during chondrogenesis where an inhibition of extracellular matrix formation was observed. In addition, a direct impact on chondrocyte metabolism, elevated magnesium concentrations also affected growth factor effectiveness by consecutive influences during chondrogenesis. All observations were dosage dependent. The results of this study indicate that magnesium may be a useful tool for cartilage tissue engineering.

Combining cluster number counts and galaxy clustering

NASA Astrophysics Data System (ADS)

Lacasa, Fabien; Rosenfeld, Rogerio

2016-08-01

The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

Emotional Awareness Moderates the Relationship Between Childhood Abuse and Borderline Personality Disorder Symptom Factors.

PubMed

Westbrook, John; Berenbaum, Howard

2017-07-01

To examine pathways to borderline personality disorder (BPD), focusing on childhood abuse and emotional attention and clarity. Among 293 community residents (mean age = 43.1; 53.9% female), measured associations between the BPD symptom factors of disturbed relatedness, affective dysregulation, and behavioral dysregulation and (a) childhood abuse (emotional, physical, and sexual); (b) emotional attention and clarity; and (c) negative affect, using structured interviews, the Schedule for Non-Adaptive and Adaptive Personality-2, the Trait Meta Mood Scale, and the Positive and Negative Affect Scale, respectively. All forms of childhood abuse were associated with BPD symptom factors. Emotional attention and clarity moderated the effects of childhood physical and emotional abuse on behavioral dysregulation and disturbed relatedness. All results held when controlling for negative affect. The relations between childhood abuse and BPD are robust. Emotional attention and clarity may help elucidate the links between childhood abuse and BPD. © 2016 Wiley Periodicals, Inc.

Outcome predictors of intra-articular glucocorticoid treatment for knee synovitis in patients with rheumatoid arthritis - a prospective cohort study.

PubMed

Weitoft, Tomas; Rönnelid, Johan; Knight, Ann; Lysholm, Jörgen; Saxne, Tore; Larsson, Anders

2014-06-20

Intra-articular glucocorticoid treatment (IAGC) is widely used for symptom relief in arthritis. However, knowledge of factors predicting treatment outcome is limited. The aim of the present study was to identify response predictors of IAGC for knee synovitis in patients with rheumatoid arthritis (RA). In this study 121 RA patients with synovitis of the knee were treated with intra-articular injections of 20 mg triamcinolone hexacetonide. They were followed for six months and the rate of clinical relapse was studied. Non-responders (relapse within 6 months) and responders were compared regarding patient characteristics and knee joint damage as determined by the Larsen-Dale index. In addition, matched samples of serum and synovial fluid were analysed for factors reflecting the inflammatory process (C-reactive protein, interleukin 6, tumour necrosis factor alpha, vascular endothelial growth factor), joint tissue turnover (cartilage oligomeric matrix protein, metalloproteinase 3), and autoimmunity (antinuclear antibodies, antibodies against citrullinated peptides, rheumatoid factor). During the observation period, 48 knees relapsed (40%). Non-responders had more radiographic joint damage than responders (P = 0.002) and the pre-treatment vascular endothelial growth factor (VEGF) level in synovial fluid was significantly higher in non-responders (P = 0.002). Joint destruction is associated with poor outcome of IAGC for knee synovitis in RA. In addition, higher levels of VEGF in synovial fluid are found in non-responders, suggesting that locally produced VEGF is a biomarker for recurrence of synovial hyperplasia and the risk for arthritis relapse.

Angiogenic Type I Collagen Extracellular Matrix Integrated with Recombinant Bacteriophages Displaying Vascular Endothelial Growth Factors.

PubMed

Yoon, Junghyo; Korkmaz Zirpel, Nuriye; Park, Hyun-Ji; Han, Sewoon; Hwang, Kyung Hoon; Shin, Jisoo; Cho, Seung-Woo; Nam, Chang-Hoon; Chung, Seok

2016-01-21

Here, a growth-factor-integrated natural extracellular matrix of type I collagen is presented that induces angiogenesis. The developed matrix adapts type I collagen nanofibers integrated with synthetic colloidal particles of recombinant bacteriophages that display vascular endothelial growth factor (VEGF). The integration is achieved during or after gelation of the type I collagen and the matrix enables spatial delivery of VEGF into a desired region. Endothelial cells that contact the VEGF are found to invade into the matrix to form tube-like structures both in vitro and in vivo, proving the angiogenic potential of the matrix. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species

USGS Publications Warehouse

Ruiz-Gutierrez, Viviana; Zipkin, Elise F.; Dhondt, Andre A.

2010-01-01

1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6.Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal and inter-patch matrix habitats to identify which species within a community are likely to be impacted most by habitat loss and fragmentation. This model can be applied to other taxa (i.e. amphibians, mammals and insects) to estimate species and community occurrence dynamics in response to current environmental conditions and to make predictions in response to future changes in habitat configurations.

scarlet: Source separation in multi-band images by Constrained Matrix Factorization

NASA Astrophysics Data System (ADS)

Melchior, Peter; Moolekamp, Fred; Jerdee, Maximilian; Armstrong, Robert; Sun, Ai-Lei; Bosch, James; Lupton, Robert

2018-03-01

SCARLET performs source separation (aka "deblending") on multi-band images. It is geared towards optical astronomy, where scenes are composed of stars and galaxies, but it is straightforward to apply it to other imaging data. Separation is achieved through a constrained matrix factorization, which models each source with a Spectral Energy Distribution (SED) and a non-parametric morphology, or multiple such components per source. The code performs forced photometry (with PSF matching if needed) using an optimal weight function given by the signal-to-noise weighted morphology across bands. The approach works well if the sources in the scene have different colors and can be further strengthened by imposing various additional constraints/priors on each source. Because of its generic utility, this package provides a stand-alone implementation that contains the core components of the source separation algorithm. However, the development of this package is part of the LSST Science Pipeline; the meas_deblender package contains a wrapper to implement the algorithms here for the LSST stack.

Effect of hysteretic and non-hysteretic negative capacitance on tunnel FETs DC performance

NASA Astrophysics Data System (ADS)

Saeidi, Ali; Jazaeri, Farzan; Stolichnov, Igor; Luong, Gia V.; Zhao, Qing-Tai; Mantl, Siegfried; Ionescu, Adrian M.

2018-03-01

This work experimentally demonstrates that the negative capacitance effect can be used to significantly improve the key figures of merit of tunnel field effect transistor (FET) switches. In the proposed approach, a matching condition is fulfilled between a trained-polycrystalline PZT capacitor and the tunnel FET (TFET) gate capacitance fabricated on a strained silicon-nanowire technology. We report a non-hysteretic switch configuration by combining a homojunction TFET and a negative capacitance effect booster, suitable for logic applications, for which the on-current is increased by a factor of 100, the transconductance by 2 orders of magnitude, and the low swing region is extended. The operation of a hysteretic negative capacitance TFET, when the matching condition for the negative capacitance is fulfilled only in a limited region of operation, is also reported and discussed. In this late case, a limited improvement in the device performance is observed. Overall, the paper demonstrates the main beneficial effects of negative capacitance on TFETs are the overdrive and transconductance amplification, which exactly address the most limiting performances of current TFETs.

