Comovements in government bond markets: A minimum spanning tree analysis

NASA Astrophysics Data System (ADS)

Gilmore, Claire G.; Lucey, Brian M.; Boscia, Marian W.

2010-11-01

The concept of a minimum spanning tree (MST) is used to study patterns of comovements for a set of twenty government bond market indices for developed North American, European, and Asian countries. We show how the MST and its related hierarchical tree evolve over time and describe the dynamic development of market linkages. Over the sample period, 1993-2008, linkages between markets have decreased somewhat. However, a subset of European Union (EU) bond markets does show increasing levels of comovements. The evolution of distinct groups within the Eurozone is also examined. The implications of our findings for portfolio diversification benefits are outlined.

Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.

PubMed

Seurinck, Sylvie; Deschepper, Ellen; Deboch, Bishaw; Verstraete, Willy; Siciliano, Steven

2006-03-01

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Structural and topological phase transitions on the German Stock Exchange

NASA Astrophysics Data System (ADS)

Wiliński, M.; Sienkiewicz, A.; Gubiec, T.; Kutner, R.; Struzik, Z. R.

2013-12-01

We find numerical and empirical evidence for dynamical, structural and topological phase transitions on the (German) Frankfurt Stock Exchange (FSE) in the temporal vicinity of the worldwide financial crash. Using the Minimal Spanning Tree (MST) technique, a particularly useful canonical tool of the graph theory, two transitions of the topology of a complex network representing the FSE were found. The first transition is from a hierarchical scale-free MST representing the stock market before the recent worldwide financial crash, to a superstar-like MST decorated by a scale-free hierarchy of trees representing the market’s state for the period containing the crash. Subsequently, a transition is observed from this transient, (meta)stable state of the crash to a hierarchical scale-free MST decorated by several star-like trees after the worldwide financial crash. The phase transitions observed are analogous to the ones we obtained earlier for the Warsaw Stock Exchange and more pronounced than those found by Onnela-Chakraborti-Kaski-Kertész for the S&P 500 index in the vicinity of Black Monday (October 19, 1987) and also in the vicinity of January 1, 1998. Our results provide an empirical foundation for the future theory of dynamical, structural and topological phase transitions on financial markets.

Structural changes in the minimal spanning tree and the hierarchical network in the Korean stock market around the global financial crisis

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Maeng, Seong Eun; Ha, Gyeong Gyun; Lee, Jae Woo

2015-04-01

This paper considers stock prices in the Korean stock market during the 2008 global financial crisis by focusing on three time periods: before, during, and after the crisis. Complex networks are extracted from cross-correlation coefficients between the normalized logarithmic return of the stock price time series of firms. The minimal spanning trees (MSTs) and the hierarchical network (HN) are generated from cross-correlation coefficients. Before and after the crisis, securities firms are located at the center of the MST. During the crisis, however, the center of the MST changes to a firm in heavy industry and construction. During the crisis, the MST shrinks in comparison to that before and that after the crisis. This topological change in the MST during the crisis reflects a distinct effect of the global financial crisis. The cophenetic correlation coefficient increases during the crisis, indicating an increase in the hierarchical structure during in this period. When crisis hits the market, firms behave synchronously, and their correlations are higher than those during a normal period.

Phase synchronization based minimum spanning trees for analysis of financial time series with nonlinear correlations

NASA Astrophysics Data System (ADS)

Radhakrishnan, Srinivasan; Duvvuru, Arjun; Sultornsanee, Sivarit; Kamarthi, Sagar

2016-02-01

The cross correlation coefficient has been widely applied in financial time series analysis, in specific, for understanding chaotic behaviour in terms of stock price and index movements during crisis periods. To better understand time series correlation dynamics, the cross correlation matrices are represented as networks, in which a node stands for an individual time series and a link indicates cross correlation between a pair of nodes. These networks are converted into simpler trees using different schemes. In this context, Minimum Spanning Trees (MST) are the most favoured tree structures because of their ability to preserve all the nodes and thereby retain essential information imbued in the network. Although cross correlations underlying MSTs capture essential information, they do not faithfully capture dynamic behaviour embedded in the time series data of financial systems because cross correlation is a reliable measure only if the relationship between the time series is linear. To address the issue, this work investigates a new measure called phase synchronization (PS) for establishing correlations among different time series which relate to one another, linearly or nonlinearly. In this approach the strength of a link between a pair of time series (nodes) is determined by the level of phase synchronization between them. We compare the performance of phase synchronization based MST with cross correlation based MST along selected network measures across temporal frame that includes economically good and crisis periods. We observe agreement in the directionality of the results across these two methods. They show similar trends, upward or downward, when comparing selected network measures. Though both the methods give similar trends, the phase synchronization based MST is a more reliable representation of the dynamic behaviour of financial systems than the cross correlation based MST because of the former's ability to quantify nonlinear relationships among time series or relations among phase shifted time series.

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

PubMed Central

Wolski, Witold E; Lalowski, Maciej; Jungblut, Peter; Reinert, Knut

2005-01-01

Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%. PMID:16102175

A new tool for post-AGB SED classification

NASA Astrophysics Data System (ADS)

Bendjoya, P.; Suarez, O.; Galluccio, L.; Michel, O.

We present the results of an unsupervised classification method applied on a set of 344 spectral energy distributions (SED) of post-AGB stars extracted from the Torun catalogue of Galactic post-AGB stars. This method aims to find a new unbiased method for post-AGB star classification based on the information contained in the IR region of the SED (fluxes, IR excess, colours). We used the data from IRAS and MSX satellites, and from the 2MASS survey. We applied a classification method based on the construction of the dataset of a minimal spanning tree (MST) with the Prim's algorithm. In order to build this tree, different metrics have been tested on both flux and color indices. Our method is able to classify the set of 344 post-AGB stars in 9 distinct groups according to their SEDs.

Connectivity Restoration in Wireless Sensor Networks via Space Network Coding.

PubMed

Uwitonze, Alfred; Huang, Jiaqing; Ye, Yuanqing; Cheng, Wenqing

2017-04-20

The problem of finding the number and optimal positions of relay nodes for restoring the network connectivity in partitioned Wireless Sensor Networks (WSNs) is Non-deterministic Polynomial-time hard (NP-hard) and thus heuristic methods are preferred to solve it. This paper proposes a novel polynomial time heuristic algorithm, namely, Relay Placement using Space Network Coding (RPSNC), to solve this problem, where Space Network Coding, also called Space Information Flow (SIF), is a new research paradigm that studies network coding in Euclidean space, in which extra relay nodes can be introduced to reduce the cost of communication. Unlike contemporary schemes that are often based on Minimum Spanning Tree (MST), Euclidean Steiner Minimal Tree (ESMT) or a combination of MST with ESMT, RPSNC is a new min-cost multicast space network coding approach that combines Delaunay triangulation and non-uniform partitioning techniques for generating a number of candidate relay nodes, and then linear programming is applied for choosing the optimal relay nodes and computing their connection links with terminals. Subsequently, an equilibrium method is used to refine the locations of the optimal relay nodes, by moving them to balanced positions. RPSNC can adapt to any density distribution of relay nodes and terminals, as well as any density distribution of terminals. The performance and complexity of RPSNC are analyzed and its performance is validated through simulation experiments.

Currency crises and the evolution of foreign exchange market: Evidence from minimum spanning tree

NASA Astrophysics Data System (ADS)

Jang, Wooseok; Lee, Junghoon; Chang, Woojin

2011-02-01

We examined the time series properties of the foreign exchange market for 1990-2008 in relation to the history of the currency crises using the minimum spanning tree (MST) approach and made several meaningful observations about the MST of currencies. First, around currency crises, the mean correlation coefficient between currencies decreased whereas the normalized tree length increased. The mean correlation coefficient dropped dramatically passing through the Asian crisis and remained at the lowered level after that. Second, the Euro and the US dollar showed a strong negative correlation after 1997, implying that the prices of the two currencies moved in opposite directions. Third, we observed that Asian countries and Latin American countries moved away from the cluster center (USA) passing through the Asian crisis and Argentine crisis, respectively.

Similarity measure and topology evolution of foreign exchange markets using dynamic time warping method: Evidence from minimal spanning tree

NASA Astrophysics Data System (ADS)

Wang, Gang-Jin; Xie, Chi; Han, Feng; Sun, Bo

2012-08-01

In this study, we employ a dynamic time warping method to study the topology of similarity networks among 35 major currencies in international foreign exchange (FX) markets, measured by the minimal spanning tree (MST) approach, which is expected to overcome the synchronous restriction of the Pearson correlation coefficient. In the empirical process, firstly, we subdivide the analysis period from June 2005 to May 2011 into three sub-periods: before, during, and after the US sub-prime crisis. Secondly, we choose NZD (New Zealand dollar) as the numeraire and then, analyze the topology evolution of FX markets in terms of the structure changes of MSTs during the above periods. We also present the hierarchical tree associated with the MST to study the currency clusters in each sub-period. Our results confirm that USD and EUR are the predominant world currencies. But USD gradually loses the most central position while EUR acts as a stable center in the MST passing through the crisis. Furthermore, an interesting finding is that, after the crisis, SGD (Singapore dollar) becomes a new center currency for the network.

The relationships between electricity consumption and GDP in Asian countries, using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Kantar, Ersin; Keskin, Mustafa

2013-11-01

This study uses hierarchical structure methods (minimal spanning tree (MST) and hierarchical tree (HT)) to examine the relationship between energy consumption and economic growth in a sample of 30 Asian countries covering the period 1971-2008. These countries are categorized into four panels based on the World Bank income classification, namely high, upper middle, lower middle, and low income. In particular, we use the data of electricity consumption and real gross domestic product (GDP) per capita to detect the topological properties of the countries. We show a relationship between electricity consumption and economic growth by using the MST and HT. We also use the bootstrap technique to investigate a value of the statistical reliability to the links of the MST. Finally, we use a clustering linkage procedure in order to observe the cluster structure. The results of the structural topologies of these trees are as follows: (i) we identified different clusters of countries according to their geographical location and economic growth, (ii) we found a strong relationship between energy consumption and economic growth for all income groups considered in this study and (iii) the results are in good agreement with the causal relationship between electricity consumption and economic growth.

What shakes the FX tree? Understanding currency dominance, dependence, and dynamics (Keynote Address)

NASA Astrophysics Data System (ADS)

Johnson, Neil F.; McDonald, Mark; Suleman, Omer; Williams, Stacy; Howison, Sam

2005-05-01

There is intense interest in understanding the stochastic and dynamical properties of the global Foreign Exchange (FX) market, whose daily transactions exceed one trillion US dollars. This is a formidable task since the FX market is characterized by a web of fluctuating exchange rates, with subtle inter-dependencies which may change in time. In practice, traders talk of particular currencies being 'in play' during a particular period of time -- yet there is no established machinery for detecting such important information. Here we apply the construction of Minimum Spanning Trees (MSTs) to the FX market, and show that the MST can capture important features of the global FX dynamics. Moreover, we show that the MST can help identify momentarily dominant and dependent currencies.

Analysis of the effects of the global financial crisis on the Turkish economy, using hierarchical methods

NASA Astrophysics Data System (ADS)

Kantar, Ersin; Keskin, Mustafa; Deviren, Bayram

2012-04-01

We have analyzed the topology of 50 important Turkish companies for the period 2006-2010 using the concept of hierarchical methods (the minimal spanning tree (MST) and hierarchical tree (HT)). We investigated the statistical reliability of links between companies in the MST by using the bootstrap technique. We also used the average linkage cluster analysis (ALCA) technique to observe the cluster structures much better. The MST and HT are known as useful tools to perceive and detect global structure, taxonomy, and hierarchy in financial data. We obtained four clusters of companies according to their proximity. We also observed that the Banks and Holdings cluster always forms in the centre of the MSTs for the periods 2006-2007, 2008, and 2009-2010. The clusters match nicely with their common production activities or their strong interrelationship. The effects of the Automobile sector increased after the global financial crisis due to the temporary incentives provided by the Turkish government. We find that Turkish companies were not very affected by the global financial crisis.

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

PubMed Central

Ji, Zhicheng; Ji, Hongkai

2016-01-01

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. PMID:27179027

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.

PubMed

Ji, Zhicheng; Ji, Hongkai

2016-07-27

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Scale free effects in world currency exchange network

NASA Astrophysics Data System (ADS)

Górski, A. Z.; Drożdż, S.; Kwapień, J.

2008-11-01

A large collection of daily time series for 60 world currencies' exchange rates is considered. The correlation matrices are calculated and the corresponding Minimal Spanning Tree (MST) graphs are constructed for each of those currencies used as reference for the remaining ones. It is shown that multiplicity of the MST graphs' nodes to a good approximation develops a power like, scale free distribution with the scaling exponent similar as for several other complex systems studied so far. Furthermore, quantitative arguments in favor of the hierarchical organization of the world currency exchange network are provided by relating the structure of the above MST graphs and their scaling exponents to those that are derived from an exactly solvable hierarchical network model. A special status of the USD during the period considered can be attributed to some departures of the MST features, when this currency (or some other tied to it) is used as reference, from characteristics typical to such a hierarchical clustering of nodes towards those that correspond to the random graphs. Even though in general the basic structure of the MST is robust with respect to changing the reference currency some trace of a systematic transition from somewhat dispersed - like the USD case - towards more compact MST topology can be observed when correlations increase.

Complexity of major UK companies between 2006 and 2010: Hierarchical structure method approach

NASA Astrophysics Data System (ADS)

Ulusoy, Tolga; Keskin, Mustafa; Shirvani, Ayoub; Deviren, Bayram; Kantar, Ersin; Çaǧrı Dönmez, Cem

2012-11-01

This study reports on topology of the top 40 UK companies that have been analysed for predictive verification of markets for the period 2006-2010, applying the concept of minimal spanning tree and hierarchical tree (HT) analysis. Construction of the minimal spanning tree (MST) and the hierarchical tree (HT) is confined to a brief description of the methodology and a definition of the correlation function between a pair of companies based on the London Stock Exchange (LSE) index in order to quantify synchronization between the companies. A derivation of hierarchical organization and the construction of minimal-spanning and hierarchical trees for the 2006-2008 and 2008-2010 periods have been used and the results validate the predictive verification of applied semantics. The trees are known as useful tools to perceive and detect the global structure, taxonomy and hierarchy in financial data. From these trees, two different clusters of companies in 2006 were detected. They also show three clusters in 2008 and two between 2008 and 2010, according to their proximity. The clusters match each other as regards their common production activities or their strong interrelationship. The key companies are generally given by major economic activities as expected. This work gives a comparative approach between MST and HT methods from statistical physics and information theory with analysis of financial markets that may give new valuable and useful information of the financial market dynamics.

Stock market network’s topological stability: Evidence from planar maximally filtered graph and minimal spanning tree

NASA Astrophysics Data System (ADS)

Yan, Xin-Guo; Xie, Chi; Wang, Gang-Jin

2015-08-01

We study the topological stability of stock market network by investigating the topological robustness, namely the ability of the network to resist structural or topological changes. The stock market network is extracted by minimal spanning tree (MST) and planar maximally filtered graph (PMFG). We find that the specific delisting thresholds of the listed companies exist in both MST and PMFG networks. In comparison with MST, PMFG provides more information and is better for the aim of exploring stock market network’s robustness. The PMFG before the US sub-prime crisis (i.e., from June 2005 to May 2007) has a stronger robustness against the intentional topological damage than the other two sub-periods (i.e., from June 2007 to May 2009 and from June 2009 to May 2011). We also find that the nonfractal property exists in MSTs of S&P 500, i.e., the highly connected nodes link with each other directly, which indicates that the MSTs are vulnerable to the removal of such important nodes. Moreover, the financial institutions and high technology companies are important in maintaining the stability of S&P 500 network.

Consistent and powerful non-Euclidean graph-based change-point test with applications to segmenting random interfered video data.

PubMed

Shi, Xiaoping; Wu, Yuehua; Rao, Calyampudi Radhakrishna

2018-06-05

The change-point detection has been carried out in terms of the Euclidean minimum spanning tree (MST) and shortest Hamiltonian path (SHP), with successful applications in the determination of authorship of a classic novel, the detection of change in a network over time, the detection of cell divisions, etc. However, these Euclidean graph-based tests may fail if a dataset contains random interferences. To solve this problem, we present a powerful non-Euclidean SHP-based test, which is consistent and distribution-free. The simulation shows that the test is more powerful than both Euclidean MST- and SHP-based tests and the non-Euclidean MST-based test. Its applicability in detecting both landing and departure times in video data of bees' flower visits is illustrated.

Analyzing systemic risk using non-linear marginal expected shortfall and its minimum spanning tree

NASA Astrophysics Data System (ADS)

Song, Jae Wook; Ko, Bonggyun; Chang, Woojin

2018-02-01

The aim of this paper is to propose a new theoretical framework for analyzing the systemic risk using the marginal expected shortfall (MES) and its correlation-based minimum spanning tree (MST). At first, we develop two parametric models of MES with their closed-form solutions based on the Capital Asset Pricing Model. Our models are derived from the non-symmetric quadratic form, which allows them to consolidate the non-linear relationship between the stock and market returns. Secondly, we discover the evidences related to the utility of our models and the possible association in between the non-linear relationship and the emergence of severe systemic risk by considering the US financial system as a benchmark. In this context, the evolution of MES also can be regarded as a reasonable proxy of systemic risk. Lastly, we analyze the structural properties of the systemic risk using the MST based on the computed series of MES. The topology of MST conveys the presence of sectoral clustering and strong co-movements of systemic risk leaded by few hubs during the crisis. Specifically, we discover that the Depositories are the majority sector leading the connections during the Non-Crisis period, whereas the Broker-Dealers are majority during the Crisis period.

Betweenness centrality in a weighted network

NASA Astrophysics Data System (ADS)

Wang, Huijuan; Hernandez, Javier Martin; van Mieghem, Piet

2008-04-01

When transport in networks follows the shortest paths, the union of all shortest path trees G∪SPT can be regarded as the “transport overlay network.” Overlay networks such as peer-to-peer networks or virtual private networks can be considered as a subgraph of G∪SPT . The traffic through the network is examined by the betweenness Bl of links in the overlay G∪SPT . The strength of disorder can be controlled by, e.g., tuning the extreme value index α of the independent and identically distributed polynomial link weights. In the strong disorder limit (α→0) , all transport flows over a critical backbone, the minimum spanning tree (MST). We investigate the betweenness distributions of wide classes of trees, such as the MST of those well-known network models and of various real-world complex networks. All these trees with different degree distributions (e.g., uniform, exponential, or power law) are found to possess a power law betweenness distribution Pr[Bl=j]˜j-c . The exponent c seems to be positively correlated with the degree variance of the tree and to be insensitive of the size N of a network. In the weak disorder regime, transport in the network traverses many links. We show that a link with smaller link weight tends to carry more traffic. This negative correlation between link weight and betweenness depends on α and the structure of the underlying topology.

Multidimensional stock network analysis: An Escoufier's RV coefficient approach

NASA Astrophysics Data System (ADS)

Lee, Gan Siew; Djauhari, Maman A.

2013-09-01

The current practice of stocks network analysis is based on the assumption that the time series of closed stock price could represent the behaviour of the each stock. This assumption leads to consider minimal spanning tree (MST) and sub-dominant ultrametric (SDU) as an indispensible tool to filter the economic information contained in the network. Recently, there is an attempt where researchers represent stock not only as a univariate time series of closed price but as a bivariate time series of closed price and volume. In this case, they developed the so-called multidimensional MST to filter the important economic information. However, in this paper, we show that their approach is only applicable for that bivariate time series only. This leads us to introduce a new methodology to construct MST where each stock is represented by a multivariate time series. An example of Malaysian stock exchange will be presented and discussed to illustrate the advantages of the method.

Changes of hierarchical network in local and world stock market

NASA Astrophysics Data System (ADS)

Patwary, Enayet Ullah; Lee, Jong Youl; Nobi, Ashadun; Kim, Doo Hwan; Lee, Jae Woo

2017-10-01

We consider the cross-correlation coefficients of the daily returns in the local and global stock markets. We generate the minimal spanning tree (MST) using the correlation matrix. We observe that the MSTs change their structure from chain-like networks to star-like networks during periods of market uncertainty. We quantify the measure of the hierarchical network utilizing the value of the hierarchy measured by the hierarchical path. The hierarchy and betweenness centrality characterize the state of the market regarding the impact of crises. During crises, the non-financial company is established as the central node of the MST. However, before the crisis and during stable periods, the financial company is occupying the central node of the MST in the Korean and the U.S. stock markets. The changes in the network structure and the central node are good indicators of an upcoming crisis.

Quantitative holographic interferometry applied to combustion and compressible flow research

NASA Astrophysics Data System (ADS)

Bryanston-Cross, Peter J.; Towers, D. P.

1993-03-01

The application of holographic interferometry to phase object analysis is described. Emphasis has been given to a method of extracting quantitative information automatically from the interferometric fringe data. To achieve this a carrier frequency has been added to the holographic data. This has made it possible, firstly to form a phase map using a fast Fourier transform (FFT) algorithm. Then to `solve,' or unwrap, this image to give a contiguous density map using a minimum weight spanning tree (MST) noise immune algorithm, known as fringe analysis (FRAN). Applications of this work to a burner flame and a compressible flow are presented. In both cases the spatial frequency of the fringes exceed the resolvable limit of conventional digital framestores. Therefore, a flatbed scanner with a resolution of 3200 X 2400 pixels has been used to produce very high resolution digital images from photographs. This approach has allowed the processing of data despite the presence of caustics, generated by strong thermal gradients at the edge of the combustion field. A similar example is presented from the analysis of a compressible transonic flow in the shock wave and trailing edge regions.

EEG functional network topology is associated with disability in patients with amyotrophic lateral sclerosis

NASA Astrophysics Data System (ADS)

Fraschini, Matteo; Demuru, Matteo; Hillebrand, Arjan; Cuccu, Lorenza; Porcu, Silvia; di Stefano, Francesca; Puligheddu, Monica; Floris, Gianluca; Borghero, Giuseppe; Marrosu, Francesco

2016-12-01

Amyotrophic Lateral Sclerosis (ALS) is one of the most severe neurodegenerative diseases, which is known to affect upper and lower motor neurons. In contrast to the classical tenet that ALS represents the outcome of extensive and progressive impairment of a fixed set of motor connections, recent neuroimaging findings suggest that the disease spreads along vast non-motor connections. Here, we hypothesised that functional network topology is perturbed in ALS, and that this reorganization is associated with disability. We tested this hypothesis in 21 patients affected by ALS at several stages of impairment using resting-state electroencephalography (EEG) and compared the results to 16 age-matched healthy controls. We estimated functional connectivity using the Phase Lag Index (PLI), and characterized the network topology using the minimum spanning tree (MST). We found a significant difference between groups in terms of MST dissimilarity and MST leaf fraction in the beta band. Moreover, some MST parameters (leaf, hierarchy and kappa) significantly correlated with disability. These findings suggest that the topology of resting-state functional networks in ALS is affected by the disease in relation to disability. EEG network analysis may be of help in monitoring and evaluating the clinical status of ALS patients.

A study of hierarchical structure on South China industrial electricity-consumption correlation

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Ji-Nan; Liu, Xiao-Feng

2016-02-01

Based on industrial electricity-consumption data of five southern provinces of China from 2005 to 2013, we study the industrial correlation mechanism with MST (minimal spanning tree) and HT (hierarchical tree) models. First, we comparatively analyze the industrial electricity-consumption correlation structure in pre-crisis and after-crisis period using MST model and Bootstrap technique of statistical reliability test of links. Results exhibit that all industrial electricity-consumption trees of five southern provinces of China in pre-crisis and after-crisis time are in formation of chain, and the "center-periphery structure" of those chain-like trees is consistent with industrial specialization in classical industrial chain theory. Additionally, the industrial structure of some provinces is reorganized and transferred in pre-crisis and after-crisis time. Further, the comparative analysis with hierarchical tree and Bootstrap technique demonstrates that as for both observations of GD and overall NF, the industrial electricity-consumption correlation is non-significant clustered in pre-crisis period, whereas it turns significant clustered in after-crisis time. Therefore we propose that in perspective of electricity-consumption, their industrial structures are directed to optimized organization and global correlation. Finally, the analysis of distance of HTs verifies that industrial reorganization and development may strengthen market integration, coordination and correlation of industrial production. Except GZ, other four provinces have a shorter distance of industrial electricity-consumption correlation in after-crisis period, revealing a better performance of regional specialization and integration.

Sanio's laws revisited. Size-dependent changes in the xylem architecture of trees.

PubMed

Mencuccini, Maurizio; Hölttä, Teemu; Petit, Giai; Magnani, Federico

2007-11-01

Early observations led Sanio [Wissen. Bot., 8, (1872) 401] to state that xylem conduit diameters and lengths in a coniferous tree increase from the apex down to a height below which they begin to decrease towards the tree base. Sanio's law of vertical tapering has been repeatedly tested with contradictory results and the debate over the scaling of conduit diameters with distance from the apex has not been settled. The debate has recently acquired new vigour, as an accurate knowledge of the vertical changes in wood anatomy has been shown to be crucial to scaling metabolic properties to plant and ecosystem levels. Contrary to Sanio's hypothesis, a well known model (MST, metabolic scaling theory) assumes that xylem conduits monotonically increase in diameter with distance from the apex following a power law. This has been proposed to explain the three-fourth power scaling between size and metabolism seen across plants. Here, we (i) summarized available data on conduit tapering in trees and (ii) propose a new numerical model that could explain the observed patterns. Data from 101 datasets grouped into 48 independent profiles supported the notions that phylogenetic group (angiosperms versus gymnosperms) and tree size strongly affected the vertical tapering of conduit diameter. For both angiosperms and gymnosperms, within-tree tapering also varied with distance from the apex. The model (based on the concept that optimal conduit tapering occurs when the difference between photosynthetic gains and wall construction costs is maximal) successfully predicted all three major empirical patterns. Our results are consistent with Sanio's law only for large trees and reject the MST assumptions that vertical tapering in conduit diameter is universal and independent of rank number.

Angle Statistics Reconstruction: a robust reconstruction algorithm for Muon Scattering Tomography

NASA Astrophysics Data System (ADS)

Stapleton, M.; Burns, J.; Quillin, S.; Steer, C.

2014-11-01

Muon Scattering Tomography (MST) is a technique for using the scattering of cosmic ray muons to probe the contents of enclosed volumes. As a muon passes through material it undergoes multiple Coulomb scattering, where the amount of scattering is dependent on the density and atomic number of the material as well as the path length. Hence, MST has been proposed as a means of imaging dense materials, for instance to detect special nuclear material in cargo containers. Algorithms are required to generate an accurate reconstruction of the material density inside the volume from the muon scattering information and some have already been proposed, most notably the Point of Closest Approach (PoCA) and Maximum Likelihood/Expectation Maximisation (MLEM) algorithms. However, whilst PoCA-based algorithms are easy to implement, they perform rather poorly in practice. Conversely, MLEM is a complicated algorithm to implement and computationally intensive and there is currently no published, fast and easily-implementable algorithm that performs well in practice. In this paper, we first provide a detailed analysis of the source of inaccuracy in PoCA-based algorithms. We then motivate an alternative method, based on ideas first laid out by Morris et al, presenting and fully specifying an algorithm that performs well against simulations of realistic scenarios. We argue this new algorithm should be adopted by developers of Muon Scattering Tomography as an alternative to PoCA.

The use of real-time, hardware-in-the-loop simulation in the design and development of the new Hughes HS601 spacecraft attitude control system

NASA Technical Reports Server (NTRS)

Slafer, Loren I.

1989-01-01

Realtime simulation and hardware-in-the-loop testing is being used extensively in all phases of the design, development, and testing of the attitude control system (ACS) for the new Hughes HS601 satellite bus. Realtime, hardware-in-the-loop simulation, integrated with traditional analysis and pure simulation activities is shown to provide a highly efficient and productive overall development program. Implementation of high fidelity simulations of the satellite dynamics and control system algorithms, capable of real-time execution (using applied Dynamics International's System 100), provides a tool which is capable of being integrated with the critical flight microprocessor to create a mixed simulation test (MST). The MST creates a highly accurate, detailed simulated on-orbit test environment, capable of open and closed loop ACS testing, in which the ACS design can be validated. The MST is shown to provide a valuable extension of traditional test methods. A description of the MST configuration is presented, including the spacecraft dynamics simulation model, sensor and actuator emulators, and the test support system. Overall system performance parameters are presented. MST applications are discussed; supporting ACS design, developing on-orbit system performance predictions, flight software development and qualification testing (augmenting the traditional software-based testing), mission planning, and a cost-effective subsystem-level acceptance test. The MST is shown to provide an ideal tool in which the ACS designer can fly the spacecraft on the ground.

Will the US economy recover in 2010? A minimal spanning tree study

NASA Astrophysics Data System (ADS)

Zhang, Yiting; Lee, Gladys Hui Ting; Wong, Jian Cheng; Kok, Jun Liang; Prusty, Manamohan; Cheong, Siew Ann

2011-06-01

We calculated the cross correlations between the half-hourly times series of the ten Dow Jones US economic sectors over the period February 2000 to August 2008, the two-year intervals 2002-2003, 2004-2005, 2008-2009, and also over 11 segments within the present financial crisis, to construct minimal spanning trees (MSTs) of the US economy at the sector level. In all MSTs, a core-fringe structure is found, with consumer goods, consumer services, and the industrials consistently making up the core, and basic materials, oil & gas, healthcare, telecommunications, and utilities residing predominantly on the fringe. More importantly, we find that the MSTs can be classified into two distinct, statistically robust, topologies: (i) star-like, with the industrials at the center, associated with low-volatility economic growth; and (ii) chain-like, associated with high-volatility economic crisis. Finally, we present statistical evidence, based on the emergence of a star-like MST in Sep 2009, and the MST staying robustly star-like throughout the Greek Debt Crisis, that the US economy is on track to a recovery.

A two-phase control algorithm for gear-shifting in a novel multi-speed transmission for electric vehicles

NASA Astrophysics Data System (ADS)

Roozegar, M.; Angeles, J.

2018-05-01

In light of the current low energy-storage capacity of electric batteries, multi-speed transmissions (MSTs) are being considered for applications in electric vehicles (EVs), since MSTs decrease the energy consumption of the EV via gear-shifting. Nonetheless, swiftness and seamlessness are the major concerns in gear-shifting. This study focuses on developing a gear-shifting control scheme for a novel MST designed for EVs. The main advantages of the proposed MST are simplicity and modularity. Firstly, the dynamics model of the transmission is formulated. Then, a two-phase algorithm is proposed for shifting between each two gear ratios, which guarantees a smooth and swift shift. In other words, a separate control set is applied for shifting between each gear pair, which includes two independent PID controllers, tuned using trial-and-error and a genetic algorithm (GA), for the two steps of the algorithm and a switch. A supervisory controller is also employed to choose the proper PID gains, called PID gain-scheduling. Simulation results for various controllers and conditions are reported and compared, indicating that the proposed scheme is highly promising for a desired gear-shifting even in the presence of an unknown external disturbance.

Hierarchical image feature extraction by an irregular pyramid of polygonal partitions

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

Skurikhin, Alexei N

2008-01-01

We present an algorithmic framework for hierarchical image segmentation and feature extraction. We build a successive fine-to-coarse hierarchy of irregular polygonal partitions of the original image. This multiscale hierarchy forms the basis for object-oriented image analysis. The framework incorporates the Gestalt principles of visual perception, such as proximity and closure, and exploits spectral and textural similarities of polygonal partitions, while iteratively grouping them until dissimilarity criteria are exceeded. Seed polygons are built upon a triangular mesh composed of irregular sized triangles, whose spatial arrangement is adapted to the image content. This is achieved by building the triangular mesh on themore » top of detected spectral discontinuities (such as edges), which form a network of constraints for the Delaunay triangulation. The image is then represented as a spatial network in the form of a graph with vertices corresponding to the polygonal partitions and edges reflecting their relations. The iterative agglomeration of partitions into object-oriented segments is formulated as Minimum Spanning Tree (MST) construction. An important characteristic of the approach is that the agglomeration of polygonal partitions is constrained by the detected edges; thus the shapes of agglomerated partitions are more likely to correspond to the outlines of real-world objects. The constructed partitions and their spatial relations are characterized using spectral, textural and structural features based on proximity graphs. The framework allows searching for object-oriented features of interest across multiple levels of details of the built hierarchy and can be generalized to the multi-criteria MST to account for multiple criteria important for an application.« less

a New Multi-Spectral Threshold Normalized Difference Water Index Mst-Ndwi Water Extraction Method - a Case Study in Yanhe Watershed

NASA Astrophysics Data System (ADS)

Zhou, Y.; Zhao, H.; Hao, H.; Wang, C.

2018-05-01

Accurate remote sensing water extraction is one of the primary tasks of watershed ecological environment study. Since the Yanhe water system has typical characteristics of a small water volume and narrow river channel, which leads to the difficulty for conventional water extraction methods such as Normalized Difference Water Index (NDWI). A new Multi-Spectral Threshold segmentation of the NDWI (MST-NDWI) water extraction method is proposed to achieve the accurate water extraction in Yanhe watershed. In the MST-NDWI method, the spectral characteristics of water bodies and typical backgrounds on the Landsat/TM images have been evaluated in Yanhe watershed. The multi-spectral thresholds (TM1, TM4, TM5) based on maximum-likelihood have been utilized before NDWI water extraction to realize segmentation for a division of built-up lands and small linear rivers. With the proposed method, a water map is extracted from the Landsat/TM images in 2010 in China. An accuracy assessment is conducted to compare the proposed method with the conventional water indexes such as NDWI, Modified NDWI (MNDWI), Enhanced Water Index (EWI), and Automated Water Extraction Index (AWEI). The result shows that the MST-NDWI method generates better water extraction accuracy in Yanhe watershed and can effectively diminish the confusing background objects compared to the conventional water indexes. The MST-NDWI method integrates NDWI and Multi-Spectral Threshold segmentation algorithms, with richer valuable information and remarkable results in accurate water extraction in Yanhe watershed.

MST's Programmable Power Supplies: Bt Update, Bp Prototype

NASA Astrophysics Data System (ADS)

Holly, D. J.; Chapman, B. E.; McCollam, K. J.; Morin, J. C.; Thomas, M. A.

2013-10-01

MST's toroidal field programmable power supply (Bt PPS) has now been in operation for several years and has provided important new capabilities. One of the primary goals for the Bt PPS is the partial optimization of inductive current profile control, involving control of the poloidal electric field. The Bt PPS has achieved fluctuation reduction over MST's entire range of Ip. At the largest Ip, the Bt PPS achieves fluctuation reduction with a smaller poloidal electric field than the previous passive system, implying that substantially longer periods of current profile control may be possible. The Bt PPS has also been used to produce Ohmic tokamak plasmas in MST. With an applied toroidal field of 0.135 T, and q(a) > 2, the estimated energy confinement time is roughly consistent with neo-Alcator scaling. Driving q(a) < 2 with larger Ip, the confinement time degrades, but the discharge duration does not terminate prematurely. To fully optimize current profile control and to test MST operational limits, a PPS is also needed for the Bp circuit. Currently in prototype stage, the Bp PPS will feature a number of innovations to increase its flexibility and performance. Isolated charging, control, and monitor systems will eliminate charging relays, reduce coupling between modules, and minimize capacitor heating. Seven-level pulse width modulation will reduce output ripple and switching losses. Solid state shorting bars will eliminate shorting relays and minimize wiring. A balanced switching algorithm will minimize capacitive noise generation. Work supported by U. S. D. o. E.

Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes.

PubMed

Sulyok, Kinga M; Kreizinger, Zsuzsa; Hornstra, Heidie M; Pearson, Talima; Szigeti, Alexandra; Dán, Ádám; Balla, Eszter; Keim, Paul S; Gyuranecz, Miklós

2014-05-07

Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis (MLVA). Phylogenetic relationships among MST genotypes show how these Hungarian samples are related to others collected around the world. Three MST genotypes were identified: sequence type (ST) 20 has also been identified in ruminants from other European countries and the USA, ST28 was previously identified in Kazakhstan, and the proposed ST37 is novel. All MST genotypes yielded different MLVA genotypes and three different MLVA genotypes were identified within ST20 samples alone. Two novel MLVA types 0-9-5-5-6-2 (AG) and 0-8-4-5-6-2 (AF) (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34) were defined in the ovine materials correlated with ST28 and ST37. Samples from different parts of the phylogenetic tree were associated with different hosts, suggesting host-specific adaptations. Even with the limited number of samples analysed, this study revealed high genetic diversity among C. burnetii in Hungary. Understanding the background genetic diversity will be essential in identifying and controlling outbreaks.

A highly efficient measure of mass segregation in star clusters

NASA Astrophysics Data System (ADS)

Olczak, C.; Spurzem, R.; Henning, Th.

2011-08-01

Context. Investigations of mass segregation are of vital interest for the understanding of the formation and dynamical evolution of stellar systems on a wide range of spatial scales. A consistent analysis requires a robust measure among different objects and well-defined comparison with theoretical expectations. Various methods have been used for this purpose but usually with limited significance, quantifiability, and application to both simulations and observations. Aims: We aim at developing a measure of mass segregation with as few parameters as possible, robustness against peculiar configurations, independence of mass determination, simple implementation, stable algorithm, and that is equally well adoptable for data from either simulations or observations. Methods: Our method is based on the minimum spanning tree (MST) that serves as a geometry-independent measure of concentration. Compared to previous such approaches we obtain a significant refinement by using the geometrical mean as an intermediate-pass. Results: The geometrical mean boosts the sensitivity compared to previous applications of the MST. It thus allows the detection of mass segregation with much higher confidence and for much lower degrees of mass segregation than other approaches. The method shows in particular very clear signatures even when applied to small subsets of the entire population. We confirm with high significance strong mass segregation of the five most massive stars in the Orion nebula cluster (ONC). Conclusions: Our method is the most sensitive general measure of mass segregation so far and provides robust results for both data from simulations and observations. As such it is ideally suited for tracking mass segregation in young star clusters and to investigate the long standing paradigm of primordial mass segregation by comparison of simulations and observations.

A Cooperative Search and Coverage Algorithm with Controllable Revisit and Connectivity Maintenance for Multiple Unmanned Aerial Vehicles.

PubMed

Liu, Zhong; Gao, Xiaoguang; Fu, Xiaowei

2018-05-08

In this paper, we mainly study a cooperative search and coverage algorithm for a given bounded rectangle region, which contains several unknown stationary targets, by a team of unmanned aerial vehicles (UAVs) with non-ideal sensors and limited communication ranges. Our goal is to minimize the search time, while gathering more information about the environment and finding more targets. For this purpose, a novel cooperative search and coverage algorithm with controllable revisit mechanism is presented. Firstly, as the representation of the environment, the cognitive maps that included the target probability map (TPM), the uncertain map (UM), and the digital pheromone map (DPM) are constituted. We also design a distributed update and fusion scheme for the cognitive map. This update and fusion scheme can guarantee that each one of the cognitive maps converges to the same one, which reflects the targets’ true existence or absence in each cell of the search region. Secondly, we develop a controllable revisit mechanism based on the DPM. This mechanism can concentrate the UAVs to revisit sub-areas that have a large target probability or high uncertainty. Thirdly, in the frame of distributed receding horizon optimizing, a path planning algorithm for the multi-UAVs cooperative search and coverage is designed. In the path planning algorithm, the movement of the UAVs is restricted by the potential fields to meet the requirements of avoiding collision and maintaining connectivity constraints. Moreover, using the minimum spanning tree (MST) topology optimization strategy, we can obtain a tradeoff between the search coverage enhancement and the connectivity maintenance. The feasibility of the proposed algorithm is demonstrated by comparison simulations by way of analyzing the effects of the controllable revisit mechanism and the connectivity maintenance scheme. The Monte Carlo method is employed to validate the influence of the number of UAVs, the sensing radius, the detection and false alarm probabilities, and the communication range on the proposed algorithm.

Man-made objects cuing in satellite imagery

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

Skurikhin, Alexei N

2009-01-01

We present a multi-scale framework for man-made structures cuing in satellite image regions. The approach is based on a hierarchical image segmentation followed by structural analysis. A hierarchical segmentation produces an image pyramid that contains a stack of irregular image partitions, represented as polygonized pixel patches, of successively reduced levels of detail (LOOs). We are jumping off from the over-segmented image represented by polygons attributed with spectral and texture information. The image is represented as a proximity graph with vertices corresponding to the polygons and edges reflecting polygon relations. This is followed by the iterative graph contraction based on Boruvka'smore » Minimum Spanning Tree (MST) construction algorithm. The graph contractions merge the patches based on their pairwise spectral and texture differences. Concurrently with the construction of the irregular image pyramid, structural analysis is done on the agglomerated patches. Man-made object cuing is based on the analysis of shape properties of the constructed patches and their spatial relations. The presented framework can be used as pre-scanning tool for wide area monitoring to quickly guide the further analysis to regions of interest.« less

Carbon-dioxide emissions trading and hierarchical structure in worldwide finance and commodities markets.

PubMed

Zheng, Zeyu; Yamasaki, Kazuko; Tenenbaum, Joel N; Stanley, H Eugene

2013-01-01

In a highly interdependent economic world, the nature of relationships between financial entities is becoming an increasingly important area of study. Recently, many studies have shown the usefulness of minimal spanning trees (MST) in extracting interactions between financial entities. Here, we propose a modified MST network whose metric distance is defined in terms of cross-correlation coefficient absolute values, enabling the connections between anticorrelated entities to manifest properly. We investigate 69 daily time series, comprising three types of financial assets: 28 stock market indicators, 21 currency futures, and 20 commodity futures. We show that though the resulting MST network evolves over time, the financial assets of similar type tend to have connections which are stable over time. In addition, we find a characteristic time lag between the volatility time series of the stock market indicators and those of the EU CO(2) emission allowance (EUA) and crude oil futures (WTI). This time lag is given by the peak of the cross-correlation function of the volatility time series EUA (or WTI) with that of the stock market indicators, and is markedly different (>20 days) from 0, showing that the volatility of stock market indicators today can predict the volatility of EU emissions allowances and of crude oil in the near future.