Position of Social Determinants of Health in Urban Man-Made Lakes

PubMed Central

Shojaei, Parisa; Karimlou, Masoud; Mohammadi, Farahnaz; Afzali, Hosein Malek; Forouzan, Ameneh Setareh

2013-01-01

Background and Objective: A social determinants approach proposes that enhancing living conditions in areas such as income, housing, transportation, employment, education, social support, and health services is central to improving the health of urban populations. Urban development projects can be costly but have health impacts. The benefit derived from the creation of man-made lakes in developing countries is usually associated with great risks; however, the evidence for physical and non-physical health benefits of urban man-made lake is unclear. The aim of this paper is to formulate a conceptual framework of associations between urban man-made lakes and social determinants of health. Method: This study was a qualitative study carried out using one focus group discussion and 16 individual interviews. Data were analyzed based on deductive-inductive content analysis approach. Results: Participants’ points of view were analyzed within 261 codes. Data analysis matrix was the conceptual framework of social determinants of health commission and its sub-groups, thus, two structural and mediating determinants categories as well as their sub-sets were created accordingly. In addition, some extra sub-sets including environment, air quality, weather changes, noise pollution, pathogenesis, quality of life, shortage of available resources, region popularity, ethnicity, tourism, social and physical development of children, unintentional injuries, aesthetic, and spirituality were extracted beyond the matrix factors, which were placed in each of above categories based on their thematic content. Conclusion: This paper has illustrated that the quality and type of man-made lake provided within communities can have a significant and sustained impact on community’s health and wellbeing. Therefore, in order to strengthen positive effects and reduce negative effects of any developmental projects within community, their impacts on public health should be taken into consideration. PMID:24171878

Position of social determinants of health in urban man-made lakes plans.

PubMed

Shojaei, Parisa; Karimloo, Masoud; Mohammadi, Farahnaz; Malek Afzali, Hossein; Forouzan, Ameneh Setareh

2013-09-04

A social determinants approach proposes that enhancing living conditions in areas such as income, housing, transportation, employment, education, social support, and health services is central to improving the health of urban populations. Urban development projects can be costly but have health impacts. The benefit derived from the creation of man-made lakes in developing countries is usually associated with great risks; however, the evidence for physical and non-physical health benefits of urban man-made lake is unclear. The aim of this paper is to formulate a conceptual framework of associations between urban man-made lakes and social determinants of health. This study was a qualitative study carried out using one focus group discussion and 16 individual interviews. Data were analyzed based on deductive-inductive content analysis approach. Participants' points of view were analyzed within 261 codes. Data analysis matrix was the conceptual framework of social determinants of health commission and its sub-groups, thus, two structural and mediating determinants categories as well as their sub-sets were created accordingly. In addition, some extra sub-sets including environment, air quality, weather changes, noise pollution, pathogenesis, quality of life, shortage of available resources, region popularity, ethnicity, tourism, social and physical development of children, unintentional injuries, aesthetic, and spirituality were extracted beyond the matrix factors, which were placed in each of above categories based on their thematic content. This paper has illustrated that the quality and type of man-made lake provided within communities can have a significant and sustained impact on community's health and wellbeing. Therefore, in order to strengthen positive effects and reduce negative effects of any developmental projects within community, their impacts on public health should be taken into consideration.

Background recovery via motion-based robust principal component analysis with matrix factorization

NASA Astrophysics Data System (ADS)

Pan, Peng; Wang, Yongli; Zhou, Mingyuan; Sun, Zhipeng; He, Guoping

2018-03-01

Background recovery is a key technique in video analysis, but it still suffers from many challenges, such as camouflage, lighting changes, and diverse types of image noise. Robust principal component analysis (RPCA), which aims to recover a low-rank matrix and a sparse matrix, is a general framework for background recovery. The nuclear norm is widely used as a convex surrogate for the rank function in RPCA, which requires computing the singular value decomposition (SVD), a task that is increasingly costly as matrix sizes and ranks increase. However, matrix factorization greatly reduces the dimension of the matrix for which the SVD must be computed. Motion information has been shown to improve low-rank matrix recovery in RPCA, but this method still finds it difficult to handle original video data sets because of its batch-mode formulation and implementation. Hence, in this paper, we propose a motion-assisted RPCA model with matrix factorization (FM-RPCA) for background recovery. Moreover, an efficient linear alternating direction method of multipliers with a matrix factorization (FL-ADM) algorithm is designed for solving the proposed FM-RPCA model. Experimental results illustrate that the method provides stable results and is more efficient than the current state-of-the-art algorithms.

Differential effect of extracellular matrix derived from papillary and reticular fibroblasts on epidermal development in vitro.

PubMed

Janson, David; Rietveld, Marion; Mahé, Christian; Saintigny, Gaëlle; El Ghalbzouri, Abdoelwaheb

2017-06-01

Papillary and reticular fibroblasts have different effects on keratinocyte proliferation and differentiation. The aim of this study was to investigate whether these effects are caused by differential secretion of soluble factors or by differential generation of extracellular matrix from papillary and reticular fibroblasts. To study the effect of soluble factors, keratinocyte monolayer cultures were grown in papillary or reticular fibroblast-conditioned medium. To study the effect of extracellular matrix, keratinocytes were grown on papillary or reticular-derived matrix. Conditioned medium from papillary or reticular fibroblasts did not differentially affect keratinocyte viability or epidermal development. However, keratinocyte viability was increased when grown on matrix derived from papillary, compared with reticular, fibroblasts. In addition, the longevity of the epidermis was increased when cultured on papillary fibroblast-derived matrix skin equivalents compared with reticular-derived matrix skin equivalents. The findings indicate that the matrix secreted by papillary and reticular fibroblasts is the main causal factor to account for the differences in keratinocyte growth and viability observed in our study. Differences in response to soluble factors between both populations were less significant. Matrix components specific to the papillary dermis may account for the preferential growth of keratinocytes on papillary dermis.

Targeting extracellular matrix remodeling in disease: Could resveratrol be a potential candidate?

PubMed

Agarwal, Renu; Agarwal, Puneet

2017-02-01

Disturbances of extracellular matrix homeostasis are associated with a number of pathological conditions. The ability of extracellular matrix to provide contextual information and hence control the individual or collective cellular behavior is increasingly being recognized. Hence, newer therapeutic approaches targeting extracellular matrix remodeling are widely investigated. We reviewed the current literature showing the effects of resveratrol on various aspects of extracellular matrix remodeling. This review presents a summary of the effects of resveratrol on extracellular matrix deposition and breakdown. Mechanisms of action of resveratrol in extracellular matrix deposition involving growth factors and their signaling pathways are discussed. Involvement of phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways and role of transcription factors and sirtuins on the effects of resveratrol on extracellular matrix homeostasis are summarized. It is evident from the literature presented in this review that resveratrol has significant effects on both the synthesis and breakdown of extracellular matrix. The major molecular targets of the action of resveratrol are growth factors and their signaling pathways, phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways, transcription factors, and SIRT-1. The effects of resveratrol on extracellular matrix and the molecular targets appear to be related to experimental models, experimental environment as well as the doses.

Targeting extracellular matrix remodeling in disease: Could resveratrol be a potential candidate?

PubMed Central

Agarwal, Puneet

2016-01-01

Disturbances of extracellular matrix homeostasis are associated with a number of pathological conditions. The ability of extracellular matrix to provide contextual information and hence control the individual or collective cellular behavior is increasingly being recognized. Hence, newer therapeutic approaches targeting extracellular matrix remodeling are widely investigated. We reviewed the current literature showing the effects of resveratrol on various aspects of extracellular matrix remodeling. This review presents a summary of the effects of resveratrol on extracellular matrix deposition and breakdown. Mechanisms of action of resveratrol in extracellular matrix deposition involving growth factors and their signaling pathways are discussed. Involvement of phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways and role of transcription factors and sirtuins on the effects of resveratrol on extracellular matrix homeostasis are summarized. It is evident from the literature presented in this review that resveratrol has significant effects on both the synthesis and breakdown of extracellular matrix. The major molecular targets of the action of resveratrol are growth factors and their signaling pathways, phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways, transcription factors, and SIRT-1. The effects of resveratrol on extracellular matrix and the molecular targets appear to be related to experimental models, experimental environment as well as the doses. PMID:27798117

Proteomic Discovery and Development of a Multiplexed Targeted MRM-LC-MS/MS Assay for Urine Biomarkers of Extracellular Matrix Disruption in Mucopolysaccharidoses I, II, and VI.

PubMed

Heywood, Wendy E; Camuzeaux, Stephane; Doykov, Ivan; Patel, Nina; Preece, Rhian-Lauren; Footitt, Emma; Cleary, Maureen; Clayton, Peter; Grunewald, Stephanie; Abulhoul, Lara; Chakrapani, Anupam; Sebire, Neil J; Hindmarsh, Peter; de Koning, Tom J; Heales, Simon; Burke, Derek; Gissen, Paul; Mills, Kevin

2015-12-15

The mucopolysaccharidoses (MPS) are lysosomal storage disorders that result from defects in the catabolism of glycosaminoglycans. Impaired muscle, bone, and connective tissue are typical clinical features of MPS due to disruption of the extracellular matrix. Markers of MPS disease pathology are needed to determine disease severity and monitor effects of existing and emerging new treatments on disease mechanisms. Urine samples from a small cohort of MPS-I, -II, and -VI patients (n = 12) were analyzed using label-free quantative proteomics. Fifty-three proteins including many associated with extracellular matrix organization were differently expressed. A targeted multiplexed peptide MRM LC-MS/MS assay was used on a larger validation cohort of patient samples (MPS-I n = 18, MPS-II n = 12, MPS-VI n = 6, control n = 20). MPS-I and -II groups were further subdivided according to disease severity. None of the markers assessed were altered significantly in the mild disease groups compared to controls. β-galactosidase, a lysosomal protein, was elevated 3.6-5.7-fold significantly (p < 0.05) in all disease groups apart from mild MPS-I and -II. Collagen type Iα, fatty-acid-binding-protein 5, nidogen-1, cartilage oligomeric matrix protein, and insulin-like growth factor binding protein 7 concentrations were elevated in severe MPS I and II groups. Cartilage oligomeric matrix protein, insulin-like growth factor binding protein 7, and β-galactosidase were able to distinguish the severe neurological form of MPS-II from the milder non-neurological form. Protein Heg1 was significantly raised only in MPS-VI. This work describes the discovery of new biomarkers of MPS that represent disease pathology and allows the stratification of MPS-II patients according to disease severity.

Second derivative time integration methods for discontinuous Galerkin solutions of unsteady compressible flows

NASA Astrophysics Data System (ADS)

Nigro, A.; De Bartolo, C.; Crivellini, A.; Bassi, F.

2017-12-01

In this paper we investigate the possibility of using the high-order accurate A (α) -stable Second Derivative (SD) schemes proposed by Enright for the implicit time integration of the Discontinuous Galerkin (DG) space-discretized Navier-Stokes equations. These multistep schemes are A-stable up to fourth-order, but their use results in a system matrix difficult to compute. Furthermore, the evaluation of the nonlinear function is computationally very demanding. We propose here a Matrix-Free (MF) implementation of Enright schemes that allows to obtain a method without the costs of forming, storing and factorizing the system matrix, which is much less computationally expensive than its matrix-explicit counterpart, and which performs competitively with other implicit schemes, such as the Modified Extended Backward Differentiation Formulae (MEBDF). The algorithm makes use of the preconditioned GMRES algorithm for solving the linear system of equations. The preconditioner is based on the ILU(0) factorization of an approximated but computationally cheaper form of the system matrix, and it has been reused for several time steps to improve the efficiency of the MF Newton-Krylov solver. We additionally employ a polynomial extrapolation technique to compute an accurate initial guess to the implicit nonlinear system. The stability properties of SD schemes have been analyzed by solving a linear model problem. For the analysis on the Navier-Stokes equations, two-dimensional inviscid and viscous test cases, both with a known analytical solution, are solved to assess the accuracy properties of the proposed time integration method for nonlinear autonomous and non-autonomous systems, respectively. The performance of the SD algorithm is compared with the ones obtained by using an MF-MEBDF solver, in order to evaluate its effectiveness, identifying its limitations and suggesting possible further improvements.

Study on invadopodia formation for lung carcinoma invasion with a microfluidic 3D culture device.

PubMed

Wang, Shanshan; Li, Encheng; Gao, Yanghui; Wang, Yan; Guo, Zhe; He, Jiarui; Zhang, Jianing; Gao, Zhancheng; Wang, Qi

2013-01-01

Invadopodia or invasive feet, which are actin-rich membrane protrusions with matrix degradation activity formed by invasive cancer cells, are a key determinant in the malignant invasive progression of tumors and represent an important target for cancer therapies. In this work, we presented a microfluidic 3D culture device with continuous supplement of fresh media via a syringe pump. The device mimicked tumor microenvironment in vivo and could be used to assay invadopodia formation and to study the mechanism of human lung cancer invasion. With this device, we investigated the effects of epidermal growth factor (EGF) and matrix metalloproteinase (MMP) inhibitor, GM6001 on invadopodia formation by human non-small cell lung cancer cell line A549 in 3D matrix model. This device was composed of three units that were capable of achieving the assays on one control group and two experimental groups' cells, which were simultaneously pretreated with EGF or GM6001 in parallel. Immunofluorescence analysis of invadopodia formation and extracellular matrix degradation was conducted using confocal imaging system. We observed that EGF promoted invadopodia formation by A549 cells in 3D matrix and that GM6001 inhibited the process. These results demonstrated that epidermal growth factor receptor (EGFR) signaling played a significant role in invadopodia formation and related ECM degradation activity. Meanwhile, it was suggested that MMP inhibitor (GM6001) might be a powerful therapeutic agent targeting invadopodia formation in tumor invasion. This work clearly demonstrated that the microfluidic-based 3D culture device provided an applicable platform for elucidating the mechanism of cancer invasion and could be used in testing other anti-invasion agents.

A new Integrated Negative Symptom structure of the Positive and Negative Syndrome Scale (PANSS) in schizophrenia using item response analysis.

PubMed

Khan, Anzalee; Lindenmayer, Jean-Pierre; Opler, Mark; Yavorsky, Christian; Rothman, Brian; Lucic, Luka

2013-10-01

Debate persists with regard to how best to categorize the syndromal dimension of negative symptoms in schizophrenia. The aim was to first review published Principle Components Analysis (PCA) of the PANSS, and extract items most frequently included in the negative domain, and secondly, to examine the quality of items using Item Response Theory (IRT) to select items that best represent a measurable dimension (or dimensions) of negative symptoms. First, 22 factor analyses and PCA met were included. Second, using a large dataset (n=7187) of participants in clinical trials with chronic schizophrenia, we extracted items loading on one or more PCA. Third, items not loading with a value of ≥ 0.5, or loading on more than one component with values of ≥ 0.5 were discarded. Fourth, resulting items were included in a non-parametric IRT and retained based on Option Characteristic Curves (OCCs) and Item Characteristic Curves (ICCs). 15 items loaded on a negative domain in at least one study, with Emotional Withdrawal loading on all studies. Non-parametric IRT retained nine items as an Integrated Negative Factor: Emotional Withdrawal, Blunted Affect, Passive/Apathetic Social Withdrawal, Poor Rapport, Lack of Spontaneity/Conversation Flow, Active Social Avoidance, Disturbance of Volition, Stereotyped Thinking and Difficulty in Abstract Thinking. This is the first study to use a psychometric IRT process to arrive at a set of negative symptom items. Future steps will include further examination of these nine items in terms of their stability, sensitivity to change, and correlations with functional and cognitive outcomes. © 2013 Elsevier B.V. All rights reserved.