Carbon-dioxide emissions trading and hierarchical structure in worldwide finance and commodities markets

NASA Astrophysics Data System (ADS)

Zheng, Zeyu; Yamasaki, Kazuko; Tenenbaum, Joel N.; Stanley, H. Eugene

2013-01-01

In a highly interdependent economic world, the nature of relationships between financial entities is becoming an increasingly important area of study. Recently, many studies have shown the usefulness of minimal spanning trees (MST) in extracting interactions between financial entities. Here, we propose a modified MST network whose metric distance is defined in terms of cross-correlation coefficient absolute values, enabling the connections between anticorrelated entities to manifest properly. We investigate 69 daily time series, comprising three types of financial assets: 28 stock market indicators, 21 currency futures, and 20 commodity futures. We show that though the resulting MST network evolves over time, the financial assets of similar type tend to have connections which are stable over time. In addition, we find a characteristic time lag between the volatility time series of the stock market indicators and those of the EU CO2 emission allowance (EUA) and crude oil futures (WTI). This time lag is given by the peak of the cross-correlation function of the volatility time series EUA (or WTI) with that of the stock market indicators, and is markedly different (>20 days) from 0, showing that the volatility of stock market indicators today can predict the volatility of EU emissions allowances and of crude oil in the near future.

Voronoi distance based prospective space-time scans for point data sets: a dengue fever cluster analysis in a southeast Brazilian town

PubMed Central

2011-01-01

Background The Prospective Space-Time scan statistic (PST) is widely used for the evaluation of space-time clusters of point event data. Usually a window of cylindrical shape is employed, with a circular or elliptical base in the space domain. Recently, the concept of Minimum Spanning Tree (MST) was applied to specify the set of potential clusters, through the Density-Equalizing Euclidean MST (DEEMST) method, for the detection of arbitrarily shaped clusters. The original map is cartogram transformed, such that the control points are spread uniformly. That method is quite effective, but the cartogram construction is computationally expensive and complicated. Results A fast method for the detection and inference of point data set space-time disease clusters is presented, the Voronoi Based Scan (VBScan). A Voronoi diagram is built for points representing population individuals (cases and controls). The number of Voronoi cells boundaries intercepted by the line segment joining two cases points defines the Voronoi distance between those points. That distance is used to approximate the density of the heterogeneous population and build the Voronoi distance MST linking the cases. The successive removal of edges from the Voronoi distance MST generates sub-trees which are the potential space-time clusters. Finally, those clusters are evaluated through the scan statistic. Monte Carlo replications of the original data are used to evaluate the significance of the clusters. An application for dengue fever in a small Brazilian city is presented. Conclusions The ability to promptly detect space-time clusters of disease outbreaks, when the number of individuals is large, was shown to be feasible, due to the reduced computational load of VBScan. Instead of changing the map, VBScan modifies the metric used to define the distance between cases, without requiring the cartogram construction. Numerical simulations showed that VBScan has higher power of detection, sensitivity and positive predicted value than the Elliptic PST. Furthermore, as VBScan also incorporates topological information from the point neighborhood structure, in addition to the usual geometric information, it is more robust than purely geometric methods such as the elliptic scan. Those advantages were illustrated in a real setting for dengue fever space-time clusters. PMID:21513556

What can we learn from the network approach in finance?

NASA Astrophysics Data System (ADS)

Janos, Kertesz

2005-03-01

Correlations between variations of stock prices reveal information about relationships between companies. Different methods of analysis have been applied to such data in order to uncover the taxonomy of the market. We use Mantegna's miminum spanning tree (MST) method for daily data in a dynamic way: By introducing a moving window we study the temporal changes in the structure of the network defined by this ``asset tree.'' The MST is scale free with a significantly changing exponent of the degree distribution for crash periods, which demonstrates the restructuring of the network due to the enhancement of correlations. This approach is compared to that based on what we call ``asset graphs:'' We start from an empty graph with no edges where the vertices correspond to stocks and then, one by one, we insert edges between the vertices according to the rank of their correlation strength. We study the properties of the creatred (weighted) networks, such as topologically different growth types, number and size of clusters and clustering coefficient. Furthermore, we define new tools like subgraph intensity and coherence to describe the role of the weights. We also investigate the time shifted cross correlation functions for high frequency data and find a characteristic time delay in many cases representing that some stocks lead the price changes while others follow them. These data can be used to construct a directed network of influence.

ITC-derived binding affinity may be biased due to titrant (nano)-aggregation. Binding of halogenated benzotriazoles to the catalytic domain of human protein kinase CK2

PubMed Central

Winiewska, Maria; Bugajska, Ewa

2017-01-01

The binding of four bromobenzotriazoles to the catalytic subunit of human protein kinase CK2 was assessed by two complementary methods: Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC). New algorithm proposed for the global analysis of MST pseudo-titration data enabled reliable determination of binding affinities for two distinct sites, a relatively strong one with the Kd of the order of 100 nM and a substantially weaker one (Kd > 1 μM). The affinities for the strong binding site determined for the same protein-ligand systems using ITC were in most cases approximately 10-fold underestimated. The discrepancy was assigned directly to the kinetics of ligand nano-aggregates decay occurring upon injection of the concentrated ligand solution to the protein sample. The binding affinities determined in the reverse ITC experiment, in which ligands were titrated with a concentrated protein solution, agreed with the MST-derived data. Our analysis suggests that some ITC-derived Kd values, routinely reported together with PDB structures of protein-ligand complexes, may be biased due to the uncontrolled ligand (nano)-aggregation, which may occur even substantially below the solubility limit. PMID:28273138

Robust tumor morphometry in multispectral fluorescence microscopy

NASA Astrophysics Data System (ADS)

Tabesh, Ali; Vengrenyuk, Yevgen; Teverovskiy, Mikhail; Khan, Faisal M.; Sapir, Marina; Powell, Douglas; Mesa-Tejada, Ricardo; Donovan, Michael J.; Fernandez, Gerardo

2009-02-01

Morphological and architectural characteristics of primary tissue compartments, such as epithelial nuclei (EN) and cytoplasm, provide important cues for cancer diagnosis, prognosis, and therapeutic response prediction. We propose two feature sets for the robust quantification of these characteristics in multiplex immunofluorescence (IF) microscopy images of prostate biopsy specimens. To enable feature extraction, EN and cytoplasm regions were first segmented from the IF images. Then, feature sets consisting of the characteristics of the minimum spanning tree (MST) connecting the EN and the fractal dimension (FD) of gland boundaries were obtained from the segmented compartments. We demonstrated the utility of the proposed features in prostate cancer recurrence prediction on a multi-institution cohort of 1027 patients. Univariate analysis revealed that both FD and one of the MST features were highly effective for predicting cancer recurrence (p <= 0.0001). In multivariate analysis, an MST feature was selected for a model incorporating clinical and image features. The model achieved a concordance index (CI) of 0.73 on the validation set, which was significantly higher than the CI of 0.69 for the standard multivariate model based solely on clinical features currently used in clinical practice (p < 0.0001). The contributions of this work are twofold. First, it is the first demonstration of the utility of the proposed features in morphometric analysis of IF images. Second, this is the largest scale study of the efficacy and robustness of the proposed features in prostate cancer prognosis.

The relationship between carbon dioxide emission and economic growth: Hierarchical structure methods

NASA Astrophysics Data System (ADS)

Deviren, Seyma Akkaya; Deviren, Bayram

2016-06-01

Carbon dioxide (CO2) emission has an essential role in the current debate on sustainable development and environmental protection. CO2 emission is also directly linked with use of energy which plays a focal role both for production and consumption in the world economy. Therefore the relationship between the CO2 emission and economic growth has a significant implication for the environmental and economical policies. In this study, within the scope of sociophysics, the topology, taxonomy and relationships among the 33 countries, which have almost the high CO2 emission and economic growth values, are investigated by using the hierarchical structure methods, such as the minimal spanning tree (MST) and hierarchical tree (HT), over the period of 1970-2010. The average linkage cluster analysis (ALCA) is also used to examine the cluster structure more clearly in HTs. According to their proximity, economic ties and economic growth, different clusters of countries are identified from the structural topologies of these trees. We have found that the high income & OECD countries are closely connected to each other and are isolated from the upper middle and lower middle income countries from the MSTs, which are obtained both for the CO2 emission and economic growth. Moreover, the high income & OECD clusters are homogeneous with respect to the economic activities and economic ties of the countries. It is also mentioned that the Group of Seven (G7) countries (CAN, ENG, FRA, GER, ITA, JPN, USA) are connected to each other and these countries are located at the center of the MST for the results of CO2 emission. The same analysis may also successfully apply to the other environmental sources and different countries.

Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

NASA Astrophysics Data System (ADS)

Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

2013-04-01

Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells

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

Yu, Teng, E-mail: tengyu33@yahoo.com; Ji, Jiang; Guo, Yong-li

2013-11-08

Highlights: •Curcumin activates MST1 in melanoma cells. •MST1 mediates curcumin-induced apoptosis of melanoma cells. •ROS production is involved in curcumin-induced MST1 activation. •MST1 mediates curcumin-induced JNK activation in melanoma cells. •MST1 mediates curcumin-induced Foxo3a nuclear translocation and Bim expression. -- Abstract: Different groups including ours have shown that curcumin induces melanoma cell apoptosis, here we focused the role of mammalian Sterile 20-like kinase 1 (MST1) in it. We observed that curcumin activated MST1-dependent apoptosis in cultured melanoma cells. MST1 silencing by RNA interference (RNAi) suppressed curcumin-induced cell apoptosis, while MST1 over-expressing increased curcumin sensitivity. Meanwhile, curcumin induced reactive oxygen speciesmore » (ROS) production in melanoma cells, and the ROS scavenger, N-acetyl-cysteine (NAC), almost blocked MST1 activation to suggest that ROS might be required for MST1 activation by curcumin. c-Jun N-terminal protein kinase (JNK) activation by curcumin was dependent on MST1, since MST1 inhibition by RNAi or NAC largely inhibited curcumin-induced JNK activation. Further, curcumin induced Foxo3 nuclear translocation and Bim-1 (Foxo3 target gene) expression in melanoma cells, such an effect by curcumin was inhibited by MST1 RNAi. In conclusion, we suggested that MST1 activation by curcumin mediates JNK activation, Foxo3a nuclear translocation and apoptosis in melanoma cells.« less

Genotyping of Coxiella burnetii from domestic ruminants in northern Spain.

PubMed

Astobiza, Ianire; Tilburg, Jeroen J H C; Piñero, Alvaro; Hurtado, Ana; García-Pérez, Ana L; Nabuurs-Franssen, Marrigje H; Klaassen, Corné H W

2012-12-10

Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). A total of 45 samples from 4 goat herds (placentas, N = 4), 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20) and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21) were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM) samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several European countries, but some of the MLVA genotypes are described here for the first time. Genotyping revealed a substantial genetic diversity among domestic ruminants from Northern Spain.

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

PubMed

Kordi, Misagh; Bansal, Mukul S

2017-06-01

Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.

Recursive algorithms for phylogenetic tree counting.

PubMed

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

SDIA: A dynamic situation driven information fusion algorithm for cloud environment

NASA Astrophysics Data System (ADS)

Guo, Shuhang; Wang, Tong; Wang, Jian

2017-09-01

Information fusion is an important issue in information integration domain. In order to form an extensive information fusion technology under the complex and diverse situations, a new information fusion algorithm is proposed. Firstly, a fuzzy evaluation model of tag utility was proposed that can be used to count the tag entropy. Secondly, a ubiquitous situation tag tree model is proposed to define multidimensional structure of information situation. Thirdly, the similarity matching between the situation models is classified into three types: the tree inclusion, the tree embedding, and the tree compatibility. Next, in order to reduce the time complexity of the tree compatible matching algorithm, a fast and ordered tree matching algorithm is proposed based on the node entropy, which is used to support the information fusion by ubiquitous situation. Since the algorithm revolve from the graph theory of disordered tree matching algorithm, it can improve the information fusion present recall rate and precision rate in the situation. The information fusion algorithm is compared with the star and the random tree matching algorithm, and the difference between the three algorithms is analyzed in the view of isomorphism, which proves the innovation and applicability of the algorithm.

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

Chen, Yen-Wei; Drury, Jeanie L.; Moussi, Joelle

Monosodium titanates (MST) are a relatively novel form of particulate titanium dioxide that have been proposed for biological use as metal sorbents or delivery agents, most recently calcium (II). In these roles, the toxicity of the titanate or its metal complex is crucial to its biological utility. The aim of this study was to determine the cytotoxicity of MST and MST-calcium complexes with MC3T3 osteoblast-like cells; MST-Ca(II) complexes could be useful to promote bone formation in various hard tissue applications. MC3T3 cells were exposed to native MST or MST-Ca(II) complexes for 24–72 h. A CellTiter-Blue ® assay was employed tomore » assess the metabolic activity of the cells. The results showed that MST and MST-Ca(II) suppressed MC3T3 metabolic activity significantly in a dose-, time-, and cell-density-dependent fashion. MST-Ca(II) suppressed MC3T3 metabolism in a statistically identical manner as native MST at all concentrations. We concluded that MST and MST-Ca(II) are significantly cytotoxic to MC3T3 cells through a mechanism yet unknown; this is a potential problem to the biological utility of these complexes.« less

Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

PubMed Central

2010-01-01

Background Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts. PMID:21143842

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

PubMed

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

Military sexual trauma among homeless veterans.

PubMed

Pavao, Joanne; Turchik, Jessica A; Hyun, Jenny K; Karpenko, Julie; Saweikis, Meghan; McCutcheon, Susan; Kane, Vincent; Kimerling, Rachel

2013-07-01

Military sexual trauma (MST) is the Veteran Health Administration's (VHA) term for sexual assault and/or sexual harassment that occurs during military service. The experience of MST is associated with a variety of mental health conditions. Preliminary research suggests that MST may be associated with homelessness among female Veterans, although to date MST has not been examined in a national study of both female and male homeless Veterans. To estimate the prevalence of MST, examine the association between MST and mental health conditions, and describe mental health utilization among homeless women and men. National, cross-sectional study of 126,598 homeless Veterans who used VHA outpatient care in fiscal year 2010. All variables were obtained from VHA administrative databases, including MST screening status, ICD-9-CM codes to determine mental health diagnoses, and VHA utilization. Of homeless Veterans in VHA, 39.7 % of females and 3.3 % of males experienced MST. Homeless Veterans who experienced MST demonstrated a significantly higher likelihood of almost all mental health conditions examined as compared to other homeless women and men, including depression, posttraumatic stress disorder, other anxiety disorders, substance use disorders, bipolar disorders, personality disorders, suicide, and, among men only, schizophrenia and psychotic disorders. Nearly all homeless Veterans had at least one mental health visit and Veterans who experienced MST utilized significantly more mental health visits compared to Veterans who did not experience MST. A substantial proportion of homeless Veterans using VHA services have experienced MST, and those who experienced MST had increased odds of mental health diagnoses. Homeless Veterans who had experienced MST had higher intensity of mental health care utilization and high rates of MST-related mental health care. This study highlights the importance of trauma-informed care among homeless Veterans and the success of VHA homeless programs in providing mental health care to homeless Veterans.

Cytotoxicity of Titanate-Calcium Complexes to MC3T3 Osteoblast-Like Cells

DOE PAGES

Chen, Yen-Wei; Drury, Jeanie L.; Moussi, Joelle; ...

2016-11-30

Monosodium titanates (MST) are a relatively novel form of particulate titanium dioxide that have been proposed for biological use as metal sorbents or delivery agents, most recently calcium (II). In these roles, the toxicity of the titanate or its metal complex is crucial to its biological utility. The aim of this study was to determine the cytotoxicity of MST and MST-calcium complexes with MC3T3 osteoblast-like cells; MST-Ca(II) complexes could be useful to promote bone formation in various hard tissue applications. MC3T3 cells were exposed to native MST or MST-Ca(II) complexes for 24–72 h. A CellTiter-Blue ® assay was employed tomore » assess the metabolic activity of the cells. The results showed that MST and MST-Ca(II) suppressed MC3T3 metabolic activity significantly in a dose-, time-, and cell-density-dependent fashion. MST-Ca(II) suppressed MC3T3 metabolism in a statistically identical manner as native MST at all concentrations. We concluded that MST and MST-Ca(II) are significantly cytotoxic to MC3T3 cells through a mechanism yet unknown; this is a potential problem to the biological utility of these complexes.« less

Cytotoxicity of Titanate-Calcium Complexes to MC3T3 Osteoblast-Like Cells

PubMed Central

Drury, Jeanie L.; Moussi, Joelle; Taylor-Pashow, Kathryn M. L.

2016-01-01

Monosodium titanates (MST) are a relatively novel form of particulate titanium dioxide that have been proposed for biological use as metal sorbents or delivery agents, most recently calcium (II). In these roles, the toxicity of the titanate or its metal complex is crucial to its biological utility. The aim of this study was to determine the cytotoxicity of MST and MST-calcium complexes with MC3T3 osteoblast-like cells; MST-Ca(II) complexes could be useful to promote bone formation in various hard tissue applications. MC3T3 cells were exposed to native MST or MST-Ca(II) complexes for 24–72 h. A CellTiter-Blue® assay was employed to assess the metabolic activity of the cells. The results showed that MST and MST-Ca(II) suppressed MC3T3 metabolic activity significantly in a dose-, time-, and cell-density-dependent fashion. MST-Ca(II) suppressed MC3T3 metabolism in a statistically identical manner as native MST at all concentrations. We concluded that MST and MST-Ca(II) are significantly cytotoxic to MC3T3 cells through a mechanism yet unknown; this is a potential problem to the biological utility of these complexes. PMID:28044136

Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling pathway

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

Hwang, Eunha; Korea University, Seoul 136-701; Cheong, Hae-Kap

2014-07-01

The heterodimeric structure of the MST1 and RASSF5 SARAH domains is presented. A comparison of homodimeric and heterodimeric interactions provides a structural basis for the preferential association of the SARAH heterodimer. Despite recent progress in research on the Hippo signalling pathway, the structural information available in this area is extremely limited. Intriguingly, the homodimeric and heterodimeric interactions of mammalian sterile 20-like (MST) kinases through the so-called ‘SARAH’ (SAV/RASSF/HPO) domains play a critical role in cellular homeostasis, dictating the fate of the cell regarding cell proliferation or apoptosis. To understand the mechanism of the heterodimerization of SARAH domains, the three-dimensional structuresmore » of an MST1–RASSF5 SARAH heterodimer and an MST2 SARAH homodimer were determined by X-ray crystallography and were analysed together with that previously determined for the MST1 SARAH homodimer. While the structure of the MST2 homodimer resembled that of the MST1 homodimer, the MST1–RASSF5 heterodimer showed distinct structural features. Firstly, the six N-terminal residues (Asp432–Lys437), which correspond to the short N-terminal 3{sub 10}-helix h1 kinked from the h2 helix in the MST1 homodimer, were disordered. Furthermore, the MST1 SARAH domain in the MST1–RASSF5 complex showed a longer helical structure (Ser438–Lys480) than that in the MST1 homodimer (Val441–Lys480). Moreover, extensive polar and nonpolar contacts in the MST1–RASSF5 SARAH domain were identified which strengthen the interactions in the heterodimer in comparison to the interactions in the homodimer. Denaturation experiments performed using urea also indicated that the MST–RASSF heterodimers are substantially more stable than the MST homodimers. These findings provide structural insights into the role of the MST1–RASSF5 SARAH domain in apoptosis signalling.« less

Network analysis of returns and volume trading in stock markets: The Euro Stoxx case

NASA Astrophysics Data System (ADS)

Brida, Juan Gabriel; Matesanz, David; Seijas, Maria Nela

2016-02-01

This study applies network analysis to analyze the structure of the Euro Stoxx market during the long period from 2002 up to 2014. The paper generalizes previous research on stock market networks by including asset returns and volume trading as the main variables to study the financial market. A multidimensional generalization of the minimal spanning tree (MST) concept is introduced, by adding the role of trading volume to the traditional approach which only includes price returns. Additionally, we use symbolization methods to the raw data to study the behavior of the market structure in different, normal and critical, situations. The hierarchical organization of the network is derived, and the MST for different sub-periods of 2002-2014 is created to illustrate how the structure of the market evolves over time. From the structural topologies of these trees, different clusters of companies are identified and analyzed according to their geographical and economic links. Two important results are achieved. Firstly, as other studies have highlighted, at the time of the financial crisis after 2008 the network becomes a more centralized one. Secondly and most important, during our second period of analysis, 2008-2014, we observe that hierarchy becomes more country-specific where different sub-clusters of stocks belonging to France, Germany, Spain or Italy are found apart from their business sector group. This result may suggest that during this period of time financial investors seem to be worried most about country specific economic circumstances.