Fluorine-free electrolytes for all-solid sodium-ion batteries based on percyano-substituted organic salts

PubMed Central

Bitner-Michalska, Anna; Nolis, Gene M.; Żukowska, Grażyna; Zalewska, Aldona; Poterała, Marcin; Trzeciak, Tomasz; Dranka, Maciej; Kalita, Michał; Jankowski, Piotr; Niedzicki, Leszek; Zachara, Janusz; Marcinek, Marek; Wieczorek, Władysław

2017-01-01

A new family of fluorine-free solid-polymer electrolytes, for use in sodium-ion battery applications, is presented. Three novel sodium salts withdiffuse negative charges: sodium pentacyanopropenide (NaPCPI), sodium 2,3,4,5-tetracyanopirolate (NaTCP) and sodium 2,4,5-tricyanoimidazolate (NaTIM) were designed andtested in a poly(ethylene oxide) (PEO) matrix as polymer electrolytes for anall-solid sodium-ion battery. Due to unique, non-covalent structural configurations of anions, improved ionic conductivities were observed. As an example, “liquid-like” high conductivities (>1 mS cm−1) were obtained above 70 °C for solid-polymer electrolyte with a PEO to NaTCP molar ratio of 16:1. All presented salts showed high thermal stability and suitable windows of electrochemical stability between 3 and 5 V. These new anions open a new class of compounds with non-covalent structure for electrolytes system applications. PMID:28067301

Fluorine-free electrolytes for all-solid sodium-ion batteries based on percyano-substituted organic salts

NASA Astrophysics Data System (ADS)

Bitner-Michalska, Anna; Nolis, Gene M.; Żukowska, Grażyna; Zalewska, Aldona; Poterała, Marcin; Trzeciak, Tomasz; Dranka, Maciej; Kalita, Michał; Jankowski, Piotr; Niedzicki, Leszek; Zachara, Janusz; Marcinek, Marek; Wieczorek, Władysław

2017-01-01

A new family of fluorine-free solid-polymer electrolytes, for use in sodium-ion battery applications, is presented. Three novel sodium salts withdiffuse negative charges: sodium pentacyanopropenide (NaPCPI), sodium 2,3,4,5-tetracyanopirolate (NaTCP) and sodium 2,4,5-tricyanoimidazolate (NaTIM) were designed andtested in a poly(ethylene oxide) (PEO) matrix as polymer electrolytes for anall-solid sodium-ion battery. Due to unique, non-covalent structural configurations of anions, improved ionic conductivities were observed. As an example, “liquid-like” high conductivities (>1 mS cm-1) were obtained above 70 °C for solid-polymer electrolyte with a PEO to NaTCP molar ratio of 16:1. All presented salts showed high thermal stability and suitable windows of electrochemical stability between 3 and 5 V. These new anions open a new class of compounds with non-covalent structure for electrolytes system applications.

Cross-Cultural Validation of the Modified Practice Attitudes Scale: Initial Factor Analysis and a New Factor Model.

PubMed

Park, Heehoon; Ebesutani, Chad K; Chung, Kyong-Mee; Stanick, Cameo

2018-01-01

The objective of this study was to create the Korean version of the Modified Practice Attitudes Scale (K-MPAS) to measure clinicians' attitudes toward evidence-based treatments (EBTs) in the Korean mental health system. Using 189 U.S. therapists and 283 members from the Korean mental health system, we examined the reliability and validity of the MPAS scores. We also conducted the first exploratory and confirmatory factor analysis on the MPAS and compared EBT attitudes across U.S. and Korean therapists. Results revealed that the inclusion of both "reversed-worded" and "non-reversed-worded" items introduced significant method effects that compromised the integrity of the one-factor MPAS model. Problems with the one-factor structure were resolved by eliminating the "non-reversed-worded" items. Reliability and validity were adequate among both Korean and U.S. therapists. Korean therapists also reported significantly more negative attitudes toward EBTs on the MPAS than U.S. therapists. The K-MPAS is the first questionnaire designed to measure Korean service providers' attitudes toward EBTs to help advance the dissemination of EBTs in Korea. The current study also demonstrated the negative impacts that can be introduced by incorporating oppositely worded items into a scale, particularly with respect to factor structure and detecting significant group differences.

The photobase generator nifedipine as a novel matrix for the detection of polyphenols in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Nguyen, Huu-Nghi; Tanaka, Mitsuru; Komabayashi, Genki; Matsui, Toshiro

2016-10-01

Matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is widely used for the detection and analysis of ionizable compounds. However, the method has less potential for the analysis of neutral compounds, such as polyphenols, owing to their lack of favorable proton-attachment or -removal groups. In this study, we reported for the first time that nifedipine (2,6-dimethyl-3,5-dicarbomethoxy-4-(2-nitrophenyl)-1,4-dihydropyridine), which is a strong photobase generator commonly used in polymerization, can abstract protons from neutral compounds in negative mode-MALDI experiments. When nifedipine (5 mg/ml) was used as a matrix reagent, the limit of detection (LOD) for epigallocatechin-3-O-gallate (EGCG) was determined to be 100 fmol/spot, which constitutes >50-fold improvement compared to the LOD obtained when trans-3-indoleacrylic acid, a matrix reagent previously reported for polyphenol detection, was used. Of the dihydropyridines investigated, only nifedipine facilitated the detection of EGCG, suggesting that the nitrosophenyl pyridine derivative of nifedipine formed by photoreduction under laser irradiation at 355 nm plays a crucial role in detecting polyphenols in negative mode. Reduced MS detection of 5-O-methylnaringenin indicated that nifedipine may preferably remove a proton from the 5-position OH group in the A ring of the flavonoid skeleton. The significant MS detection by nifedipine was extensively observed for polyphenols including flavones, flavonones, chalcones, stilbenoids and phenolic acids. In conclusion, nifedipine can act as a novel matrix for improving polyphenol detection by MALDI-MS in negative mode. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation

PubMed Central

Kiss, Gergely; Konrad, Csaba; Doczi, Judit; Starkov, Anatoly A.; Kawamata, Hibiki; Manfredi, Giovanni; Zhang, Steven F.; Gibson, Gary E.; Beal, M. Flint; Adam-Vizi, Vera; Chinopoulos, Christos

2013-01-01

A decline in α-ketoglutarate dehydrogenase complex (KGDHC) activity has been associated with neurodegeneration. Provision of succinyl-CoA by KGDHC is essential for generation of matrix ATP (or GTP) by substrate-level phosphorylation catalyzed by succinyl-CoA ligase. Here, we demonstrate ATP consumption in respiration-impaired isolated and in situ neuronal somal mitochondria from transgenic mice with a deficiency of either dihydrolipoyl succinyltransferase (DLST) or dihydrolipoyl dehydrogenase (DLD) that exhibit a 20–48% decrease in KGDHC activity. Import of ATP into the mitochondrial matrix of transgenic mice was attributed to a shift in the reversal potential of the adenine nucleotide translocase toward more negative values due to diminished matrix substrate-level phosphorylation, which causes the translocase to reverse prematurely. Immunoreactivity of all three subunits of succinyl-CoA ligase and maximal enzymatic activity were unaffected in transgenic mice as compared to wild-type littermates. Therefore, decreased matrix substrate-level phosphorylation was due to diminished provision of succinyl-CoA. These results were corroborated further by the finding that mitochondria from wild-type mice respiring on substrates supporting substrate-level phosphorylation exhibited ∼30% higher ADP-ATP exchange rates compared to those obtained from DLST+/− or DLD+/− littermates. We propose that KGDHC-associated pathologies are a consequence of the inability of respiration-impaired mitochondria to rely on “in-house” mitochondrial ATP reserves.—Kiss, G., Konrad, C., Doczi, J., Starkov, A. A., Kawamata, H., Manfredi, G., Zhang, S. F., Gibson, G. E., Beal, M. F., Adam-Vizi, V., Chinopoulos, C. The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation. PMID:23475850

The Development and Evaluation of the Psychometric Properties of the Negative Beliefs about Post-Event Processing Scale.