Finding Frequent Closed Itemsets in Sliding Window in Linear Time

NASA Astrophysics Data System (ADS)

Chen, Junbo; Zhou, Bo; Chen, Lu; Wang, Xinyu; Ding, Yiqun

One of the most well-studied problems in data mining is computing the collection of frequent itemsets in large transactional databases. Since the introduction of the famous Apriori algorithm [14], many others have been proposed to find the frequent itemsets. Among such algorithms, the approach of mining closed itemsets has raised much interest in data mining community. The algorithms taking this approach include TITANIC [8], CLOSET+[6], DCI-Closed [4], FCI-Stream [3], GC-Tree [15], TGC-Tree [16] etc. Among these algorithms, FCI-Stream, GC-Tree and TGC-Tree are online algorithms work under sliding window environments. By the performance evaluation in [16], GC-Tree [15] is the fastest one. In this paper, an improved algorithm based on GC-Tree is proposed, the computational complexity of which is proved to be a linear combination of the average transaction size and the average closed itemset size. The algorithm is based on the essential theorem presented in Sect. 4.2. Empirically, the new algorithm is several orders of magnitude faster than the state of art algorithm, GC-Tree.

Cordilleran forest scaling dynamics and disturbance regimes quantified by aerial lidar

NASA Astrophysics Data System (ADS)

Swetnam, Tyson L.

Semi-arid forests are in a period of rapid transition as a result of unprecedented landscape scale fires, insect outbreaks, drought, and anthropogenic land use practices. Understanding how historically episodic disturbances led to coherent forest structural and spatial patterns that promoted resilience and resistance is a critical part of addressing change. Here my coauthors and I apply metabolic scaling theory (MST) to examine scaling behavior and structural patterns of semi-arid conifer forests in Arizona and New Mexico. We conceptualize a linkage to mechanistic drivers of forest assembly that incorporates the effects of low-intensity disturbance, and physiologic and resource limitations as an extension of MST. We use both aerial LiDAR data and field observations to quantify changes in forest structure from the sub-meter to landscape scales. We found: (1) semi-arid forest structure exhibits MST-predicted behaviors regardless of disturbance and that MST can help to quantitatively measure the level of disturbance intensity in a forest, (2) the application of a power law to a forest overstory frequency distribution can help predict understory presence/absence, (3) local indicators of spatial association can help to define first order effects (e.g. topographic changes) and map where recent disturbances (e.g. logging and fire) have altered forest structure. Lastly, we produced a comprehensive set of above-ground biomass and carbon models for five distinct forest types and ten common species of the southwestern US that are meant for use in aerial LiDAR forest inventory projects. This dissertation presents both a conceptual framework and applications for investigating local scales (stands of trees) up to entire ecosystems for diagnosis of current carbon balances, levels of departure from historical norms, and ecological stability. These tools and models will become more important as we prepare our ecosystems for a future characterized by increased climatic variability with an associated increase in frequency and severity of ecological disturbances.

An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree

PubMed Central

2016-01-01

Motivation: Gene tree represents the evolutionary history of gene lineages that originate from multiple related populations. Under the multispecies coalescent model, lineages may coalesce outside the species (population) boundary. Given a species tree (with branch lengths), the gene tree probability is the probability of observing a specific gene tree topology under the multispecies coalescent model. There are two existing algorithms for computing the exact gene tree probability. The first algorithm is due to Degnan and Salter, where they enumerate all the so-called coalescent histories for the given species tree and the gene tree topology. Their algorithm runs in exponential time in the number of gene lineages in general. The second algorithm is the STELLS algorithm (2012), which is usually faster but also runs in exponential time in almost all the cases. Results: In this article, we present a new algorithm, called CompactCH, for computing the exact gene tree probability. This new algorithm is based on the notion of compact coalescent histories: multiple coalescent histories are represented by a single compact coalescent history. The key advantage of our new algorithm is that it runs in polynomial time in the number of gene lineages if the number of populations is fixed to be a constant. The new algorithm is more efficient than the STELLS algorithm both in theory and in practice when the number of populations is small and there are multiple gene lineages from each population. As an application, we show that CompactCH can be applied in the inference of population tree (i.e. the population divergence history) from population haplotypes. Simulation results show that the CompactCH algorithm enables efficient and accurate inference of population trees with much more haplotypes than a previous approach. Availability: The CompactCH algorithm is implemented in the STELLS software package, which is available for download at http://www.engr.uconn.edu/ywu/STELLS.html. Contact: ywu@engr.uconn.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307621

Hypermethylation of MST1 in IgG4-related autoimmune pancreatitis and rheumatoid arthritis

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

Fukuhara, Takataro; Tomiyama, Takashi; Yasuda, Kaneki

The serine/threonine kinase Mst1 plays important roles in the control of immune cell trafficking, proliferation, and differentiation. Previously, we reported that Mst1 was required for thymocyte selection and regulatory T-cell functions, thereby the prevention of autoimmunity in mice. In humans, MST1 null mutations cause T-cell immunodeficiency and hypergammaglobulinemia with autoantibody production. RASSF5C(RAPL) is an activator of MST1 and it is frequently methylated in some tumors. Herein, we investigated methylation of the promoter regions of MST1 and RASSF5C(RAPL) in leukocytes from patients with IgG4-related autoimmune pancreatitis (AIP) and rheumatoid arthritis (RA). Increased number of CpG methylation in the 5′ region ofmore » MST1 was detected in AIP patients with extrapancreatic lesions, whereas AIP patients without extrapancreatic lesions were similar to controls. In RA patients, we detected a slight increased CpG methylation in MST1, although the overall number of methylation sites was lower than that of AIP patients with extrapancreatic lesions. There were no significant changes of the methylation levels of the CpG islands in the 5′ region of RASSF5C(RAPL) in leukocytes from AIP and RA patients. Consistently, we found a significantly down-regulated expression of MST1 in regulatory T cells of AIP patients. Our results suggest that the decreased expression of MST1 in regulatory T cells due to hypermethylation of the promoter contributes to the pathogenesis of IgG4-related AIP. - Highlights: • Mst1 controls immune cells trafficking, cell proliferation and differentiation. • Autoimmune pancreatitis (AIP) is an idiopathic pancreatitis affecting multiple organs. • Decreased MST1 expression and increased CpG methylation of promoter of MST1 in AIP. • Slight increased CpG methylation of MST1 in rheumatoid arthritis patients. • MST1 contributes pathogenesis of IgG4-related AIP.« less

Finding Minimum-Power Broadcast Trees for Wireless Networks

NASA Technical Reports Server (NTRS)

Arabshahi, Payman; Gray, Andrew; Das, Arindam; El-Sharkawi, Mohamed; Marks, Robert, II

2004-01-01

Some algorithms have been devised for use in a method of constructing tree graphs that represent connections among the nodes of a wireless communication network. These algorithms provide for determining the viability of any given candidate connection tree and for generating an initial set of viable trees that can be used in any of a variety of search algorithms (e.g., a genetic algorithm) to find a tree that enables the network to broadcast from a source node to all other nodes while consuming the minimum amount of total power. The method yields solutions better than those of a prior algorithm known as the broadcast incremental power algorithm, albeit at a slightly greater computational cost.

Involvement of Mst1 in tumor necrosis factor-{alpha}-induced apoptosis of endothelial cells

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

Ohtsubo, Hideki; Ichiki, Toshihiro; Imayama, Ikuyo

2008-03-07

Mammalian sterile 20-kinase 1 (Mst1), a member of the sterile-20 family protein kinase, plays an important role in the induction of apoptosis. However, little is know about the physiological activator of Mst1 and the role of Mst1 in endothelial cells (ECs). We examined whether Mst1 is involved in the tumor necrosis factor (TNF)-{alpha}-induced apoptosis of ECs. Western blot analysis revealed that TNF-{alpha} induced activation of caspase 3 and Mst1 in a time- and dose-dependent manner. TNF-{alpha}-induced Mst1 activation is almost completely prevented by pretreatment with Z-DEVD-FMK, a caspase 3 inhibitor. Nuclear staining with Hoechst 33258 and fluorescence-activated cell sorting ofmore » propidium iodide-stained cells showed that TNF-{alpha} induced apoptosis of EC. Diphenyleneiodonium, an inhibitor of NADPH oxidase, and N-acetylcysteine, a potent antioxidant, also inhibited TNF-{alpha}-induced activation of Mst1 and caspase 3, as well as apoptosis. Knockdown of Mst1 expression by short interfering RNA attenuated TNF-{alpha}-induced apoptosis but not cleavage of caspase 3. These results suggest that Mst1 plays an important role in the induction of TNF-{alpha}-induced apoptosis of EC. However, positive feedback mechanism between Mst1 and caspase 3, which was shown in the previous studies, was not observed. Inhibition of Mst1 function may be beneficial for maintaining the endothelial integrity and inhibition of atherogenesis.« less

A Decision Processing Algorithm for CDC Location Under Minimum Cost SCM Network

NASA Astrophysics Data System (ADS)

Park, N. K.; Kim, J. Y.; Choi, W. Y.; Tian, Z. M.; Kim, D. J.

Location of CDC in the matter of network on Supply Chain is becoming on the high concern these days. Present status of methods on CDC has been mainly based on the calculation manually by the spread sheet to achieve the goal of minimum logistics cost. This study is focused on the development of new processing algorithm to overcome the limit of present methods, and examination of the propriety of this algorithm by case study. The algorithm suggested by this study is based on the principle of optimization on the directive GRAPH of SCM model and suggest the algorithm utilizing the traditionally introduced MST, shortest paths finding methods, etc. By the aftermath of this study, it helps to assess suitability of the present on-going SCM network and could be the criterion on the decision-making process for the optimal SCM network building-up for the demand prospect in the future.

1. GENERAL VIEW OF SLC3W SHOWING SOUTH FACE AND EAST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. GENERAL VIEW OF SLC-3W SHOWING SOUTH FACE AND EAST SIDE OF A-FRAME MOBILE SERVICE TOWER (MST). MST IN SERVICE POSITION OVER LAUNCHER AND FLAME BUCKET. CABLE TRAYS BETWEEN LAUNCH OPERATIONS BUILDING (BLDG. 763) AND SLC-3W IN FOREGROUND. LIQUID OXYGEN APRON VISIBLE IMMEDIATELY EAST (RIGHT) OF MST; FUEL APRON VISIBLE IMMEDIATELY WEST (LEFT) OF MST. A PORTION OF THE FLAME BUCKET VISIBLE BELOW THE SOUTH FACE OF THE MST. CAMERA TOWERS VISIBLE EAST OF MST BETWEEN ROAD AND CABLE TRAY, AND SOUTH OF MST NEAR LEFT MARGIN OF PHOTOGRAPH. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

PubMed Central

Krsticevic, Flavia J.; Schrago, Carlos G.; Carvalho, A. Bernardo

2015-01-01

The autosomal gene Mst77F of Drosophila melanogaster is essential for male fertility. In 2010, Krsticevic et al. (Genetics 184: 295−307) found 18 Y-linked copies of Mst77F (“Mst77Y”), which collectively account for 20% of the functional Mst77F-like mRNA. The Mst77Y genes were severely misassembled in the then-available genome assembly and were identified by cloning and sequencing polymerase chain reaction products. The genomic structure of the Mst77Y region and the possible existence of additional copies remained unknown. The recent publication of two long-read assemblies of D. melanogaster prompted us to reinvestigate this challenging region of the Y chromosome. We found that the Illumina Synthetic Long Reads assembly failed in the Mst77Y region, most likely because of its tandem duplication structure. The PacBio MHAP assembly of the Mst77Y region seems to be very accurate, as revealed by comparisons with the previously found Mst77Y genes, a bacterial artificial chromosome sequence, and Illumina reads of the same strain. We found that the Mst77Y region spans 96 kb and originated from a 3.4-kb transposition from chromosome 3L to the Y chromosome, followed by tandem duplications inside the Y chromosome and invasion of transposable elements, which account for 48% of its length. Twelve of the 18 Mst77Y genes found in 2010 were confirmed in the PacBio assembly, the remaining six being polymerase chain reaction−induced artifacts. There are several identical copies of some Mst77Y genes, coincidentally bringing the total copy number to 18. Besides providing a detailed picture of the Mst77Y region, our results highlight the utility of PacBio technology in assembling difficult genomic regions such as tandemly repeated genes. PMID:25858959

Morin impedes Yap nuclear translocation and fosters apoptosis through suppression of Wnt/β-catenin and NF-κB signaling in Mst1 overexpressed HepG2 cells

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

Perumal, NaveenKumar; Perumal, MadanKumar; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas 75390

Recent clinical and experimental evidences strongly acclaim Yes-associated protein (Yap), a key oncogenic driver in liver carcinogenesis, as a therapeutic target. Of the known multiple schemes to inhibit Yap activity, activation of Mammalian Sterile 20-like Kinase 1 (Mst1), an upstream regulator of Yap, appears to be a promising one. In this study, we hypothesize that morin, a bioflavonoid, mediates its anti-cancer effect through the activation of Mst1/hippo signaling in liver cancer cells. To test this hypothesis, both full length Mst1 (F-Mst1) and kinase active N-terminal Mst1 (N-Mst1)-overexpressed HepG2 cells were used. Exposure of F-Mst1 overexpressed HepG2 cells to morin activatedmore » Mst1 by caspase-3 cleavage and thereby inhibited Yap nuclear translocation and fostered apoptosis. Morin suppressed NF-κB p65 and Wnt/β-catenin signaling through Mst1 activation via cleavage and phosphorylation, leading to cell death. Annexin-V/PI staining further confirmed the induction of apoptosis in morin treated F-Mst1 overexpressed cells. The present study shows that morin targets cell survival molecules such as NF-κB p65 and β-catenin through activation of hippo signaling. Therefore, morin could be considered as a potential anti-cancer agent against liver cancer. - Highlights: • Morin induced cytotoxicity in cultured HepG2 cells. • Morin activated hippo pathway via Mst1 activation in transfected HepG2 cells. • Morin suppressed Wnt/β-catenin signaling and induced G0/G1 cell cycle arrest. • Morin inhibited NF-κB signaling through Mst1 activation in transfected HepG2 cells. • Morin potentiates apoptosis through Mst1-JNK-caspase mediated mechanism in HepG2 cells.« less

Adsorption of biometals to monosodium titanate in biological environments

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

HOBBS, D.T.; MESSER, R. L. W.; LEWIS, J. B.

2005-06-06

Monosodium titanate (MST) is an inorganic sorbent/ion exchanger developed for the removal of radionuclides from nuclear wastes. We investigated the ability of MST to bind Cd(II), Hg(II), or Au(III) to establish the utility of MST for applications in environmental decontamination or medical therapy (drug delivery). Adsorption isotherms for MST were determined at pH 7-7.5 in water or phosphate-buffered saline. The extent of metal binding was determined spectroscopically by measuring the concentrations of the metals in solution before and after contact with the MST. Cytotoxic responses to MST were assessed using THP1 monocytes and succinate dehydrogenase activity. Monocytic activation by MSTmore » was assessed by TNF{alpha} secretion (ELISA) with or without lipopolysaccharide (LPS) activation. MST sorbed Cd(II), Hg(II), and Au(III) under conditions similar to that in physiological systems. MST exhibited the highest affinity for Cd(II) followed by Hg(II) and Au (III). MST (up to 100 mg/L) exhibited only minor (< 25% suppression of succinate dehydrogenase) cytotoxicity and did not trigger TNF{alpha} secretion nor modulate LPS-induced TNF{alpha} secretion from monocytes. MST exhibits high affinity for biometals with no significant biological liabilities in these introductory studies. MST deserves further scrutiny as a substance with the capacity to decontaminate biological environments or deliver metals in a controlled fashion.« less

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

PubMed Central

Cui, Yun; Jansson, Jesper

2012-01-01

Abstract A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host–parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists. PMID:22963134

Polynomial-time algorithms for building a consensus MUL-tree.

PubMed

Cui, Yun; Jansson, Jesper; Sung, Wing-Kin

2012-09-01

A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host-parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists.

Autumn Algorithm-Computation of Hybridization Networks for Realistic Phylogenetic Trees.

PubMed

Huson, Daniel H; Linz, Simone

2018-01-01

A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and "realistic" trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of "realistic" rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of "autumn trees", a nice framework for the formulation of algorithms based on the mathematics of "maximum acyclic agreement forests". While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.

Direct evaluation of fault trees using object-oriented programming techniques

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1989-01-01

Object-oriented programming techniques are used in an algorithm for the direct evaluation of fault trees. The algorithm combines a simple bottom-up procedure for trees without repeated events with a top-down recursive procedure for trees with repeated events. The object-oriented approach results in a dynamic modularization of the tree at each step in the reduction process. The algorithm reduces the number of recursive calls required to solve trees with repeated events and calculates intermediate results as well as the solution of the top event. The intermediate results can be reused if part of the tree is modified. An example is presented in which the results of the algorithm implemented with conventional techniques are compared to those of the object-oriented approach.

Negative posttraumatic cognitions among military sexual trauma survivors.

PubMed

Carroll, Kathryn K; Lofgreen, Ashton M; Weaver, Darian C; Held, Philip; Klassen, Brian J; Smith, Dale L; Karnik, Niranjan S; Pollack, Mark H; Zalta, Alyson K

2018-05-19

Unique aspects of military sexual trauma (MST) may result in specific maladaptive cognitions among survivors. Understanding which posttraumatic cognitions are particularly strong among MST survivors could help clinicians target and improve treatment for these individuals. This study explored the impact of experiencing MST on posttraumatic cognitions among veterans with posttraumatic stress disorder (PTSD). Veterans enrolled in an Intensive Outpatient Program for PTSD (N = 226) were assessed for MST, PTSD severity, depression severity, and posttraumatic cognitions as part of a standard clinical intake. Multivariate analyses examined differences in posttraumatic cognitions between veterans who did and did not experience MST. MST survivors (n = 88) endorsed significantly stronger posttraumatic cognitions related to self-blame compared to non-MST counterparts (n = 138), even when accounting for current symptom severity. Specifically, MST predicted the following cognitions: "The event happened to me because of the sort of person I am," "Somebody else would have stopped the event from happening," "Somebody else would not have gotten into this situation," and "There is something about me that made the event happen," after controlling for severity of PTSD and depression. Study population was a treatment-seeking sample of veterans diagnosed with PTSD from a non-VA clinic. Veterans in MST group endorsed either sexual harassment, sexual assault, or both. Sample size of males who endorsed MST (n = 21) may be too small to generalize to all males. Beliefs related to self-blame may be important treatment targets for MST survivors. Copyright © 2018. Published by Elsevier B.V.

Cell Polarity Kinase MST4 Cooperates with cAMP-dependent Kinase to Orchestrate Histamine-stimulated Acid Secretion in Gastric Parietal Cells*

PubMed Central

Jiang, Hao; Wang, Wenwen; Zhang, Yin; Yao, William W.; Jiang, Jiying; Qin, Bo; Yao, Wendy Y.; Liu, Fusheng; Wu, Huihui; Ward, Tarsha L.; Chen, Chun Wei; Liu, Lifang; Ding, Xia; Liu, Xing; Yao, Xuebiao

2015-01-01

The digestive function of the stomach depends on acidification of the gastric lumen. Acid secretion into the lumen is triggered by activation of the PKA cascade, which ultimately results in the insertion of gastric H,K-ATPases into the apical plasma membranes of parietal cells. A coupling protein is ezrin, whose phosphorylation at Ser-66 by PKA is required for parietal cell activation. However, little is known regarding the molecular mechanism(s) by which this signaling pathway operates in gastric acid secretion. Here we show that PKA cooperates with MST4 to orchestrate histamine-elicited acid secretion by phosphorylating ezrin at Ser-66 and Thr-567. Histamine stimulation activates PKA, which phosphorylates MST4 at Thr-178 and then promotes MST4 kinase activity. Interestingly, activated MST4 then phosphorylates ezrin prephosphorylated by PKA. Importantly, MST4 is important for acid secretion in parietal cells because either suppression of MST4 or overexpression of non-phosphorylatable MST4 prevents the apical membrane reorganization and proton pump translocation elicited by histamine stimulation. In addition, overexpressing MST4 phosphorylation-deficient ezrin results in an inhibition of gastric acid secretion. Taken together, these results define a novel molecular mechanism linking the PKA-MST4-ezrin signaling cascade to polarized epithelial secretion in gastric parietal cells. PMID:26405038

Within-unit relationship quality mediates the association between military sexual trauma and posttraumatic stress symptoms in veterans separating from military service.