PubMed

Rodriguez, Hayley; Kissell, Kellie; Lucas, Lloyd; Fisak, Brian

2017-11-01

Although negative beliefs have been found to be associated with worry symptoms and depressive rumination, negative beliefs have yet to be examined in relation to post-event processing and social anxiety symptoms. The purpose of the current study was to examine the psychometric properties of the Negative Beliefs about Post-Event Processing Questionnaire (NB-PEPQ). A large, non-referred undergraduate sample completed the NB-PEPQ along with validation measures, including a measure of post-event processing and social anxiety symptoms. Based on factor analysis, a single-factor model was obtained, and the NB-PEPQ was found to exhibit good validity, including positive associations with measures of post-event processing and social anxiety symptoms. These findings add to the literature on the metacognitive variables that may lead to the development and maintenance of post-event processing and social anxiety symptoms, and have relevant clinical applications.

Emotional rigidity negatively impacts remission from anxiety and recovery of well-being.

PubMed

Wiltgen, Anika; Shepard, Christopher; Smith, Ryan; Fowler, J Christopher

2018-08-15

Emotional rigidity is described in clinical literature as a significant barrier to recovery; however, few there are few empirical measures of the construct. The current study had two aims: Study 1 aimed to identify latent factors that may bear on the construct of emotional rigidity while Study 2 assessed the potential impact of the latent factor(s) on anxiety remission rates and well-being. This study utilized data from 2472 adult inpatients (1176 females and 1296 males) with severe psychopathology. Study 1 utilized exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to identify latent factors of emotional rigidity. Study 2 utilized hierarchical logistic regression analyses to assess the relationships among emotional rigidity factors and anxiety remission and well-being recovery at discharge. Study 1 yielded a two-factor solution identified in EFA was confirmed with CFA. Factor 1 consisted of neuroticism, experiential avoidance, non-acceptance of emotions, impaired goal-directed behavior, impulse control difficulties and limited access to emotion regulation strategies when experiencing negative emotions. Factor 2 consisted of lack of emotional awareness and lack of emotional clarity when experiencing negative emotions. Results of Study 2 indicated higher scores on Factor 1 was associated with lower remission rates from anxiety and poorer well-being upon discharge. Factor 2 was not predictive of outcome. Emotional rigidity appears to be a latent construct that negatively impacts remission rates from anxiety. Limitations of the present study include its retrospective design, and inefficient methods of assessing emotional rigidity. Copyright © 2018. Published by Elsevier B.V.

Characteristics and source apportionment of fine haze aerosol in Beijing during the winter of 2013

NASA Astrophysics Data System (ADS)

Shang, Xiaona; Zhang, Kai; Meng, Fan; Wang, Shihao; Lee, Meehye; Suh, Inseon; Kim, Daigon; Jeon, Kwonho; Park, Hyunju; Wang, Xuezhong; Zhao, Yuxi

2018-02-01

For PM2.5 filter samples collected daily at the Chinese Research Academy of Environmental Sciences (Beijing, China) from December of 2013 to February of 2014 (the winter period), chemical characteristics and sources were investigated with an emphasis on haze events in different alert levels. During the 3 months, the average PM2.5 concentration was 89 µg m-3, exceeding the Chinese national standard of 75 µg m-3 in 24  h. The maximum PM2.5 concentration was 307 µg m-3, which characterizes developed-type pollution (PM2.5 / PM10>0.5) in the World Health Organization criteria. PM2.5 was dominated by SO42-, NO3-, and pseudo-carbonaceous compounds with obvious differences in concentrations and proportions between non-haze and haze episodes. The non-negative matrix factorization (NMF) analysis provided reasonable PM2.5 source profiles, by which five sources were identified: soil dust, traffic emission, biomass combustion, industrial emission, and coal combustion accounting for 13, 22, 12, 28, and 25  % of the total, respectively. The dust impact increased with northwesterlies during non-haze periods and decreased under stagnant conditions during haze periods. A blue alert of heavy air pollution was characterized by the greatest contribution from industrial emissions (61  %). During the Chinese Lantern Festival, an orange alert was issued and biomass combustion was found to be the major source owing to firework explosions. Red-alert haze was almost equally contributed by local traffic and transported coal combustion emissions from the vicinity of Beijing (approximately 40  % each) that was distinguished by the highest levels of NO3- and SO42-, respectively. This study also reveals that the severity and source of haze are largely dependent on meteorological conditions.

[Effect of non-genetically modified (non-GM) soy varieties on the measured value of GM soy by a quantitative PCR method].

PubMed

Watanabe, Takahiro; Sekino, Ayako; Shiramasa, Yuko; Matsuda, Rieko; Maitani, Tamio

2008-08-01

It is very important to examine the effect of non-genetically modified (non-GM) soy varieties, which constitute the matrix of the testing sample used to quantify GM soy (RRS), on the measured value of RRS by quantitative PCR methods. Therefore, we quantified the amount of RRS in powder-mixed samples containing 1 or 5% RRS prepared by using 10 different varieties of non-GM soy as the matrix. The results revealed that the measured values were not in agreement with the powder-mixing levels and that the extent of the difference depended on the variety of non-GM soy used as the matrix. The yields of DNA extracted differed among the soy varieties. On the other hand, analysis of DNA-mixed samples, that were prepared with the DNAs extracted from RRS and non-GM soy varieties, showed that the measured values of RRS were in agreement with the DNA-mixing levels. These results strongly suggest that the proportions of DNA derived from RRS and non-GM soy were not consistent with the powder-mixing ratio in the case of some non-GM soy varieties used as a matrix, resulting in the discrepancy between the measured values and the powder-mixing levels.

Generation of a non-transmissive Borna disease virus vector lacking both matrix and glycoprotein genes.

PubMed

Fujino, Kan; Yamamoto, Yusuke; Daito, Takuji; Makino, Akiko; Honda, Tomoyuki; Tomonaga, Keizo

2017-09-01

Borna disease virus (BoDV), a prototype of mammalian bornavirus, is a non-segmented, negative strand RNA virus that often causes severe neurological disorders in infected animals, including horses and sheep. Unique among animal RNA viruses, BoDV transcribes and replicates non-cytopathically in the cell nucleus, leading to establishment of long-lasting persistent infection. This striking feature of BoDV indicates its potential as an RNA virus vector system. It has previously been demonstrated by our team that recombinant BoDV (rBoDV) lacking an envelope glycoprotein (G) gene develops persistent infections in transduced cells without loss of the viral genome. In this study, a novel non-transmissive rBoDV, rBoDV ΔMG, which lacks both matrix (M) and G genes in the genome, is reported. rBoDV-ΔMG expressing green fluorescence protein (GFP), rBoDV ΔMG-GFP, was efficiently generated in Vero/MG cells stably expressing both BoDV M and G proteins. Infection with rBoDV ΔMG-GFP was persistently maintained in the parent Vero cells without propagation within cell culture. The optimal ratio of M and G for efficient viral particle production by transient transfection of M and G expression plasmids into cells persistently infected with rBoDV ΔMG-GFP was also demonstrated. These findings indicate that the rBoDV ΔMG-based BoDV vector may provide an extremely safe virus vector system and could be a novel strategy for investigating the function of M and G proteins and the host range of bornaviruses. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

Robust infrared targets tracking with covariance matrix representation

NASA Astrophysics Data System (ADS)

Cheng, Jian

2009-07-01

Robust infrared target tracking is an important and challenging research topic in many military and security applications, such as infrared imaging guidance, infrared reconnaissance, scene surveillance, etc. To effectively tackle the nonlinear and non-Gaussian state estimation problems, particle filtering is introduced to construct the theory framework of infrared target tracking. Under this framework, the observation probabilistic model is one of main factors for infrared targets tracking performance. In order to improve the tracking performance, covariance matrices are introduced to represent infrared targets with the multi-features. The observation probabilistic model can be constructed by computing the distance between the reference target's and the target samples' covariance matrix. Because the covariance matrix provides a natural tool for integrating multiple features, and is scale and illumination independent, target representation with covariance matrices can hold strong discriminating ability and robustness. Two experimental results demonstrate the proposed method is effective and robust for different infrared target tracking, such as the sensor ego-motion scene, and the sea-clutter scene.