PubMed

Laws, Holly; Mazure, Carolyn M; McKee, Sherry A; Park, Crystal L; Hoff, Rani

2016-09-01

Few studies have examined the impact of military sexual trauma (MST) on social functioning during deployment. Yet consideration of unit relationships during deployment may be important, given that military unit cohesion and support can provide protective effects against the stress of combat, and reduce the likelihood of developing posttraumatic stress disorder. Although prior research has posited that depleted social resources are one pathway through which MST is associated with posttraumatic stress symptoms (PTSS), no studies have statistically tested this theory. This study examined the association of MST and PTSS and evaluated the potential mediating role of decreased unit relationship quality. Mediational analyses were conducted on a sample of veterans following discharge from military service (N = 818; 328 women, 490 men). Women were significantly more likely to experience MST than men. As hypothesized, experiences of MST during deployment were associated with higher PTSS. MST experiences were associated with less trust in and support from one's military unit, which partially mediated the association between MST and PTSS. The indirect effect of MST on PTSS through lower unit relationship quality accounted for 20.4% of the total effect of MST on PTSS. While the retrospective study design precludes tests of causality, mediational findings provided statistical evidence that lower unit relationship quality partially explains the association between MST and PTSS. This finding is consistent with interpersonal theories of trauma response suggesting that the deleterious effects of MST may be in part due to its erosion of social resources during deployment. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Military Sexual Trauma Among Recent Veterans: Correlates of Sexual Assault and Sexual Harassment.

PubMed

Barth, Shannon K; Kimerling, Rachel E; Pavao, Joanne; McCutcheon, Susan J; Batten, Sonja V; Dursa, Erin; Peterson, Michael R; Schneiderman, Aaron I

2016-01-01

Military sexual trauma (MST) includes sexual harassment or sexual assault that occurs during military service and is of increasing public health concern. The population prevalence of MST among female and male veterans who served during Operations Enduring Freedom and Iraqi Freedom (OEF/OIF) has not been estimated to our knowledge. The purpose of this study is to assess the population prevalence and identify military correlates of MST, sexual harassment, and sexual assault among OEF/OIF veterans. MST was assessed in the 2009-2011 National Health Study for a New Generation of U.S. Veterans, a survey of 60,000 veterans who served during the OEF/OIF eras (response rate, 34%, n=20,563). Weighted prevalence estimates and AORs of MST, sexual harassment, and sexual assault among women and men were calculated. Gender-stratified logistic regression models controlled for military and demographic characteristics. Data analyses were conducted in 2013-2014. Approximately 41% of women and 4% of men reported experiencing MST. Deployed men had lower risk for MST compared with non-deployed men, though no difference was found among women. However, veterans reporting combat exposure during deployment had increased risk for MST compared with those without, while controlling for OEF/OIF deployment. Among women, Marines and Navy veterans had increased risk for MST compared with Air Force veterans. MST was significantly higher among veterans who reported using Veterans Affairs healthcare services. These prevalence estimates underscore the importance of public awareness and continued investigation of the public health impact of MST. Published by Elsevier Inc.

A Fast Exact k-Nearest Neighbors Algorithm for High Dimensional Search Using k-Means Clustering and Triangle Inequality.

PubMed

Wang, Xueyi

2012-02-08

The k-nearest neighbors (k-NN) algorithm is a widely used machine learning method that finds nearest neighbors of a test object in a feature space. We present a new exact k-NN algorithm called kMkNN (k-Means for k-Nearest Neighbors) that uses the k-means clustering and the triangle inequality to accelerate the searching for nearest neighbors in a high dimensional space. The kMkNN algorithm has two stages. In the buildup stage, instead of using complex tree structures such as metric trees, kd-trees, or ball-tree, kMkNN uses a simple k-means clustering method to preprocess the training dataset. In the searching stage, given a query object, kMkNN finds nearest training objects starting from the nearest cluster to the query object and uses the triangle inequality to reduce the distance calculations. Experiments show that the performance of kMkNN is surprisingly good compared to the traditional k-NN algorithm and tree-based k-NN algorithms such as kd-trees and ball-trees. On a collection of 20 datasets with up to 10(6) records and 10(4) dimensions, kMkNN shows a 2-to 80-fold reduction of distance calculations and a 2- to 60-fold speedup over the traditional k-NN algorithm for 16 datasets. Furthermore, kMkNN performs significant better than a kd-tree based k-NN algorithm for all datasets and performs better than a ball-tree based k-NN algorithm for most datasets. The results show that kMkNN is effective for searching nearest neighbors in high dimensional spaces.

Longitudinal Multistage Testing

ERIC Educational Resources Information Center

Pohl, Steffi

2013-01-01

This article introduces longitudinal multistage testing (lMST), a special form of multistage testing (MST), as a method for adaptive testing in longitudinal large-scale studies. In lMST designs, test forms of different difficulty levels are used, whereas the values on a pretest determine the routing to these test forms. Since lMST allows for…

Decision tree and ensemble learning algorithms with their applications in bioinformatics.

PubMed

Che, Dongsheng; Liu, Qi; Rasheed, Khaled; Tao, Xiuping

2011-01-01

Machine learning approaches have wide applications in bioinformatics, and decision tree is one of the successful approaches applied in this field. In this chapter, we briefly review decision tree and related ensemble algorithms and show the successful applications of such approaches on solving biological problems. We hope that by learning the algorithms of decision trees and ensemble classifiers, biologists can get the basic ideas of how machine learning algorithms work. On the other hand, by being exposed to the applications of decision trees and ensemble algorithms in bioinformatics, computer scientists can get better ideas of which bioinformatics topics they may work on in their future research directions. We aim to provide a platform to bridge the gap between biologists and computer scientists.

Learning receptive fields using predictive feedback.

PubMed

Jehee, Janneke F M; Rothkopf, Constantin; Beck, Jeffrey M; Ballard, Dana H

2006-01-01

Previously, it was suggested that feedback connections from higher- to lower-level areas carry predictions of lower-level neural activities, whereas feedforward connections carry the residual error between the predictions and the actual lower-level activities [Rao, R.P.N., Ballard, D.H., 1999. Nature Neuroscience 2, 79-87.]. A computational model implementing the hypothesis learned simple cell receptive fields when exposed to natural images. Here, we use predictive feedback to explain tuning properties in medial superior temporal area (MST). We implement the hypothesis using a new, biologically plausible, algorithm based on matching pursuit, which retains all the features of the previous implementation, including its ability to efficiently encode input. When presented with natural images, the model developed receptive field properties as found in primary visual cortex. In addition, when exposed to visual motion input resulting from movements through space, the model learned receptive field properties resembling those in MST. These results corroborate the idea that predictive feedback is a general principle used by the visual system to efficiently encode natural input.

Military sexual trauma research: a proposed agenda.

PubMed

Allard, Carolyn B; Nunnink, Sarah; Gregory, Amber M; Klest, Bridget; Platt, Melissa

2011-01-01

Military sexual trauma (MST) is a widespread problem associated with negative psychological and physical health problems. This article presents the current state of MST research and highlights specific areas in need of more focused study. Areas that have produced the greatest body of knowledge include MST prevalence and psychological and physical health correlates. We propose a research agenda based on gaps noted in our research review and empirical and theoretical evidence of issues relevant to but not studied directly in MST populations. We present evidence that MST is qualitatively distinct from other forms of sexual maltreatment in terms of its relational and vocational context as well as the severity of associated psychological distress, examine underexplored gender and sexual issues in MST, and discuss the lack of treatment and prevention studies specific to MST. Specific recommendations are made throughout in an attempt to guide and advance the field.

A Hybrid Shared-Memory Parallel Max-Tree Algorithm for Extreme Dynamic-Range Images.

PubMed

Moschini, Ugo; Meijster, Arnold; Wilkinson, Michael H F

2018-03-01

Max-trees, or component trees, are graph structures that represent the connected components of an image in a hierarchical way. Nowadays, many application fields rely on images with high-dynamic range or floating point values. Efficient sequential algorithms exist to build trees and compute attributes for images of any bit depth. However, we show that the current parallel algorithms perform poorly already with integers at bit depths higher than 16 bits per pixel. We propose a parallel method combining the two worlds of flooding and merging max-tree algorithms. First, a pilot max-tree of a quantized version of the image is built in parallel using a flooding method. Later, this structure is used in a parallel leaf-to-root approach to compute efficiently the final max-tree and to drive the merging of the sub-trees computed by the threads. We present an analysis of the performance both on simulated and actual 2D images and 3D volumes. Execution times are about better than the fastest sequential algorithm and speed-up goes up to on 64 threads.

Mobility based multicast routing in wireless mesh networks

NASA Astrophysics Data System (ADS)

Jain, Sanjeev; Tripathi, Vijay S.; Tiwari, Sudarshan

2013-01-01

There exist two fundamental approaches to multicast routing namely minimum cost trees and shortest path trees. The (MCT's) minimum cost tree is one which connects receiver and sources by providing a minimum number of transmissions (MNTs) the MNTs approach is generally used for energy constraint sensor and mobile ad hoc networks. In this paper we have considered node mobility and try to find out simulation based comparison of the (SPT's) shortest path tree, (MST's) minimum steiner trees and minimum number of transmission trees in wireless mesh networks by using the performance metrics like as an end to end delay, average jitter, throughput and packet delivery ratio, average unicast packet delivery ratio, etc. We have also evaluated multicast performance in the small and large wireless mesh networks. In case of multicast performance in the small networks we have found that when the traffic load is moderate or high the SPTs outperform the MSTs and MNTs in all cases. The SPTs have lowest end to end delay and average jitter in almost all cases. In case of multicast performance in the large network we have seen that the MSTs provide minimum total edge cost and minimum number of transmissions. We have also found that the one drawback of SPTs, when the group size is large and rate of multicast sending is high SPTs causes more packet losses to other flows as MCTs.

SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK

PubMed Central

Osinski, Adam; Tomchick, Diana R; Brautigam, Chad A

2017-01-01

The Hippo pathway controls tissue growth and homeostasis through a central MST-LATS kinase cascade. The scaffold protein SAV1 promotes the activation of this kinase cascade, but the molecular mechanisms remain unknown. Here, we discover SAV1-mediated inhibition of the PP2A complex STRIPAKSLMAP as a key mechanism of MST1/2 activation. SLMAP binding to autophosphorylated MST2 linker recruits STRIPAK and promotes PP2A-mediated dephosphorylation of MST2 at the activation loop. Our structural and biochemical studies reveal that SAV1 and MST2 heterodimerize through their SARAH domains. Two SAV1–MST2 heterodimers further dimerize through SAV1 WW domains to form a heterotetramer, in which MST2 undergoes trans-autophosphorylation. SAV1 directly binds to STRIPAK and inhibits its phosphatase activity, protecting MST2 activation-loop phosphorylation. Genetic ablation of SLMAP in human cells leads to spontaneous activation of the Hippo pathway and alleviates the need for SAV1 in Hippo signaling. Thus, SAV1 promotes Hippo activation through counteracting the STRIPAKSLMAP PP2A phosphatase complex. PMID:29063833

SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK

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

Bae, Sung Jun; Ni, Lisheng; Osinski, Adam

The Hippo pathway controls tissue growth and homeostasis through a central MST-LATS kinase cascade. The scaffold protein SAV1 promotes the activation of this kinase cascade, but the molecular mechanisms remain unknown. Here, we discover SAV1-mediated inhibition of the PP2A complex STRIPAKSLMAP as a key mechanism of MST1/2 activation. SLMAP binding to autophosphorylated MST2 linker recruits STRIPAK and promotes PP2A-mediated dephosphorylation of MST2 at the activation loop. Our structural and biochemical studies reveal that SAV1 and MST2 heterodimerize through their SARAH domains. Two SAV1–MST2 heterodimers further dimerize through SAV1 WW domains to form a heterotetramer, in which MST2 undergoes trans-autophosphorylation. SAV1more » directly binds to STRIPAK and inhibits its phosphatase activity, protecting MST2 activation-loop phosphorylation. Genetic ablation of SLMAP in human cells leads to spontaneous activation of the Hippo pathway and alleviates the need for SAV1 in Hippo signaling. Thus, SAV1 promotes Hippo activation through counteracting the STRIPAKSLMAP PP2A phosphatase complex.« less

Dendritic cell MST1 inhibits Th17 differentiation

PubMed Central

Li, Chunxiao; Bi, Yujing; Li, Yan; Yang, Hui; Yu, Qing; Wang, Jian; Wang, Yu; Su, Huilin; Jia, Anna; Hu, Ying; Han, Linian; Zhang, Jiangyuan; Li, Simin; Tao, Wufan; Liu, Guangwei

2017-01-01

Although the differentiation of CD4+T cells is widely studied, the mechanisms of antigen-presenting cell-dependent T-cell modulation are unclear. Here, we investigate the role of dendritic cell (DC)-dependent T-cell differentiation in autoimmune and antifungal inflammation and find that mammalian sterile 20-like kinase 1 (MST1) signalling from DCs negatively regulates IL-17 producing-CD4+T helper cell (Th17) differentiation. MST1 deficiency in DCs increases IL-17 production by CD4+T cells, whereas ectopic MST1 expression in DCs inhibits it. Notably, MST1-mediated DC-dependent Th17 differentiation regulates experimental autoimmune encephalomyelitis and antifungal immunity. Mechanistically, MST1-deficient DCs promote IL-6 secretion and regulate the activation of IL-6 receptor α/β and STAT3 in CD4+T cells in the course of inducing Th17 differentiation. Activation of the p38 MAPK signal is responsible for IL-6 production in MST1-deficient DCs. Thus, our results define the DC MST1–p38MAPK signalling pathway in directing Th17 differentiation. PMID:28145433

Mst1 shuts off cytosolic antiviral defense through IRF3 phosphorylation

PubMed Central

Meng, Fansen; Zhou, Ruyuan; Wu, Shiying; Zhang, Qian; Jin, Qiuheng; Zhou, Yao; Plouffe, Steven W.; Liu, Shengduo; Song, Hai; Xia, Zongping; Zhao, Bin; Ye, Sheng; Feng, Xin-Hua; Guan, Kun-Liang; Zou, Jian

2016-01-01

Cytosolic RNA/DNA sensing elicits primary defense against viral pathogens. Interferon regulatory factor 3 (IRF3), a key signal mediator/transcriptional factor of the antiviral-sensing pathway, is indispensible for interferon production and antiviral defense. However, how the status of IRF3 activation is controlled remains elusive. Through a functional screen of the human kinome, we found that mammalian sterile 20-like kinase 1 (Mst1), but not Mst2, profoundly inhibited cytosolic nucleic acid sensing. Mst1 associated with IRF3 and directly phosphorylated IRF3 at Thr75 and Thr253. This Mst1-mediated phosphorylation abolished activated IRF3 homodimerization, its occupancy on chromatin, and subsequent IRF3-mediated transcriptional responses. In addition, Mst1 also impeded virus-induced activation of TANK-binding kinase 1 (TBK1), further attenuating IRF3 activation. As a result, Mst1 depletion or ablation enabled an enhanced antiviral response and defense in cells and mice. Therefore, the identification of Mst1 as a novel physiological negative regulator of IRF3 activation provides mechanistic insights into innate antiviral defense and potential antiviral prevention strategies. PMID:27125670

Synthesis and Reaction Chemistry of Nanosize Monosodium Titanate

PubMed Central

Elvington, Mark C.; Taylor-Pashow, Kathryn M. L.; Tosten, Michael H.; Hobbs, David T.

2016-01-01

This paper describes the synthesis and peroxide-modification of nanosize monosodium titanate (nMST), along with an ion-exchange reaction to load the material with Au(III) ions. The synthesis method was derived from a sol-gel process used to produce micron-sized monosodium titanate (MST), with several key modifications, including altering reagent concentrations, omitting a particle seed step, and introducing a non-ionic surfactant to facilitate control of particle formation and growth. The resultant nMST material exhibits spherical-shaped particle morphology with a monodisperse distribution of particle diameters in the range from 100 to 150 nm. The nMST material was found to have a Brunauer-Emmett-Teller (BET) surface area of 285 m2g-1, which is more than an order of magnitude higher than the micron-sized MST. The isoelectric point of the nMST measured 3.34 pH units, which is a pH unit lower than that measured for the micron-size MST. The nMST material was found to serve as an effective ion exchanger under weakly acidic conditions for the preparation of an Au(III)-exchange nanotitanate. In addition, the formation of the corresponding peroxotitanate was demonstrated by reaction of the nMST with hydrogen peroxide. PMID:26967828

MST1, a key player, in enhancing fast skeletal muscle atrophy

PubMed Central

2013-01-01

Background Skeletal muscle undergoes rapid atrophy upon denervation and the underlying mechanisms are complicated. FOXO3a has been implicated as a major mediator of muscle atrophy, but how its subcellular location and activity is controlled during the pathogenesis of muscle atrophy remains largely unknown. MST1 (Mammalian Sterile 20-like kinase 1) is identified as a central component of the Hippo signaling pathway. MST1 has been shown to mediate phosphorylation of FOXO3a at Ser207. Whether this MST1-FOXO signaling cascade exerts any functional consequence on cellular homeostasis remains to be investigated. Result We identified that MST1 kinase was expressed widely in skeletal muscles and was dramatically up-regulated in fast- but not slow-dominant skeletal muscles immediately following denervation. The results of our histological and biochemical studies demonstrated that deletion of MST1 significantly attenuated denervation-induced skeletal muscle wasting and decreased expression of Atrogin-1 and LC3 genes in fast-dominant skeletal muscles from three- to five-month-old adult mice. Further studies indicated that MST1, but not MST2, remarkably increased FOXO3a phosphorylation level at Ser207 and promoted its nuclear translocation in atrophic fast-dominant muscles. Conclusions We have established that MST1 kinase plays an important role in regulating denervation-induced skeletal muscle atrophy. During the early stage of muscle atrophy, the up-regulated MST1 kinase promoted progression of neurogenic atrophy in fast-dominant skeletal muscles through activation of FOXO3a transcription factors. PMID:23374633

Efficacy of multisystemic therapy in youths aged 10-17 with severe antisocial behaviour and emotional disorders: systematic review.

PubMed

Tan, Jia Xuan; Fajardo, Maria Lourdes Restrepo

2017-11-01

Antisocial behaviour and conduct disorders are the most common behavioural and mental health problems in children and young people globally. An efficacious intervention is needed to manage these antisocial behaviours that have costly consequences. Multisystemic Therapy (MST), an intensive home-based intervention for youths with psychosocial and behavioural problems, is recommended under National Institute for Health and Clinical Excellence guidelines for conduct disorder. However, reviews on the efficacy of MST are mixed. To review randomised controlled trials (RCTs) reporting efficacy of MST among youths presenting with antisocial behaviour and emotional disorder respectively. A systematic map term to subject heading search was conducted in PsycINFO, Embase, and Ovid Medline databases for articles up to November 2015. RCTs comparing MST vs.treatment as usual (TAU) in youths presenting with antisocial behaviour and emotional disorder were included. 12 RCTs ( n  = 1425) reported efficacy of MST vs. TAU in youths presenting with antisocial behaviour and emotional disorder. Clinically significant treatment effects of MST showed a reduction of antisocial behaviour which includes delinquency. MST, vs. psychiatric hospitalisation, was associated with a reduction of suicidal attempts in youths presenting with psychiatric emergencies. 4 studies showed that MST was less costly than TAU in the short term, with further analysis required for long-term cost-effectiveness. MST is an efficacious intervention for severe antisocial behaviours in reduction of delinquency and should be included in clinical practices. MST was shown to have a positive effect on emotional disorder but further research is needed to evaluate the efficacy of MST with emotional disorder. Further analysis is required to assess the services utilized for long-term cost effectiveness.

Pervanadate induces Mammalian Ste20 Kinase 3 (MST3) tyrosine phosphorylation but not activation.

PubMed

Kan, Wei-Chih; Lu, Te-Ling; Ling, Pin; Lee, Te-Hsiu; Cho, Chien-Yu; Huang, Chi-Ying F; Jeng, Wen-Yih; Weng, Yui-Ping; Chiang, Chun-Yen; Wu, Jin Bin; Lu, Te-Jung

2016-07-01

The yeast Ste20 (sterile) protein kinase, which is a serine/threonine kinase, responds to the stimulation of the G proteincoupled receptor (GPCR) pheromone receptor. Ste20 protein kinase serves as the critical component that links signaling from the GPCR/G proteins to the mitogen-activated protein kinase (MAPK) cascade in yeast. The yeast Ste20p functions as a MAP kinase kinase kinase kinase (MAP4K) in the pheromone response. Ste20-like kinases are structurally conserved from yeast to mammals. The mechanism by which MAP4K links GPCR to the MAPK pathway is less clearly defined in vertebrates. In addition to MAP4K, the tyrosine kinase cascade bridges G proteins and the MAPK pathway in vertebrate cells. Mammalian Ste20 Kinase 3 (MST3) has been categorized into the Ste20 family and has been reported to function in the regulation of cell polarity and migration. However, whether MST3 tyrosine phosphorylation regulates diverse signaling pathways is unknown. In this study, the tyrosine phosphatase inhibitor pervanadate was found to induce MST3 tyrosine phosphorylation in intact cells, and the activity of tyrosine-phosphorylated MST3 was measured. This tyrosine-directed phosphorylation was independent of MST3 activity. Parameters including protein conformation, Triton concentration and ionic concentration influenced the sensitivity of MST3 activity. Taken together, our data suggests that the serine/threonine kinase MST3 undergoes tyrosinedirected phosphorylation. The tyrosine-phosphorylated MST3 may create a docking site for the structurally conserved SH2/SH3 (Src Homology 2 and 3) domains within the Src oncoprotein. The unusual tyrosinephosphorylated MST3 may recruit MST3 to various signaling components. Copyright © 2016. Published by Elsevier Inc.

The Protective Effect of Poloxamer-188 on Platelet Functions.

PubMed

Guler, Nil; Abro, Schuharazad; Emanuele, Marty; Iqbal, Omer; Hoppensteadt, Debra; Fareed, Jawed

2017-11-01

Poloxamer-188 (MST-188) is effective in the repair/recovery of damaged cell membranes. MST-188 is a promising agent for protecting blood cell viability. The aim of the study is to test the hypothesis that MST-188 can extend the duration of platelet function. Blood samples were collected from 20 healthy volunteers. MST-188 (10 or 2 mg/mL) containing platelet-rich plasma (PRP) was prepared with 2 procedures. First, PRP prepared from MST-188 added whole blood (WB); second, MST-188 was added to PRP. These were referred to MST-188-WB preparation (WBP) and MST-188-PRP preparation (PRPP), respectively. For control, saline was used in the same manner. Agonist-induced aggregation (AIA) studies were performed at 30, 180, and 300 minutes using Platelet Aggregation Profiler (PAP-8) aggregometer (Bio/Data Corporation, Horsham, Pennsylvania) and Adenosine diphosphate (ADP), arachidonic acid, collagen, and epinephrine as agonists at final concentration of 20 µM, 500 µg/mL, 0.19 mg/mL, and 100 µM, respectively. There was a protective effect of MST-188 on ADP and collagen AIA. At 300 minutes, ADP AIA was found to be 50.2% higher than saline control in 2-mg WBP, 43% at 10-mg PRPP, and 10.4% at 2-mg PRPP. Protective effect of on collagen AIA was 65.9% in 2-mg WBP, 42.74% at 10-mg PRPP, and 11.42% at 2-mg PRPP. In comparison between 30 and 300 minutes, MST-188 showed significant protection in terms of ADP and collagen receptors and for both types of preparations (WBP and PRPP). The protective effects of MST-188 on ADP- and collagen-induced platelet aggregation may contribute to the preservation of platelet functionality upon storage in blood banks.

MST4 kinase phosphorylates ACAP4 protein to orchestrate apical membrane remodeling during gastric acid secretion.

PubMed

Yuan, Xiao; Yao, Phil Y; Jiang, Jiying; Zhang, Yin; Su, Zeqi; Yao, Wendy; Wang, Xueying; Gui, Ping; Mullen, McKay; Henry, Calmour; Ward, Tarsha; Wang, Wenwen; Brako, Larry; Tian, Ruijun; Zhao, Xuannv; Wang, Fengsong; Cao, Xinwang; Wang, Dongmei; Liu, Xing; Ding, Xia; Yao, Xuebiao

2017-09-29

Digestion in the stomach depends on acidification of the lumen. Histamine-elicited acid secretion is triggered by activation of the PKA cascade, which ultimately results in the insertion of gastric H,K-ATPases into the apical plasma membranes of parietal cells. Our recent study revealed the functional role of PKA-MST4-ezrin signaling axis in histamine-elicited acid secretion. However, it remains uncharacterized how the PKA-MST4-ezrin signaling axis operates the insertion of H,K-ATPases into the apical plasma membranes of gastric parietal cells. Here we show that MST4 phosphorylates ACAP4, an ARF6 GTPase-activating protein, at Thr 545 Histamine stimulation activates MST4 and promotes MST4 interaction with ACAP4. ACAP4 physically interacts with MST4 and is a cognate substrate of MST4 during parietal cell activation. The phosphorylation site of ACAP4 by MST4 was mapped to Thr 545 by mass spectrometric analyses. Importantly, phosphorylation of Thr 545 is essential for acid secretion in parietal cells because either suppression of ACAP4 or overexpression of non-phosphorylatable ACAP4 prevents the apical membrane reorganization and proton pump translocation elicited by histamine stimulation. In addition, persistent overexpression of MST4 phosphorylation-deficient ACAP4 results in inhibition of gastric acid secretion and blockage of tubulovesicle fusion to the apical membranes. Significantly, phosphorylation of Thr 545 enables ACAP4 to interact with ezrin. Given the location of Thr 545 between the GTPase-activating protein domain and the first ankyrin repeat, we reason that MST4 phosphorylation elicits a conformational change that enables ezrin-ACAP4 interaction. Taken together, these results define a novel molecular mechanism linking the PKA-MST4-ACAP4 signaling cascade to polarized acid secretion in gastric parietal cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Bayes Forest: a data-intensive generator of morphological tree clones

PubMed Central

Järvenpää, Marko; Åkerblom, Markku; Raumonen, Pasi; Kaasalainen, Mikko

2017-01-01

Abstract Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree “clones” based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research. PMID:29020742

MST with Conduct Disordered Youth in Sweden: Costs and Benefits after 2 Years

ERIC Educational Resources Information Center

Olsson, Tina M.

2010-01-01

Objectives: The purpose of this study was to investigate the costs and benefits associated with multisystemic therapy (MST) for conduct disordered youth, 2 years following intake. Methods: The study employed a secondary analysis of 156 youth enrolled in a randomized trial assessing the psychosocial and behavioral outcomes of MST. Results: MST cost…

Transportability of Multisystemic Therapy to Community Settings: Can a Program Sustain Outcomes without MST Services Oversight?

ERIC Educational Resources Information Center

Smith-Boydston, Julianne M.; Holtzman, Rochelle J.; Roberts, Michael C.

2014-01-01

Background: Multisystemic therapy (MST) has been shown to be effective in treating delinquent behavior in youth. However, some community agencies with MST programs are unable to afford the ongoing costs of licensure and quality assurance oversight provided by MST services. Objective: The present study utilized retrospective archival analyses of…

Detection and Counting of Orchard Trees from Vhr Images Using a Geometrical-Optical Model and Marked Template Matching

NASA Astrophysics Data System (ADS)

Maillard, Philippe; Gomes, Marília F.

2016-06-01

This article presents an original algorithm created to detect and count trees in orchards using very high resolution images. The algorithm is based on an adaptation of the "template matching" image processing approach, in which the template is based on a "geometricaloptical" model created from a series of parameters, such as illumination angles, maximum and ambient radiance, and tree size specifications. The algorithm is tested on four images from different regions of the world and different crop types. These images all have < 1 meter spatial resolution and were downloaded from the GoogleEarth application. Results show that the algorithm is very efficient at detecting and counting trees as long as their spectral and spatial characteristics are relatively constant. For walnut, mango and orange trees, the overall accuracy was clearly above 90%. However, the overall success rate for apple trees fell under 75%. It appears that the openness of the apple tree crown is most probably responsible for this poorer result. The algorithm is fully explained with a step-by-step description. At this stage, the algorithm still requires quite a bit of user interaction. The automatic determination of most of the required parameters is under development.

Hierarchical cluster-tendency analysis of the group structure in the foreign exchange market

NASA Astrophysics Data System (ADS)

Wu, Xin-Ye; Zheng, Zhi-Gang

2013-08-01

A hierarchical cluster-tendency (HCT) method in analyzing the group structure of networks of the global foreign exchange (FX) market is proposed by combining the advantages of both the minimal spanning tree (MST) and the hierarchical tree (HT). Fifty currencies of the top 50 World GDP in 2010 according to World Bank's database are chosen as the underlying system. By using the HCT method, all nodes in the FX market network can be "colored" and distinguished. We reveal that the FX networks can be divided into two groups, i.e., the Asia-Pacific group and the Pan-European group. The results given by the hierarchical cluster-tendency method agree well with the formerly observed geographical aggregation behavior in the FX market. Moreover, an oil-resource aggregation phenomenon is discovered by using our method. We find that gold could be a better numeraire for the weekly-frequency FX data.

A tool for filtering information in complex systems

NASA Astrophysics Data System (ADS)

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-07-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. This paper was submitted directly (Track II) to the PNAS office.Abbreviations: MST, minimum spanning tree; PMFG, Planar Maximally Filtered Graph; r-clique, clique of r elements.

Global Interactions Analysis of Epileptic ECoG Data

NASA Astrophysics Data System (ADS)

Ortega, Guillermo J.; Sola, Rafael G.; Pastor, Jesús

2007-05-01

Localization of the epileptogenic zone is an important issue in epileptology, even though there is not a unique definition of the epileptic focus. The objective of the present study is to test ultrametric analysis to uncover cortical interactions in human epileptic data. Correlation analysis has been carried out over intraoperative Electro-Corticography (ECoG) data in 2 patients suffering from temporal lobe epilepsy (TLE). Recordings were obtained using a grid of 20 electrodes (5×4) covering the lateral temporal lobe and a strip of either 4 or 8 electrodes at the mesial temporal lobe. Ultrametric analysis was performed in the averaged final correlation matrices. By using the matrix of linear correlation coefficients and the appropriate metric distance between pairs of electrodes time series, we were able to construct Minimum Spanning Trees (MST). The topological connectivity displayed by these trees gives useful and valuable information regarding physiological and pathological information in the temporal lobe of epileptic patients.

A Modified Decision Tree Algorithm Based on Genetic Algorithm for Mobile User Classification Problem

PubMed Central

Liu, Dong-sheng; Fan, Shu-jiang

2014-01-01

In order to offer mobile customers better service, we should classify the mobile user firstly. Aimed at the limitations of previous classification methods, this paper puts forward a modified decision tree algorithm for mobile user classification, which introduced genetic algorithm to optimize the results of the decision tree algorithm. We also take the context information as a classification attributes for the mobile user and we classify the context into public context and private context classes. Then we analyze the processes and operators of the algorithm. At last, we make an experiment on the mobile user with the algorithm, we can classify the mobile user into Basic service user, E-service user, Plus service user, and Total service user classes and we can also get some rules about the mobile user. Compared to C4.5 decision tree algorithm and SVM algorithm, the algorithm we proposed in this paper has higher accuracy and more simplicity. PMID:24688389

Using Microbial Source Tracking to Enhance Environmental Stewardship of Agriculture

NASA Astrophysics Data System (ADS)

Martin, Sherry; Rose, Joan; Flood, Matthew; Aw, Tiong; Hyndman, David

2016-04-01

Large scale agriculture relies on the application of chemical fertilizers and animal manure. It is well known that nutrients in excess of a plant's uptake and soil retention capacity can travel to nearby waterways via surface run-off and groundwater pathways, indirectly fertilizing these aquatic ecosystems. It has not yet been possible to distinguish water quality impacts of fertilizer from those derived from human and animal waste sources. However, new microbial source tracking (MST) tools allow specific identification of fecal pollution. Our objective was to examine pollution risks at the regional scale using MST, mapping and classification and regression tree analysis. We present results Bovine M2 genetic marker data from three flow regimes (baseflow, snow melt, and post-planting rain). Key landscape characteristics were related to the presence of the bovine markers and appear to be related to fate and transport. Impacts at this regional watershed scale will be discussed. Our research aims to identify the impacts of agricultural management practices on water quality by linking nutrient concentrations with fecal pollution sources. We hope that our research will provide guidance that will help improve water quality through agricultural best management practices to reduce pathogen contamination.

Differential Effects of High Dose Magnetic Seizure Therapy (MST) and Electroconvulsive Shock (ECS) on Cognitive Function

PubMed Central

Spellman, Timothy; McClintock, Shawn M.; Terrace, Herbert; Luber, Bruce; Husain, Mustafa M.; Lisanby, Sarah H.

2008-01-01

Background Magnetic seizure therapy (MST) is under investigation as an alternative form of convulsive therapy that induces more focal seizures and spares cortical regions involved in memory. Using a newly expanded version of the Columbia University Primate Cognitive Profile, we compared the cognitive effects of high-dose MST delivered at 100 Hz (6X seizure threshold) with electroconvulsive shock (ECS) delivered at 2.5X seizure threshold. Methods Daily high-dose MST, ECS, and Sham (anesthesia-only) were administered for 4 weeks each in a within-subject cross-over design. Rhesus macaques (n = 3) were trained on five cognitive tasks assessing automatic memory, anterograde learning and memory, combined anterograde and retrograde simultaneous chaining, and spatial and serial working memory. Acutely following each intervention, monkeys were tested on the cognitive battery twice daily, separated by a 3-hour retention interval. Results Subjects were slower to complete criterion tasks (p’s<0.0001) following ECS, compared to sham and high-dose MST. Moreover, time to task-completion following high-dose MST did not differ from sham. Out of 6 measures of accuracy, treatment effects were found in 4; in all of these, ECS, but not MST, fared worse than Sham. On all accuracy and time to completion measurements, subjects performed as well as following high-dose MST as did subjects from a previous study on moderate-dose MST. Conclusion These findings provide evidence that high-dose MST results in benign acute cognitive side-effect profile relative to ECS, and are in line with our previous studies. PMID:18262171

Military Sexual Trauma Among US Servicewomen During Deployment: A Qualitative Study

PubMed Central

Grindlay, Kate; Holt, Kelsey; Manski, Ruth; Grossman, Daniel

2014-01-01

Objectives. We explored qualitatively US servicewomen’s experiences with and perceptions of military sexual trauma (MST), reporting, and related services. Methods. From May 2011 to January 2012, we conducted 22 telephone interviews with US servicewomen deployed overseas between 2002 and 2011. We analyzed data thematically with modified grounded theory methods. Results. Factors identified as contributing to MST included deployment dynamics, military culture, and lack of consequences for perpetrators. Participants attributed low MST reporting to negative reactions and blame from peers and supervisors, concerns about confidentiality, and stigma. Unit cohesion was cited as both a facilitator and a barrier to reporting. Availability and awareness of MST services during deployment varied. Barriers to care seeking were similar to reporting barriers and included confidentiality concerns and stigma. We identified several avenues to address MST, including strengthening consequences for perpetrators. Conclusions. We identified barriers to MST reporting and services. Better understanding of these issues will allow policymakers to improve MST prevention and services. PMID:24328617

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

Multi-state trajectory approach to non-adiabatic dynamics: General formalism and the active state trajectory approximation

NASA Astrophysics Data System (ADS)

Tao, Guohua

2017-07-01

A general theoretical framework is derived for the recently developed multi-state trajectory (MST) approach from the time dependent Schrödinger equation, resulting in equations of motion for coupled nuclear-electronic dynamics equivalent to Hamilton dynamics or Heisenberg equation based on a new multistate Meyer-Miller (MM) model. The derived MST formalism incorporates both diabatic and adiabatic representations as limiting cases and reduces to Ehrenfest or Born-Oppenheimer dynamics in the mean-field or the single-state limits, respectively. In the general multistate formalism, nuclear dynamics is represented in terms of a set of individual state-specific trajectories, while in the active state trajectory (AST) approximation, only one single nuclear trajectory on the active state is propagated with its augmented images running on all other states. The AST approximation combines the advantages of consistent nuclear-coupled electronic dynamics in the MM model and the single nuclear trajectory in the trajectory surface hopping (TSH) treatment and therefore may provide a potential alternative to both Ehrenfest and TSH methods. The resulting algorithm features in a consistent description of coupled electronic-nuclear dynamics and excellent numerical stability. The implementation of the MST approach to several benchmark systems involving multiple nonadiabatic transitions and conical intersection shows reasonably good agreement with exact quantum calculations, and the results in both representations are similar in accuracy. The AST treatment also reproduces the exact results reasonably, sometimes even quantitatively well, with a better performance in the adiabatic representation.

Concurrent computation of attribute filters on shared memory parallel machines.

PubMed

Wilkinson, Michael H F; Gao, Hui; Hesselink, Wim H; Jonker, Jan-Eppo; Meijster, Arnold

2008-10-01

Morphological attribute filters have not previously been parallelized, mainly because they are both global and non-separable. We propose a parallel algorithm that achieves efficient parallelism for a large class of attribute filters, including attribute openings, closings, thinnings and thickenings, based on Salembier's Max-Trees and Min-trees. The image or volume is first partitioned in multiple slices. We then compute the Max-trees of each slice using any sequential Max-Tree algorithm. Subsequently, the Max-trees of the slices can be merged to obtain the Max-tree of the image. A C-implementation yielded good speed-ups on both a 16-processor MIPS 14000 parallel machine, and a dual-core Opteron-based machine. It is shown that the speed-up of the parallel algorithm is a direct measure of the gain with respect to the sequential algorithm used. Furthermore, the concurrent algorithm shows a speed gain of up to 72 percent on a single-core processor, due to reduced cache thrashing.

Phylogenetic search through partial tree mixing

PubMed Central

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

Responsiveness and Minimally Important Difference of the 6-Minute Stepper Test in Patients with Chronic Obstructive Pulmonary Disease.

PubMed

Pichon, Romain; Couturaud, Francis; Mialon, Philippe; Le Ber-Moy, Catherine; Péran, Loïc; Lochon, Chantal; Nowak, Emmanuel; Beaumont, Marc

2016-01-01

The validity and reproducibility of the 6-minute stepper test (6MST) have already been demonstrated in patients with chronic obstructive pulmonary disease (COPD). The aim of this study was to evaluate the responsiveness of the 6MST to pulmonary rehabilitation (PR) in patients with COPD, to determine a minimal important difference (MID) for the 6MST, and to compare the 6MST and the 6-minute walk test (6MWT). Sixty-two patients with COPD were included in a prospective experimental study. Participants underwent a 3-week inpatient PR program. The primary outcome was the change in the number of steps during the 6MST measured before and after PR. The secondary outcome included the change in the 6-minute walking distance (6MWD) pulse oximetry, heart rate, dyspnea, and leg discomfort during the tests measured before and after PR. MID was determined by anchor-based and distribution approaches. After PR, we observed a significant increase in the number of steps during the 6MST (22.5 steps; 95% CI 13.8-31.3; p < 0.0001) and in the 6MWD (26.6 m; 95% CI 17.6-35.5; p < 0.0001). The 6MST and 6MWT were improved by 10.1 and 6.5%, respectively. The number of steps during the 6MST was significantly correlated with the 6MWD before (r = 0.72; p < 0.0001) and after PR (r = 0.66; p < 0.0001). MID was estimated to be around 20 steps. The 6MST appears to be as responsive as the 6MWT in assessing functional improvement during PR in patients with COPD. The 6MST is a low-cost assessment and requires limited space. © 2016 S. Karger AG, Basel.

Characterization of in vivo metabolites in rat urine following an oral dose of masitinib by liquid chromatography tandem mass spectrometry.

PubMed

Kadi, Adnan A; Amer, Sawsan M; Darwish, Hany W; Attwa, Mohamed W

2018-05-15

Masitinib (MST) is an orally administered drug that targets mast cells and macrophages, important cells for immunity, by inhibiting a limited number of tyrosine kinases. It is currently registered in Europe and USA for the treatment of mast cell tumors in dogs. AB Science announced that the European Medicines Agency has accepted a conditional marketing authorization application for MST to treat amyotrophic lateral sclerosis. In our work, we focused on studying in vivo metabolism of MST in Sprague-Dawley rats. Single oral dose of MST (33 mg kg -1 ) was given to Sprague-Dawley rats (kept in metabolic cages) using oral gavage. Urine was collected and filtered at 0, 6, 12, 18, 24, 48, 72 and 96 h from MST dosing. An equal amount of ACN was added to urine samples. Both organic and aqueous layers were injected into liquid chromatography-tandem mass spectrometry (LC-MS/MS) to detect in vivo phase I and phase II MST metabolites. The current work reports the identification and characterization of twenty in vivo phase I and four in vivo phase II metabolites of MST by LC-MS/MS. Phase I metabolic pathways were reduction, demethylation, hydroxylation, oxidative deamination, oxidation and N-oxide formation. Phase II metabolic pathways were the direct conjugation of MST, N-demethyl metabolites and oxidative metabolites with glucuronic acid. Part of MST dose was excreted unchanged in urine. The literature review showed no previous articles have been made on in vivo metabolism of MST or detailed structural identification of the formed in vivo phase I and phase II metabolites.

Military sexual trauma as a determinant in the development of mental and physical illness in male and female veterans.