Acid-Base and the Skeleton

NASA Astrophysics Data System (ADS)

Bushinsky, David A.

2008-09-01

Chronic metabolic acidosis increases urine calcium (Ca) excretion in the absence of a concomitant increase in intestinal Ca absorption resulting in a net loss of total body. The source of this additional urine Ca is almost certainly the skeleton, the primary reservoir of body Ca. In vitro metabolic acidosis, modeled as a primary reduction in medium bicarbonate concentration, acutely (<24 h) stimulates Ca efflux primarily through physicochemical mineral dissolution while at later time periods (>24 h) cell-mediated mechanisms predominate. In cultured neonatal mouse calvariae, acidosis-induced, cell-mediated Ca efflux is mediated by effects on both osteoblasts and osteoclasts. Metabolic acidosis inhibits extracellular matrix production by osteoblasts, as determined by measurement of collagen levels and levels for the non-collagenous matrix proteins osteopontin and matrix gla protein. Metabolic acidosis upregulates osteoblastic expression of RANKL (Receptor Activator of NFκB Ligand), an important osteoclastogenic and osteoclast-activating factor. Acidosis also increases osteoclastic activity as measured by release of β-glucuronidase, an enzyme whose secretion correlates with osteoclast-mediated bone resorption.

Negative thinking as a coping strategy mediator of pain and internalizing symptoms in adolescents with sickle cell disease.

PubMed

Barakat, Lamia P; Schwartz, Lisa A; Simon, Katherine; Radcliffe, Jerilynn

2007-06-01

The objective of this study was to examine the role of coping strategies, specifically negative thinking, in mediating the association of pain with symptoms of anxiety and depression in adolescents with sickle cell disease. Fifty-two 12-18-year-old adolescents with sickle cell disease completed a daily pain diary and paper-and-pencil measures of pain, pain coping, depression and anxiety. Symptoms of depression and anxiety were within the non-clinical range. Preliminary analyses indicated that lower family income was associated with higher reports of pain and negative thinking. Mediation regression analyses supported negative thinking as mediating the association of: (1) pain intensity with depression, and (2) pain interference with daily activities with anxiety. Findings highlight negative thinking as a factor compromising adolescents' adaptation to sickle cell pain; however, further investigation is required to determine the mediating influence of pain coping. Associations for lower income emphasize the multiple risk factors experienced by many of these adolescents.

Extracellular matrix regenerative graft attenuates the negative impact of polypropylene prolapse mesh on vagina in rhesus macaque.

PubMed

Liang, Rui; Knight, Katrina; Barone, William; Powers, Robert W; Nolfi, Alexis; Palcsey, Stacy; Abramowitch, Steven; Moalli, Pamela A

2017-02-01

The use of wide pore lightweight polypropylene mesh to improve anatomical outcomes in the surgical repair of prolapse has been hampered by mesh complications. One of the prototype prolapse meshes has been found to negatively impact the vagina by inducing a decrease in smooth muscle volume and contractility and the degradation of key structural proteins (collagen and elastin), resulting in vaginal degeneration. Recently, bioscaffolds derived from extracellular matrix have been used to mediate tissue regeneration and have been widely adopted in tissue engineering applications. Here we aimed to: (1) define whether augmentation of a polypropylene prolapse mesh with an extracellular matrix regenerative graft in a primate sacrocolpopexy model could mitigate the degenerative changes; and (2) determine the impact of the extracellular matrix graft on vagina when implanted alone. A polypropylene-extracellular matrix composite graft (n = 9) and a 6-layered extracellular matrix graft alone (n = 8) were implanted in 17 middle-aged parous rhesus macaques via sacrocolpopexy and compared to historical data obtained from sham (n = 12) and the polypropylene mesh (n = 12) implanted by the same method. Vaginal function was measured in passive (ball-burst test) and active (smooth muscle contractility) mechanical tests. Vaginal histomorphologic/biochemical assessments included hematoxylin-eosin and trichrome staining, immunofluorescent labeling of α-smooth muscle actin and apoptotic cells, measurement of total collagen, collagen subtypes (ratio III/I), mature elastin, and sulfated glycosaminoglycans. Statistical analyses included 1-way analysis of variance, Kruskal-Wallis, and appropriate post-hoc tests. The host inflammatory response in the composite mesh-implanted vagina was reduced compared to that following implantation with the polypropylene mesh alone. The increase in apoptotic cells observed with the polypropylene mesh was blunted in the composite (overall P < .001). Passive mechanical testing showed inferior parameters for both polypropylene mesh alone and the composite compared to sham whereas the contractility and thickness of smooth muscle layer in the composite were improved with a value similar to sham, which was distinct from the decreases observed with polypropylene mesh alone. Biochemically, the composite had similar mature elastin content, sulfated glycosaminoglycan content, and collagen subtype III/I ratio but lower total collagen content when compared to sham (P = .011). Multilayered extracellular matrix graft alone showed overall comparable values to sham in aspects of the biomechanical, histomorphologic, or biochemical endpoints of the vagina. The increased collagen subtype ratio III/I with the extracellular matrix graft alone (P = .033 compared to sham) is consistent with an ongoing active remodeling response. Mesh augmentation with a regenerative extracellular matrix graft attenuated the negative impact of polypropylene mesh on the vagina. Application of the extracellular matrix graft alone had no measurable negative effects suggesting that the benefits of this extracellular matrix graft occur when used without a permanent material. Future studies will focus on understanding mechanisms. Copyright © 2016. Published by Elsevier Inc.

Extracellular matrix regenerative graft attenuates the negative impact of polypropylene prolapse mesh on vagina in rhesus macaque

PubMed Central

Liang, Rui; Knight, Katrina; Barone, William; Powers, Robert W.; Nolfi, Alexis; Palcsey, Stacy; Abramowitch, Steven; Moalli, Pamela A.