PubMed

O'Brien, Betsy S; Sher, Leo

2013-01-01

Military Sexual Trauma (MST) is defined as sexual harassment and or sexual assault experienced by a military service member. It is much more widespread and common than reported. It is associated with pre-combat traumatic experiences and pathologic sequelae including mental and medical illness. An electronic search of the major behavioral science databases was conducted to retrieve studies detailing the social, epidemiological and clinical characteristics of MST and its relationship to psychiatric and medical illness. Studies indicate that military sexual trauma is related to an increase in psychiatric pathology, including posttraumatic stress disorder (PTSD), substance abuse and dependence, depression, anxiety, eating disorders and suicidal behavior. MST is also related to an increase in medical illness, primarily pain-related symptoms involving multiple organ systems, including gastrointestinal, neurological, genitourinary and musculoskeletal. MST is associated with an increased prevalence of mental and physical illness. Although there are some gender differences in the reported rates of MST and there may be some variables, such as prior traumatic experiences, that may make an individual more vulnerable to the psychiatric and medical sequela of MST, it is clear that MST is a major healthcare issue that affects both sexes and warrants further attention and an increase in clinical resources devoted to it. Some preventive measures for decreasing the prevalence of MST may include increasing education and legal prosecution of perpetrators in the military, and increasing access to mental health services for individuals who have suffered from MST.

An independent randomized clinical trial of multisystemic therapy with non-court-referred adolescents with serious conduct problems.

PubMed

Weiss, Bahr; Han, Susan; Harris, Vicki; Catron, Thomas; Ngo, Victoria K; Caron, Annalise; Gallop, Robert; Guth, Carol

2013-12-01

Adolescent conduct problems exact serious social as well as personal costs, and effective treatments are essential. One of the most widely disseminated and effective programs for the treatment of serious conduct problems in adolescents is Multisystemic Therapy (MST). However, most evaluations of MST have involved the developers of MST. The purpose of the present study was to conduct an independent evaluation of MST, with non-court-referred adolescents with conduct problems. Participants were 164 adolescents ages 11-18 years who were recruited from self-contained behavior intervention classrooms in public schools. Adolescents and their families were randomly assigned to receive MST or services as usual. Outcome measures assessed conduct problems, school functioning, and court records of criminal behavior. Participants were followed for 18 months after baseline using parent, adolescent, and teacher reports; arrest data were collected for 2.5 years postbaseline. Two of 4 primary outcome measures focused on externalizing problems showed significant treatment effects favoring MST. Several secondary and intervention targets pertaining to family functioning and parent psychopathology showed positive effects of MST, and no negative effects were identified. Results provide some further support for the effectiveness of MST, although smaller effect sizes than previous studies also suggest the complexity of successful dissemination, particularly to non-court-referred populations.

Selection and application of microbial source tracking tools for water-quality investigations

USGS Publications Warehouse

Stoeckel, Donald M.

2005-01-01

Microbial source tracking (MST) is a complex process that includes many decision-making steps. Once a contamination problem has been defined, the potential user of MST tools must thoroughly consider study objectives before deciding upon a source identifier, a detection method, and an analytical approach to apply to the problem. Regardless of which MST protocol is chosen, underlying assumptions can affect the results and interpretation. It is crucial to incorporate tests of those assumptions in the study quality-control plan to help validate results and facilitate interpretation. Detailed descriptions of MST objectives, protocols, and assumptions are provided in this report to assist in selection and application of MST tools for water-quality investigations. Several case studies illustrate real-world applications of MST protocols over a range of settings, spatial scales, and types of contamination. Technical details of many available source identifiers and detection methods are included as appendixes. By use of this information, researchers should be able to formulate realistic expectations for the information that MST tools can provide and, where possible, successfully execute investigations to characterize sources of fecal contamination to resource waters.

Fuzzy α-minimum spanning tree problem: definition and solutions

NASA Astrophysics Data System (ADS)

Zhou, Jian; Chen, Lu; Wang, Ke; Yang, Fan

2016-04-01

In this paper, the minimum spanning tree problem is investigated on the graph with fuzzy edge weights. The notion of fuzzy ? -minimum spanning tree is presented based on the credibility measure, and then the solutions of the fuzzy ? -minimum spanning tree problem are discussed under different assumptions. First, we respectively, assume that all the edge weights are triangular fuzzy numbers and trapezoidal fuzzy numbers and prove that the fuzzy ? -minimum spanning tree problem can be transformed to a classical problem on a crisp graph in these two cases, which can be solved by classical algorithms such as the Kruskal algorithm and the Prim algorithm in polynomial time. Subsequently, as for the case that the edge weights are general fuzzy numbers, a fuzzy simulation-based genetic algorithm using Prüfer number representation is designed for solving the fuzzy ? -minimum spanning tree problem. Some numerical examples are also provided for illustrating the effectiveness of the proposed solutions.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

PubMed

Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

2012-09-15

Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

A stochastic multiple imputation algorithm for missing covariate data in tree-structured survival analysis.

PubMed

Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati

2010-12-20

Missing covariate data present a challenge to tree-structured methodology due to the fact that a single tree model, as opposed to an estimated parameter value, may be desired for use in a clinical setting. To address this problem, we suggest a multiple imputation algorithm that adds draws of stochastic error to a tree-based single imputation method presented by Conversano and Siciliano (Technical Report, University of Naples, 2003). Unlike previously proposed techniques for accommodating missing covariate data in tree-structured analyses, our methodology allows the modeling of complex and nonlinear covariate structures while still resulting in a single tree model. We perform a simulation study to evaluate our stochastic multiple imputation algorithm when covariate data are missing at random and compare it to other currently used methods. Our algorithm is advantageous for identifying the true underlying covariate structure when complex data and larger percentages of missing covariate observations are present. It is competitive with other current methods with respect to prediction accuracy. To illustrate our algorithm, we create a tree-structured survival model for predicting time to treatment response in older, depressed adults. Copyright © 2010 John Wiley & Sons, Ltd.

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

Grabaskas, David; Bucknor, Matthew; Jerden, James

A mechanistic source term (MST) calculation attempts to realistically assess the transport and release of radionuclides from a reactor system to the environment during a specific accident sequence. The U.S. Nuclear Regulatory Commission (NRC) has repeatedly stated its expectation that advanced reactor vendors will utilize an MST during the U.S. reactor licensing process. As part of a project to examine possible impediments to sodium fast reactor (SFR) licensing in the U.S., an analysis was conducted regarding the current capabilities to perform an MST for a metal fuel SFR. The purpose of the project was to identify and prioritize any gapsmore » in current computational tools, and the associated database, for the accurate assessment of an MST. The results of the study demonstrate that an SFR MST is possible with current tools and data, but several gaps exist that may lead to possibly unacceptable levels of uncertainty, depending on the goals of the MST analysis.« less

Routing Algorithm based on Minimum Spanning Tree and Minimum Cost Flow for Hybrid Wireless-optical Broadband Access Network

NASA Astrophysics Data System (ADS)

Le, Zichun; Suo, Kaihua; Fu, Minglei; Jiang, Ling; Dong, Wen

2012-03-01

In order to minimize the average end to end delay for data transporting in hybrid wireless optical broadband access network, a novel routing algorithm named MSTMCF (minimum spanning tree and minimum cost flow) is devised. The routing problem is described as a minimum spanning tree and minimum cost flow model and corresponding algorithm procedures are given. To verify the effectiveness of MSTMCF algorithm, extensively simulations based on OWNS have been done under different types of traffic source.

Increased Health Care Utilization and Costs Among Veterans With a Positive Screen for Military Sexual Trauma.

PubMed

Brignone, Emily; Gundlapalli, Adi V; Blais, Rebecca K; Kimerling, Rachel; Barrett, Tyson S; Nelson, Richard E; Carter, Marjorie E; Samore, Matthew H; Fargo, Jamison D

2017-09-01

The effects of sexual trauma on long-term health care utilization and costs are not well understood due to infrequent documentation of sexual trauma history in health care systems. The Veteran's Health Administration provides a unique opportunity to address this constraint as sexual trauma is actively screened for as part of routine care. We used a retrospective cohort design to analyze Veteran's Health Administration mental health and medical service utilization and costs as a function of a positive screen for exposure to military sexual trauma (MST) among Veterans of recent conflicts in Iraq and Afghanistan. We computed adjusted 5-year estimates of overall utilization and costs, and utilization and costs determined not to be related to MST. The cohort included 426,223 men and 59,611 women. A positive MST screen was associated with 50% higher health care utilization and costs relative to a negative screen. Overall, a positive relative to negative MST screen was associated with a 5-year incremental difference of 34.6 encounters and $10,734 among women, and 33.5 encounters and $11,484 among men. After accounting for MST-related treatment, positive MST screen was associated with 11.9 encounters and $4803 among women, and 19.5 encounters and $8001 among men. Results demonstrate significant and consistent differences in health care utilization and costs between Veterans with a positive relative to negative MST screen. Even after accounting for MST-related care, a positive screen was associated with significantly higher utilization and costs. MST-related needs may be more readily recognized in women relative to men.

Inhibition of in vitro and in vivo brown fat differentiation program by myostatin.

PubMed

Braga, Melissa; Pervin, Shehla; Norris, Keith; Bhasin, Shalender; Singh, Rajan

2013-06-01

Obesity arises mainly due to the imbalance between energy storage and its expenditure. Metabolically active brown adipose tissue (BAT) has recently been detected in humans and has been proposed as a new target for anti-obesity therapy because of its unique capacity to regulate energy expenditure. Myostatin (Mst), a negative regulator of muscle mass, has been identified as a potential target to regulate overall body composition. Although the beneficial effects of Mst inhibition on muscle mass are well known, its role in the regulation of lipid metabolism, and energy expenditure is not very clear. We tested the effects of Mst inhibition on the gene regulatory networks that control BAT differentiation using both in vivo and in vitro model systems. PRDM16 and UCP1, two key regulators of brown fat differentiation were significantly up regulated in levator-ani (LA) and gastrocnemius (Gastroc) muscles as well as in epididymal (Epi) and subcutaneous (SC) fat pads isolated from Mst knock out (Mst KO) male mice compared with wild type (WT) mice. Using mouse embryonic fibroblast (MEFs) primary cultures obtained from Mst KO group compared to the WT group undergoing adipogenic differentiation, we also demonstrate a significant increase in select genes and proteins that improve lipid metabolism and energy expenditure. Treatment of Mst KO MEFs with recombinant Mst protein significantly inhibited the gene expression levels of UCP1, PRDM16, PGC1-α/β as well as BMP7. Future studies to extend these findings and explore the therapeutic potential of Mst inhibition on metabolic disorders are warranted. Copyright © 2012 The Obesity Society.

Economic evaluation of multisystemic therapy for young people at risk for continuing criminal activity in the UK.

PubMed

Cary, Maria; Butler, Stephen; Baruch, Geoffrey; Hickey, Nicole; Byford, Sarah

2013-01-01

To evaluate whether multisystemic therapy (MST) is more cost-effective than statutory interventions that are currently available for young offenders in England. A cost-offset evaluation of MST based on data from a randomised controlled trial conducted in North London, England, comparing MST with usual services provided by two youth offending teams (YOT). Service costs were compared to cost savings in terms of rates of criminal re-offending. 108 adolescents, aged 11-17 years, were randomly allocated to MST+YOT (n = 56) or YOT alone (n = 52). Reductions in offending were evident in both groups, but were higher in the MST+YOT group. At 18-month follow-up, the MST+YOT group cost less in terms of criminal activity (£9,425 versus £11,715, p = 0.456). The MST+YOT group were significantly cheaper in terms of YOT services than the YOT group (£3,402 versus £4,619, p = 0.006), but more expensive including the cost of MST, although not significantly so (£5,687 versus £4,619, p = 0.195). The net benefit per young person for the 18-month follow-up was estimated to be £1,222 (95% CI -£5,838 to £8,283). The results reported in this study support the finding that MST+YOT has scope for cost-savings when compared to YOT alone. However, the limitations of the study in terms of method of economic evaluation, outcome measures used and data quality support the need for further research.

Exact solutions for species tree inference from discordant gene trees.

PubMed

Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

2013-10-01

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions.

A grey incidence algorithm to detect high-Z material using cosmic ray muons

NASA Astrophysics Data System (ADS)

He, W.; Xiao, S.; Shuai, M.; Chen, Y.; Lan, M.; Wei, M.; An, Q.; Lai, X.

2017-10-01

Muon scattering tomography (MST) is a method for using cosmic muons to scan cargo containers and vehicles for special nuclear materials. However, the flux of cosmic ray muons is low, in the real life application, the detection has to be done a short timescale with small numbers of muons. In this paper, we present a novel approach to detection of special nuclear material by using cosmic ray muons. We use the degree of grey incidence to distinguish typical waste fuel material, uranium, from low-Z material, medium-Z material and other high-Z materials of tungsten and lead. The result shows that using this algorithm, it is possible to detect high-Z materials with an acceptable timescale.

Assailant Identity and Self-Reported Nondisclosure of Military Sexual Trauma in Partnered Women Veterans.

PubMed

Blais, Rebecca K; Brignone, Emily; Fargo, Jamison D; Galbreath, Nathan W; Gundlapalli, Adi V

2017-10-09

Department of Veterans Affairs estimates of military sexual trauma (MST) suggest 27% of female veterans have experienced MST. However, Department of Defense data (Department of Defense, 2014) show that a subgroup of active-duty women do not report sexual assaults to a military authority, suggesting barriers to disclosure exist among military samples. No study of female veterans has examined rates of nondisclosure among those with previous screens for MST; these data could inform screening efforts and establishment of safe havens for candid disclosures. Using an explanatory sequential mixed-methods survey, a history of MST, and postservice MST disclosures during screening and their associations with demographic, assault, and screening-setting characteristics were evaluated in 359 female veterans. Open-ended responses regarding barriers to disclosure were analyzed using editing analysis style. Eighty-one percent (n = 289) reported MST. Of these, 50% (n = 143) reported a prior screening and 25% (n = 35) reported they did not disclose their true MST status. Veterans who experienced MST by a unit-member assailant were significantly less likely to disclose (adjusted odds ratio = 4.75, 95% confidence interval = 1.20-18.30). Disclosure barriers included stigma, experiential avoidance, and discomfort with the screening setting. Creative interventions to reduce nondisclosure among female veterans, with specific attention to those assaulted by a unit member, are urgently needed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Structure and Kinetic Analysis of H2S Production by Human Mercaptopyruvate Sulfurtransferase*

PubMed Central

Yadav, Pramod Kumar; Yamada, Kazuhiro; Chiku, Taurai; Koutmos, Markos; Banerjee, Ruma

2013-01-01

Mercaptopyruvate sulfurtransferase (MST) is a source of endogenous H2S, a gaseous signaling molecule implicated in a wide range of physiological processes. The contribution of MST versus the other two H2S generators, cystathionine β-synthase and γ-cystathionase, has been difficult to evaluate because many studies on MST have been conducted at high pH and have used varied reaction conditions. In this study, we have expressed, purified, and crystallized human MST in the presence of the substrate 3-mercaptopyruvate (3-MP). The kinetics of H2S production by MST from 3-MP was studied at pH 7.4 in the presence of various physiological persulfide acceptors: cysteine, dihydrolipoic acid, glutathione, homocysteine, and thioredoxin, and in the presence of cyanide. The crystal structure of MST reveals a mixture of the product complex containing pyruvate and an active site cysteine persulfide (Cys248-SSH) and a nonproductive intermediate in which 3-MP is covalently linked via a disulfide bond to an active site cysteine. The crystal structure analysis allows us to propose a detailed mechanism for MST in which an Asp-His-Ser catalytic triad is positioned to activate the nucleophilic cysteine residue and participate in general acid-base chemistry, whereas our kinetic analysis indicates that thioredoxin is likely to be the major physiological persulfide acceptor for MST. PMID:23698001

Algorithm for protecting light-trees in survivable mesh wavelength-division-multiplexing networks

NASA Astrophysics Data System (ADS)

Luo, Hongbin; Li, Lemin; Yu, Hongfang

2006-12-01

Wavelength-division-multiplexing (WDM) technology is expected to facilitate bandwidth-intensive multicast applications such as high-definition television. A single fiber cut in a WDM mesh network, however, can disrupt the dissemination of information to several destinations on a light-tree based multicast session. Thus it is imperative to protect multicast sessions by reserving redundant resources. We propose a novel and efficient algorithm for protecting light-trees in survivable WDM mesh networks. The algorithm is called segment-based protection with sister node first (SSNF), whose basic idea is to protect a light-tree using a set of backup segments with a higher priority to protect the segments from a branch point to its children (sister nodes). The SSNF algorithm differs from the segment protection scheme proposed in the literature in how the segments are identified and protected. Our objective is to minimize the network resources used for protecting each primary light-tree such that the blocking probability can be minimized. To verify the effectiveness of the SSNF algorithm, we conduct extensive simulation experiments. The simulation results demonstrate that the SSNF algorithm outperforms existing algorithms for the same problem.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data.

PubMed

Barros, Rodrigo C; Winck, Ana T; Machado, Karina S; Basgalupp, Márcio P; de Carvalho, André C P L F; Ruiz, Duncan D; de Souza, Osmar Norberto

2012-11-21

This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

PubMed Central

2012-01-01

Background This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor. PMID:23171000

21. DETAIL OF AIR HANDLER 1 (MST AIRCONDITIONING SYSTEM) INTERIOR, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

21. DETAIL OF AIR HANDLER 1 (MST AIR-CONDITIONING SYSTEM) INTERIOR, SOUTHEAST CORNER, STATION 30, SLC-3W MST - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

AWIWPCA STATES HELPING STATES CLL ON MST

EPA Science Inventory

Several Microbial Source Tracking (MST) tools are now being applied in the development of TMDL plans and in the evaluation of best management practices. However, due to the relatively recent development of MST most environmental managers and scientists have little training and ...

Learning classification trees

NASA Technical Reports Server (NTRS)

Buntine, Wray

1991-01-01

Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

Shikonin regulates C-MYC and GLUT1 expression through the MST1-YAP1-TEAD1 axis

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

Vališ, Karel, E-mail: karel.valis@biomed.cas.cz; Faculty of Science, Charles University, Prague; Talacko, Pavel

The general mechanism underlying the tumor suppressor activity of the Hippo signaling pathway remains unclear. In this study, we explore the molecular mechanisms connecting the Hippo signaling pathway with glucose metabolism. We have found that two key regulators of glycolysis, C-MYC and GLUT1, are targets of the Hippo signaling pathway in human leukemia cells. Our results revealed that activation of MST1 by the natural compound shikonin inhibited the expression of GLUT1 and C-MYC. Furthermore, RNAi experiments confirmed the regulation of GLUT1 and C-MYC expression via the MST1-YAP1-TEAD1 axis. Surprisingly, YAP1 was found to positively regulate C-MYC mRNA levels in complexmore » with TEAD1, while it negatively regulates C-MYC levels in cooperation with MST1. Hence, YAP1 serves as a rheostat for C-MYC, which is regulated by MST1. In addition, depletion of MST1 stimulates lactate production, whereas the specific depletion of TEAD1 has an opposite effect. The inhibition of lactate production and cellular proliferation induced by shikonin also depends on the Hippo pathway activity. Finally, a bioinformatic analysis revealed conserved TEAD-binding motifs in the C-MYC and GLUT1 promoters providing another molecular data supporting our observations. In summary, regulation of glucose metabolism could serve as a new tumor suppressor mechanism orchestrated by the Hippo signaling pathway. - Highlights: • Shikonin inhibits C-MYC and GLUT1 expression in MST1 and YAP1 dependent manner. • YAP1-TEAD1 interaction activates C-MYC and GLUT1 expression. • MST1 in cooperation with YAP1 inhibits C-MYC and GLUT1 expression. • MST1-YAP1-TEAD1 axis regulates lactate production by leukemic cells. • MST1 and YAP1 proteins block proliferation of leukemic cells.« less

Mammalian Ste20-like protein kinase 3 mediates trophoblast apoptosis in spontaneous delivery.

PubMed

Wu, Hung-Yi; Lin, Chia-Ying; Lin, Tze-Yi; Chen, Tai-Chang; Yuan, Chiun-Jye

2008-02-01

The placenta is essential in transferring gases and nutrients from the mother to the developing fetus. Trophoblast apoptosis may cause labor or other pregnancy-related disorders. This study demonstrated the essential role of Mst3, a human Ste20-like protein kinase, in the oxidative stress-induced apoptosis of trophoblasts of term placenta in normal spontaneous delivery. Oxidative stress, but not hormones released during labor such as prostaglandin E1, oxytocin or angiotensin II, induces the expression of Mst3 and apoptosis of human term placenta after elective Cesarean section without labor pain. The role of Mst3 in oxidative stress-induced apoptosis was further demonstrated in the 3A-sub-E, a human trophoblast cell line. The H2O2-induced apoptosis of 3A-sub-E cells was largely suppressed by overexpressed Mst3KR, the kinase-dead mutant or by selective knockdown of endogenous Mst3. Further studies showed that Jun N-terminal kinase (JNK) may participate in the signaling pathway of H2O2-induced apoptosis by mediating the level of Mst3. Subsequently, caspase 3 and other downstream apoptotic components may be activated by Mst3 and trigger the apoptotic process in human trophoblasts.