2016-01-01

BACKGROUND The use of wide pore lightweight polypropylene mesh to improve anatomical outcomes in the surgical repair of prolapse has been hampered by mesh complications. One of the prototype prolapse meshes has been found to negatively impact the vagina by inducing a decrease in smooth muscle volume and contractility and the degradation of key structural proteins (collagen and elastin), resulting in vaginal degeneration. Recently, bioscaffolds derived from extracellular matrix have been used to mediate tissue regeneration and have been widely adopted in tissue engineering applications. OBJECTIVE Here we aimed to: (1) define whether augmentation of a polypropylene prolapse mesh with an extracellular matrix regenerative graft in a primate sacrocolpopexy model could mitigate the degenerative changes; and (2) determine the impact of the extracellular matrix graft on vagina when implanted alone. STUDY DESIGN A polypropylene-extracellular matrix composite graft (n = 9) and a 6-layered extracellular matrix graft alone (n = 8) were implanted in 17 middle-aged parous rhesus macaques via sacrocolpopexy and compared to historical data obtained from sham (n = 12) and the polypropylene mesh (n = 12) implanted by the same method. Vaginal function was measured in passive (ball-burst test) and active (smooth muscle contractility) mechanical tests. Vaginal histomorphologic/ biochemical assessments included hematoxylin-eosin and trichrome staining, immunofluorescent labeling of α-smooth muscle actin and apoptotic cells, measurement of total collagen, collagen subtypes (ratio III/ I), mature elastin, and sulfated glycosaminoglycans. Statistical analyses included 1-way analysis of variance, Kruskal-Wallis, and appropriate posthoc tests. RESULTS The host inflammatory response in the composite mesh-implanted vagina was reduced compared to that following implantation with the polypropylene mesh alone. The increase in apoptotic cells observed with the polypropylene mesh was blunted in the composite (overall P < .001). Passive mechanical testing showed inferior parameters for both polypropylene mesh alone and the composite compared to sham whereas the contractility and thickness of smooth muscle layer in the composite were improved with a value similar to sham, which was distinct from the decreases observed with polypropylene mesh alone. Biochemically, the composite had similar mature elastin content, sulfated glycosaminoglycan content, and collagen subtype III/I ratio but lower total collagen content when compared to sham (P = .011). Multilayered extracellular matrix graft alone showed overall comparable values to sham in aspects of the biomechanical, histomorphologic, or biochemical end-points of the vagina. The increased collagen subtype ratio III/I with the extracellular matrix graft alone (P = .033 compared to sham) is consistent with an ongoing active remodeling response. CONCLUSION Mesh augmentation with a regenerative extracellular matrix graft attenuated the negative impact of polypropylene mesh on the vagina. Application of the extracellular matrix graft alone had no measurable negative effects suggesting that the benefits of this extra-cellular matrix graft occur when used without a permanent material. Future studies will focus on understanding mechanisms. PMID:27615441

Examining significant factors in micro and small enterprises performance: case study in Amhara region, Ethiopia

NASA Astrophysics Data System (ADS)

Cherkos, Tomas; Zegeye, Muluken; Tilahun, Shimelis; Avvari, Muralidhar

2017-07-01

Furniture manufacturing micro and small enterprises are confronted with several factors that affect their performance. Some enterprises fail to sustain, some others remain for long period of time without transforming, and most are producing similar and non-standard products. The main aim of this manuscript is on improving the performance and contribution of MSEs by analyzing impact of significant internal and external factors. Data was collected via a questionnaire, group discussion with experts and interviewing process. Randomly selected eight representative main cities of Amhara region with 120 furniture manufacturing enterprises are considered. Data analysis and presentation was made using SPSS tools (correlation, proximity, and T test) and impact-effort analysis matrix tool. The correlation analysis shows that politico-legal with infrastructure, leadership with entrepreneurship skills and finance and credit with marketing factors are those factors, which result in high correlation with Pearson correlation values of r = 0.988, 0.983, and 0.939, respectively. The study investigates that the most critical factors faced by MSEs are work premises, access to finance, infrastructure, entrepreneurship and business managerial problems. The impact of these factors is found to be high and is confirmed by the 50% drop-out rate in 2014/2015. Furthermore, more than 25% work time losses due to power interruption daily and around 65% work premises problems challenged MSEs. Further, an impact-effort matrix was developed to help the MSEs to prioritize the affecting factors.

A public health framework to translate risk factors related to political violence and war into multi-level preventive interventions.

PubMed

De Jong, Joop T V M

2010-01-01

Political violence, armed conflicts and human rights violations are produced by a variety of political, economic and socio-cultural factors. Conflicts can be analyzed with an interdisciplinary approach to obtain a global understanding of the relative contribution of risk and protective factors. A public health framework was designed to address these risk factors and protective factors. The framework resulted in a matrix that combined primary, secondary and tertiary interventions with their implementation on the levels of the society-at-large, the community, and the family and individual. Subsequently, the risk and protective factors were translated into multi-sectoral, multi-modal and multi-level preventive interventions involving the economy, governance, diplomacy, the military, human rights, agriculture, health, and education. Then the interventions were slotted in their appropriate place in the matrix. The interventions can be applied in an integrative form by international agencies, governments and non-governmental organizations, and molded to meet the requirements of the historic, political-economic and socio-cultural context. The framework maps the complementary fit among the different actors while engaging themselves in preventive, rehabilitative and reconstructive interventions. The framework shows how the economic, diplomatic, political, criminal justice, human rights, military, health and rural development sectors can collaborate to promote peace or prevent the aggravation or continuation of violence. A deeper understanding of the association between risk and protective factors and the developmental pathways of generic, country-specific and culture-specific factors leading to political violence is needed.

Examining significant factors in micro and small enterprises performance: case study in Amhara region, Ethiopia

NASA Astrophysics Data System (ADS)

Cherkos, Tomas; Zegeye, Muluken; Tilahun, Shimelis; Avvari, Muralidhar

2018-07-01

Furniture manufacturing micro and small enterprises are confronted with several factors that affect their performance. Some enterprises fail to sustain, some others remain for long period of time without transforming, and most are producing similar and non-standard products. The main aim of this manuscript is on improving the performance and contribution of MSEs by analyzing impact of significant internal and external factors. Data was collected via a questionnaire, group discussion with experts and interviewing process. Randomly selected eight representative main cities of Amhara region with 120 furniture manufacturing enterprises are considered. Data analysis and presentation was made using SPSS tools (correlation, proximity, and T test) and impact-effort analysis matrix tool. The correlation analysis shows that politico-legal with infrastructure, leadership with entrepreneurship skills and finance and credit with marketing factors are those factors, which result in high correlation with Pearson correlation values of r = 0.988, 0.983, and 0.939, respectively. The study investigates that the most critical factors faced by MSEs are work premises, access to finance, infrastructure, entrepreneurship and business managerial problems. The impact of these factors is found to be high and is confirmed by the 50% drop-out rate in 2014/2015. Furthermore, more than 25% work time losses due to power interruption daily and around 65% work premises problems challenged MSEs. Further, an impact-effort matrix was developed to help the MSEs to prioritize the affecting factors.

Asymmetric correlation matrices: an analysis of financial data

NASA Astrophysics Data System (ADS)

Livan, G.; Rebecchi, L.

2012-06-01

We analyse the spectral properties of correlation matrices between distinct statistical systems. Such matrices are intrinsically non-symmetric, and lend themselves to extend the spectral analyses usually performed on standard Pearson correlation matrices to the realm of complex eigenvalues. We employ some recent random matrix theory results on the average eigenvalue density of this type of matrix to distinguish between noise and non-trivial correlation structures, and we focus on financial data as a case study. Namely, we employ daily prices of stocks belonging to the American and British stock exchanges, and look for the emergence of correlations between two such markets in the eigenvalue spectrum of their non-symmetric correlation matrix. We find several non trivial results when considering time-lagged correlations over short lags, and we corroborate our findings by additionally studying the asymmetric correlation matrix of the principal components of our datasets.

The interstitial distribution of macromolecules in rat tumours is influenced by the negatively charged matrix components

PubMed Central

Wiig, Helge; Gyenge, Christina C; Tenstad, Olav

2005-01-01

Knowledge of macromolecular distribution volumes is essential in understanding fluid transport within normal and pathological tissues. In this study in vivo we determined the distribution volumes of several macromolecules, including one monoclonal antibody, in tumours and tested whether charges associated with the tumour extracellular matrix influence their available volumes. Steady state levels of the monoclonal antibody trastuzumab (Herceptin) (pI = 9.2), IgG (pI = 7.6) as well as native (pI = 5.0) and cationized albumin (pI = 7.6) were established in rats bearing dimethylbenzanthracene (DMBA)-induced mammary tumours by continuous infusion using osmotic minipumps. After a 5–7 day infusion period, the rats were nephrectomized and the extracellular volume was determined with 51Cr-labelled EDTA. Plasma volumes were measured with 125I-labelled human serum albumin or rat IgM in a separate series. Steady state concentrations of probes were determined in the interstitial fluid that was isolated by centrifugation from tumours or by post mortem wick implantation in the back skin. Calculations were made for interstitial fluid volume (Vi), along with the available (Va/Vi) and excluded (Ve/Vi) relative interstitial volume fractions. The Ve/Vi for the positively charged trastuzumab in tumours averaged 0.29 ± 0.03 (n = 16), a value which was significantly lower than the corresponding one for IgG of 0.36 ± 0.02 (n = 16). Native albumin was excluded from 38% of the tumour interstitial fluid, whereas cationization of albumin reduced the excluded volume by ∼50%. Our experiments suggest that the tumour interstitium acts as a negatively charged matrix and is an important factor in determining the macromolecular distribution volume. PMID:15994186

The interstitial distribution of macromolecules in rat tumours is influenced by the negatively charged matrix components.

PubMed

Wiig, Helge; Gyenge, Christina C; Tenstad, Olav

2005-09-01

Knowledge of macromolecular distribution volumes is essential in understanding fluid transport within normal and pathological tissues. In this study in vivo we determined the distribution volumes of several macromolecules, including one monoclonal antibody, in tumours and tested whether charges associated with the tumour extracellular matrix influence their available volumes. Steady state levels of the monoclonal antibody trastuzumab (Herceptin) (pI = 9.2), IgG (pI = 7.6) as well as native (pI = 5.0) and cationized albumin (pI = 7.6) were established in rats bearing dimethylbenzanthracene (DMBA)-induced mammary tumours by continuous infusion using osmotic minipumps. After a 5-7 day infusion period, the rats were nephrectomized and the extracellular volume was determined with 51Cr-labelled EDTA. Plasma volumes were measured with 125I-labelled human serum albumin or rat IgM in a separate series. Steady state concentrations of probes were determined in the interstitial fluid that was isolated by centrifugation from tumours or by post mortem wick implantation in the back skin. Calculations were made for interstitial fluid volume (Vi), along with the available (Va/Vi) and excluded (Ve/Vi) relative interstitial volume fractions. The Ve/Vi for the positively charged trastuzumab in tumours averaged 0.29 +/- 0.03 (n = 16), a value which was significantly lower than the corresponding one for IgG of 0.36 +/- 0.02 (n = 16). Native albumin was excluded from 38% of the tumour interstitial fluid, whereas cationization of albumin reduced the excluded volume by approximately 50%. Our experiments suggest that the tumour interstitium acts as a negatively charged matrix and is an important factor in determining the macromolecular distribution volume.

[Emotional processes in schizophrenia: investigation of the evaluative component].

PubMed

Sander, D; Koenig, O; Georgieff, N; Terra, J-L; Franck, N

2005-01-01

Schizophrenia is a disease that constitutes a particularly relevant way to investigate emotional processing. Indeed, major clinical signs of emotional disturbance (eg, anhedonia) suggest that some emotional mechanisms are defective in patients with schizophrenia. Evaluation can be considered as a fundamental component of the emotional system (28) and the first aim of the present study was to test the polarity hypothesis according to which different mechanisms are involved in the evaluation of positive vs negative emotional events. The second aim was to disentangle a -paradox emerging from the schizophrenia literature. On one hand, the tendency that schizophrenic patients have to under-evaluate the level of unpleasantness of negative stimuli suggests a deficit in the evaluation of negative events. For instance, it was proposed that patients with schizophrenia show a major deficit in the recognition of negative emotions, but a preserved recognition of positive emotions. On the other hand, the fact that anhedonia constitutes a critical cli-nical feature of schizophrenia suggests a deficit in the eva-luation of positive events. For instance, Crespo-Facorro et al. showed that patients with schizophrenia had a tendency to under-evaluate the level of pleasantness of positive stimuli but correctly evaluated the level of unpleasantness of negative stimuli. Given the importance of the social component in the analysis of deficits in patients with schizophrenia, we hypothesized that the variation of this component in stimuli used in the literature could explain the apparently inconsistent results described above. For example, the Bell et al. study used social stimuli whereas the Crespo-Facorro et al. study used non-social stimuli. Therefore, in our study, we have decided to manipulate the social component of stimuli. Another research issue of the present experiment was to study the explicit and/or implicit mode of processing of eva-luation in schizophrenic patients. In general, the experimental logic was to expect interaction effects between the factors polarity (negative vs positive) and participants (schizophrenic patients vs controls). Moreover, given the potential importance of the social component, a three-way interaction of the factors polarity, participants, and social component was expected. Finally, the experimental paradigm allowed us to search for dissociations in the context of both explicit and implicit evaluation. Stimuli used were negative and positive emotional pictures from the International Affective Picture System. Stimuli were chosen so that the mean valence -ratings of negative and positive pictures were at the same distance from neutrality. The factor arousal was controlled so that negative and positive pictures had equivalent mean arousal ratings. The social component factor was operatio-nalized by selecting pictures that either depicted or not a social scene. A fundamental criterion was that all social pictures were depicting at least one human being (eg, a wedding or a funeral), whereas non-social pictures never depicted any human being (eg, animals and landscapes). An upper and a lower border, that were either identical or different, were added to each picture. In a first experiment (the "implicit-task experiment"), patients with schizophrenia and matched controls were requested to decide whether the two borders surrounding the pictures were identical or different. Asking participants to process the borders was an experimental ruse to test if emotional processing takes place even when it is not task-relevant, and therefore if it is implicit. In a second experiment (the "explicit-task experiment"), the same participants were requested to evaluate whether the pictures were pleasant or unpleasant. Analyses of variance (ANOVA) were computed on response time and number of correct responses for both tasks. An important result was the observation of the expected three-way interaction effect of the factors polarity, participants, and social component on response time in the explicit task F(1, 19)=4.8, p<0.05. Critically, we observed that, for non-social stimuli, the interaction effect of the factors participants and polarity on response time was significant in the explicit task, F(1, 8)=4.9, p<0.05. These results are consistent with the polarity hypothesis and suggest a deficit in the processing of non-social positive stimuli in patients with schizophrenia. The expected three-way interaction effect was also observed on the number of correct responses in the explicit task F(1, 19)=5, p<0.04. For this task, we critically observed that, for social stimuli, the interaction effect of the factors participants and polarity on the number of correct responses was significant F(1, 19)=8.4, p<0.04. These results are also consistent with the polarity hypothesis and suggest a deficit in the processing of social negative stimuli in patients with schizophrenia. Moreover, let us notice that a comparison of the performances of the two groups revealed that patients made significantly more errors than controls for the evaluation of non-social positive stimuli, F(1, 19)=10,5, p<0.001, but not for the evaluation of non-social negative stimuli, F<1. In the implicit-task experiment, the analysis revealed that patients had a tendency to make more errors in the judgment of borders configuration for negative than for positive stimuli, whereas control participants showed the opposite tendency F(1, 19)=5.7, p<0.03, for the interaction of the factors polarity and participants. This result is consistent with the idea that distinct cognitive mechanisms are involved in the evaluation of positive vs negative emotional events even in the context of implicit processing. In conclusion, results obtained support the hypothesis according to which different cognitive mechanisms are involved in the evaluation of positive vs negative emotional events. Moreover, results suggest that patients with schizophrenia show a deficit in hedonic judgment of social negative and non-social positive stimuli. The later result indicates that the paradox described above becomes clearer whenever the social component of emotional stimuli happens to be taken into account. Results suggest that the polarity and the social component of events evaluated by patients with schizophrenia are critical parameters that should be considered in forthcoming studies that investigate affect disorders in schizophrenia.