22. DETAIL OF CHILLERS 1 AND 2 (MST AIRCONDITIONING SYSTEM) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. DETAIL OF CHILLERS 1 AND 2 (MST AIR-CONDITIONING SYSTEM) INTERIOR, NORTHEAST CORNER, STATION 30, SLC-3W MST - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Hydrogen peroxide modified sodium titanates with improved sorption capabilities

DOEpatents

Nyman, May D [Albuquerque, NM; Hobbs, David T [North Augusta, SC

2009-02-24

The sorption capabilities (e.g., kinetics, selectivity, capacity) of the baseline monosodium titanate (MST) sorbent material currently being used to sequester Sr-90 and alpha-emitting radioisotopes at the Savannah River Site are significantly improved when treated with hydrogen peroxide; either during the original synthesis of MST, or, as a post-treatment step after the MST has been synthesized. It is expected that these peroxide-modified MST sorbent materials will have significantly improved sorption capabilities for non-radioactive cations found in industrial processes and waste streams.

A new approach to enhance the performance of decision tree for classifying gene expression data.

PubMed

Hassan, Md; Kotagiri, Ramamohanarao

2013-12-20

Gene expression data classification is a challenging task due to the large dimensionality and very small number of samples. Decision tree is one of the popular machine learning approaches to address such classification problems. However, the existing decision tree algorithms use a single gene feature at each node to split the data into its child nodes and hence might suffer from poor performance specially when classifying gene expression dataset. By using a new decision tree algorithm where, each node of the tree consists of more than one gene, we enhance the classification performance of traditional decision tree classifiers. Our method selects suitable genes that are combined using a linear function to form a derived composite feature. To determine the structure of the tree we use the area under the Receiver Operating Characteristics curve (AUC). Experimental analysis demonstrates higher classification accuracy using the new decision tree compared to the other existing decision trees in literature. We experimentally compare the effect of our scheme against other well known decision tree techniques. Experiments show that our algorithm can substantially boost the classification performance of the decision tree.

Differential neurophysiological effects of magnetic seizure therapy (MST) and electroconvulsive shock (ECS) in non-human primates.

PubMed

Cycowicz, Yael M; Luber, Bruce; Spellman, Timothy; Lisanby, Sarah H

2008-07-01

Magnetic seizure therapy (MST) is under development as a means of reducing the side effects of electroconvulsive therapy (ECT) through enhanced control over patterns of seizure induction and spread. We previously reported that chronic treatment with MST resulted in less impairment in cognitive function than electroconvulsive shock (ECS) in a non-human primate model of convulsive therapy. Here we present quantitative analyses of ictal expression and post-ictal suppression following ECS, MST, and anesthesia-alone sham in the same model to test whether differential neurophysiological characteristics of the seizures could be identified. Rhesus monkeys received 4 weeks of daily treatment with ECS, MST, and anesthesia-alone sham in a counterbalanced order separated by a recovery period. Both ECS and MST were given bilaterally at 2.5 x seizure threshold. Neurophysiological characteristics were derived from two scalp EEG electrode recording sites during and immediately following the ictal period, and were compared to sham treatment. EEG power within four frequencies (delta, theta, alpha and beta) was calculated. Our results support earlier findings from intracerebral electrode recordings demonstrating that MST- and ECS- induced seizures elicit differential patterns of EEG activation. Specifically, we found that ECS shows significantly more marked ictal expression, and more intense post-ictal suppression than MST in the theta, alpha, and beta frequency bands (Ps < .05). However, the ECS and MST were indistinguishable in the delta frequency band during both ictal and post-ictal periods. These results demonstrate that magnetic seizure induction can result in seizures that differ in some neurophysiological respects compared with ECS, but that these modalities share some aspects of seizure expression. The clinical significance of these similarities and differences awaits clinical correlation.

Placement and Delinquency Outcomes Among System-Involved Youth Referred to Multisystemic Therapy: A Propensity Score Matching Analysis.

PubMed

Vidal, Sarah; Steeger, Christine M; Caron, Colleen; Lasher, Leanne; Connell, Christian M

2017-11-01

Multisystemic therapy (MST) was developed to help youth with serious social, emotional, and behavioral problems. Research on the efficacy and effectiveness of MST has shown positive outcomes in different domains of development and functioning among various populations of youth. Nonetheless, even with a large body of literature investigating the treatment effects of MST, few studies have focused on the effectiveness of MST through large-scale dissemination efforts. Utilizing a large sample of youth involved in a statewide dissemination of MST (n = 740; 43% females; 14% Black; 29% Hispanic; 49% White; M age  = 14.9 years), propensity score matching was employed to account for baseline differences between the treatment (n = 577) and comparison (n = 163) groups. Treatment effects were examined based on three outcomes: out-of-home placement, adjudication, and placement in a juvenile training school over a 6-year period. Significant group differences remained after adjusting for baseline differences, with youth who received MST experiencing better outcomes in offending rates than youth who did not have an opportunity to complete MST due to non-clinical or administrative reasons. Survival analyses revealed rates of all three outcomes were approximately 40% lower among the treatment group. Overall, this study adds to the body of literature supporting the long-term effectiveness of MST in reducing offending among high-risk youth. The findings underscore the potential benefits of taking evidence-based programs such as MST to scale to improve the well-being and functioning of high-risk youth. However, strategies to effectively deliver the program in mental health service settings, and to address the specific needs of high-risk youth are necessary.

Mammalian Sterile 20-like Kinase 1 (Mst1) Enhances the Stability of Forkhead Box P3 (Foxp3) and the Function of Regulatory T Cells by Modulating Foxp3 Acetylation.

PubMed

Li, Jiang; Du, Xingrong; Shi, Hao; Deng, Kejing; Chi, Hongbo; Tao, Wufan

2015-12-25

Regulatory T cells (Tregs) play crucial roles in maintaining immune tolerance. The transcription factor Foxp3 is a critical regulator of Treg development and function, and its expression is regulated at both transcriptional and post-translational levels. Acetylation by lysine acetyl transferases/lysine deacetylases is one of the main post-translational modifications of Foxp3, which regulate Foxp3's stability and transcriptional activity. However, the mechanism(s) by which the activities of these lysine acetyl transferases/lysine deacetylases are regulated to preserve proper Foxp3 acetylation during Treg development and maintenance of Treg function remains to be determined. Here we report that Mst1 can enhance Foxp3 stability, its transcriptional activity, and Treg function by modulating the Foxp3 protein at the post-translational level. We discovered that Mst1 could increase the acetylation of Foxp3 by inhibiting Sirt1 activity, which requires the Mst1 kinase activity. We also found that Mst1 could attenuate Sirt1-mediated deacetylation of Foxp3 through directly interacting with Foxp3 to prevent or interfere the interaction between Sirt1 and Foxp3. Therefore, Mst1 can regulate Foxp3 stability in kinase-dependent and kinase-independent manners. Finally, we showed that treatment of Mst1(-/-) Tregs with Ex-527, a Sirt1-specific inhibitor, partially restored the suppressive function of Mst1(-/-) Tregs. Our studies reveal a novel mechanism by which Mst1 enhances Foxp3 expression and Treg function at the post-translational level. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Misato Controls Mitotic Microtubule Generation by Stabilizing the TCP-1 Tubulin Chaperone Complex [corrected].

PubMed

Palumbo, Valeria; Pellacani, Claudia; Heesom, Kate J; Rogala, Kacper B; Deane, Charlotte M; Mottier-Pavie, Violaine; Gatti, Maurizio; Bonaccorsi, Silvia; Wakefield, James G

2015-06-29

Mitotic spindles are primarily composed of microtubules (MTs), generated by polymerization of α- and β-Tubulin hetero-dimers. Tubulins undergo a series of protein folding and post-translational modifications in order to fulfill their functions. Defects in Tubulin polymerization dramatically affect spindle formation and disrupt chromosome segregation. We recently described a role for the product of the conserved misato (mst) gene in regulating mitotic MT generation in flies, but the molecular function of Mst remains unknown. Here, we use affinity purification mass spectrometry (AP-MS) to identify interacting partners of Mst in the Drosophila embryo. We demonstrate that Mst associates stoichiometrically with the hetero-octameric Tubulin Chaperone Protein-1 (TCP-1) complex, with the hetero-hexameric Tubulin Prefoldin complex, and with proteins having conserved roles in generating MT-competent Tubulin. We show that RNAi-mediated in vivo depletion of any TCP-1 subunit phenocopies the effects of mutations in mst or the Prefoldin-encoding gene merry-go-round (mgr), leading to monopolar and disorganized mitotic spindles containing few MTs. Crucially, we demonstrate that Mst, but not Mgr, is required for TCP-1 complex stability and that both the efficiency of Tubulin polymerization and Tubulin stability are drastically compromised in mst mutants. Moreover, our structural bioinformatic analyses indicate that Mst resembles the three-dimensional structure of Tubulin monomers and might therefore occupy the TCP-1 complex central cavity. Collectively, our results suggest that Mst acts as a co-factor of the TCP-1 complex, playing an essential role in the Tubulin-folding processes required for proper assembly of spindle MTs. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.

PubMed

Li, Jinghui; Nagamochi, Hiroshi; Akutsu, Tatsuya

2018-01-01

Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph with no other cycles than benzene rings is called tree-like, and becomes a tree possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation are called the substituted benzene isomers of . When we replace each virtual atom in with a benzene ring to obtain a substituted benzene isomer, distinct isomers of are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation . Our algorithm first counts the number of all the isomers of the tree representation by a dynamic programming method. To enumerate all the isomers, for each , our algorithm then generates the th isomer by backtracking the counting phase of the dynamic programming. We also implemented our algorithm for computational experiments.

Do Extremely Violent Juveniles Respond Differently to Treatment?

PubMed Central

Asscher, Jessica J.; Deković, M.; Van den Akker, Alithe L.; Prins, Pier J. M.; Van der Laan, Peter H.

2016-01-01

This study increases knowledge on effectiveness of treatment for extremely violent (EV) youth by investigating their response to multisystemic therapy (MST). Using data of a randomized controlled trial on effectiveness of MST, we investigated differences in treatment response between EV youth and not extremely violent (NEV) youth. Pre- to post-treatment comparison indicated MST was equally effective for EV and NEV youth, whereas treatment as usual was not effective for either group. Growth curves of within-treatment changes indicated EV youth responded differently to MST than NEV youth. The within-treatment change was for EV youth non-linear: Initially, they show a deterioration; however, after one month, EV juveniles respond positively to MST, indicating longer lasting, intensive programs may be effective in treating extreme violence. PMID:27794135

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

The influence of conifer forest canopy cover on the accuracy of two individual tree measurement algorithms using lidar data

Treesearch

Michael J. Falkowski; Alistair M.S. Smith; Paul E. Gessler; Andrew T. Hudak; Lee A. Vierling; Jeffrey S. Evans

2008-01-01

Individual tree detection algorithms can provide accurate measurements of individual tree locations, crown diameters (from aerial photography and light detection and ranging (lidar) data), and tree heights (from lidar data). However, to be useful for forest management goals relating to timber harvest, carbon accounting, and ecological processes, there is a need to...

Distance-Based Phylogenetic Methods Around a Polytomy.

PubMed

Davidson, Ruth; Sullivant, Seth

2014-01-01

Distance-based phylogenetic algorithms attempt to solve the NP-hard least-squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean space properly containing the space of all tree metrics as a polyhedral fan. Outputs of distance-based tree reconstruction algorithms such as UPGMA and neighbor-joining are points in the maximal cones in the fan. Tree metrics with polytomies lie at the intersections of maximal cones. A phylogenetic algorithm divides the space of all dissimilarity maps into regions based upon which combinatorial tree is reconstructed by the algorithm. Comparison of phylogenetic methods can be done by comparing the geometry of these regions. We use polyhedral geometry to compare the local nature of the subdivisions induced by least-squares phylogeny, UPGMA, and neighbor-joining when the true tree has a single polytomy with exactly four neighbors. Our results suggest that in some circumstances, UPGMA and neighbor-joining poorly match least-squares phylogeny.

Utilization and intensity of outpatient care related to military sexual trauma for veterans from Afghanistan and Iraq.

PubMed

Turchik, Jessica A; Pavao, Joanne; Hyun, Jenny; Mark, Hanna; Kimerling, Rachel

2012-07-01

Little research has examined factors associated with the utilization of outpatient health care services related to sexual assault experiences. The Veterans Health Administration provides free outpatient treatment services to veterans who report military sexual trauma (MST); this system provides a unique opportunity to examine factors related to the utilization of mental health and non-mental health outpatient services by patients with sexual trauma. The current study examined sociodemographic, military service factors, and primary diagnoses related to utilization and utilization intensity of MST-related care among 4,458 Operation Enduring Freedom/Operation Iraqi Freedom Veterans in a 1-year period after reporting an experience of MST. Of the veterans who reported MST, 75.9% received MST-related care. The most notable factor that influenced receipt and intensity of MST-related care was gender, where male veterans used less care than female veterans. These results have important treatment implications for both veteran and civilian sexual trauma survivors.

Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees.

PubMed

Fokkema, M; Smits, N; Zeileis, A; Hothorn, T; Kelderman, H

2017-10-25

Identification of subgroups of patients for whom treatment A is more effective than treatment B, and vice versa, is of key importance to the development of personalized medicine. Tree-based algorithms are helpful tools for the detection of such interactions, but none of the available algorithms allow for taking into account clustered or nested dataset structures, which are particularly common in psychological research. Therefore, we propose the generalized linear mixed-effects model tree (GLMM tree) algorithm, which allows for the detection of treatment-subgroup interactions, while accounting for the clustered structure of a dataset. The algorithm uses model-based recursive partitioning to detect treatment-subgroup interactions, and a GLMM to estimate the random-effects parameters. In a simulation study, GLMM trees show higher accuracy in recovering treatment-subgroup interactions, higher predictive accuracy, and lower type II error rates than linear-model-based recursive partitioning and mixed-effects regression trees. Also, GLMM trees show somewhat higher predictive accuracy than linear mixed-effects models with pre-specified interaction effects, on average. We illustrate the application of GLMM trees on an individual patient-level data meta-analysis on treatments for depression. We conclude that GLMM trees are a promising exploratory tool for the detection of treatment-subgroup interactions in clustered datasets.

Multiple subpial transection for intractable partial epilepsy: an international meta-analysis.

PubMed

Spencer, Susan S; Schramm, Johannes; Wyler, Allen; O'Connor, Michael; Orbach, Darren; Krauss, Gregory; Sperling, Michael; Devinsky, Orrin; Elger, Christian; Lesser, Ronald; Mulligan, Lisa; Westerveld, Michael

2002-02-01

Because the number and variety of patients at any single facility is not sufficient for clinical or statistical analysis, data from six major epilepsy centers that performed multiple subpial transections (MSTs) for medically intractable epilepsy were collected. A meta-analysis was performed to elucidate the indications and outcome, and to assess the results of the procedure. Overall, 211 patients were represented with data regarding preoperative evaluation, procedures, seizure types and frequencies before and after surgery, postoperative deficits, and demographic information. Fifty-three patients underwent MST without resection. In patients with MST plus resection, excellent outcome (>95% reduction in seizure frequency) was obtained in 87% of patients for generalized seizures, 68% for complex partial seizures, and 68% for simple partial seizures. For the patients who underwent MST without resection, the rate of excellent outcome was only slightly lower, at 71% for generalized, 62% for complex partial, and 63% for simple partial seizures. EEG localization, age at epilepsy onset, duration of epilepsy, and location of MST were not significant predictors of outcome for any kinds of seizures after MST, with or without resection. New neurologic deficits were found in 47 patients overall, comparable in MST with resection (23%) or without (19%). These preliminary results suggest that MST has efficacy by itself, with minimal neurologic compromise, in cases in which resective surgery cannot be used to treat uncontrolled epilepsy. MST should be investigated as a stand-alone procedure to allow further development of criteria and predictive factors for outcome.

73. LIQUID NITROGEN PUMPING STATION ON WEST SIDE OF MST; ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

73. LIQUID NITROGEN PUMPING STATION ON WEST SIDE OF MST; NITROGEN EXCHANGERS ON RIGHT. SOUTHWEST CORNER OF MST VISIBLE; ENVIRONMENTAL CURTAIN SWING AND PLATFORM EXTENDED. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

17. VIEW OF INTERIOR, EAST SIDE, DECK LEVEL OF MST. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. VIEW OF INTERIOR, EAST SIDE, DECK LEVEL OF MST. NOTE CANVAS CURTAIN (RIGHT) USED TO COVER SOUTH SIDE OF MST BELOW LOWEST ENVIRONMENTAL DOORS. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Low-dose maintenance steroid treatment could reduce the relapse rate in patients with type 1 autoimmune pancreatitis: a long-term Japanese multicenter analysis of 510 patients.

PubMed

Kubota, Kensuke; Kamisawa, Terumi; Okazaki, Kazuichi; Kawa, Shigeyuki; Hirano, Kenji; Hirooka, Yoshiki; Uchida, Kazushige; Shiomi, Hideyuki; Ohara, Hirotaka; Shimizu, Kyoko; Arakura, Norikazu; Kanno, Atsushi; Sakagami, Junichi; Itoi, Takao; Ito, Tetsuhide; Ueki, Toshiharu; Nishino, Takayoshi; Inui, Kazuo; Mizuno, Nobumasa; Yoshida, Hitoshi; Sugiyama, Masanori; Iwasaki, Eisuke; Irisawa, Atshishi; Shimosegawa, Toru; Takeyama, Yoshifumi; Chiba, Tsutomu

2017-08-01

The effect of maintenance steroid treatment (MST) in reducing the risk of relapse in patients with autoimmune pancreatitis (AIP) remains under debate. The aim of this study was to validate the effect of MST on AIP administered in accordance with the 2010 Japanese consensus guidelines. The clinical data of patients with (n = 510) from 22 high-volume centers in Japan were studied. The primary endpoints were the relapse rates (RRs) in patients administered MST versus those not administered MST. The secondary endpoints were the optimal dose and duration of MST in terms of steroid toxicity and the predictors of relapse. The RRs were 10.0% within 1 year, 25.8% within 3 years and 35.1% within 5 years. The RR in the steroid therapy group reached a plateau at 42.7% at 7 years. In terms of the optimal dosage, the overall RR in the MST 5 mg/day group was 26.1%, which was significantly lower than that in the group which had discontinued steroid therapy (45.2%; p = 0.023) or was receiving MST at 2.5 mg/day (43.4%, p = 0.001). The RRs in the group receiving MST at ≥5 mg/day versus the patient group receiving MST at <5 mg/day were 10.6 vs. 10.3% within 1 year, 23.5 vs. 32.9% within 3 years and 32.2 vs. 41.3% within 5 years, respectively (log-rank, p = 0.028). The best cutoff value of the total steroid dose for serious steroid toxicity was 6405 mg, with a moderate accuracy of 0.717 determined using the area under the curve. Presence of diffuse pancreatic swelling [odds ratio OR) 1.745; p = 0.008) and MST at >5 mg/day were identified as predictors of relapse (OR 0.483; p = 0.001). The RR could continue to increase for 7 years even under MST. Based on our analysis of the side effects of steroid therapy, MST at 5 mg/day for 2 (total 4625 mg) to 3 (total 6425 mg) years might be a rational and safe therapeutic strategy in terms of keeping the RR to <30% while avoiding potential steroid toxicity.

Image compression using quad-tree coding with morphological dilation

NASA Astrophysics Data System (ADS)

Wu, Jiaji; Jiang, Weiwei; Jiao, Licheng; Wang, Lei

2007-11-01

In this paper, we propose a new algorithm which integrates morphological dilation operation to quad-tree coding, the purpose of doing this is to compensate each other's drawback by using quad-tree coding and morphological dilation operation respectively. New algorithm can not only quickly find the seed significant coefficient of dilation but also break the limit of block boundary of quad-tree coding. We also make a full use of both within-subband and cross-subband correlation to avoid the expensive cost of representing insignificant coefficients. Experimental results show that our algorithm outperforms SPECK and SPIHT. Without using any arithmetic coding, our algorithm can achieve good performance with low computational cost and it's more suitable to mobile devices or scenarios with a strict real-time requirement.

Decision tree methods: applications for classification and prediction.

PubMed

Song, Yan-Yan; Lu, Ying

2015-04-25

Decision tree methodology is a commonly used data mining method for establishing classification systems based on multiple covariates or for developing prediction algorithms for a target variable. This method classifies a population into branch-like segments that construct an inverted tree with a root node, internal nodes, and leaf nodes. The algorithm is non-parametric and can efficiently deal with large, complicated datasets without imposing a complicated parametric structure. When the sample size is large enough, study data can be divided into training and validation datasets. Using the training dataset to build a decision tree model and a validation dataset to decide on the appropriate tree size needed to achieve the optimal final model. This paper introduces frequently used algorithms used to develop decision trees (including CART, C4.5, CHAID, and QUEST) and describes the SPSS and SAS programs that can be used to visualize tree structure.

Greedy algorithms in disordered systems

NASA Astrophysics Data System (ADS)

Duxbury, P. M.; Dobrin, R.

1999-08-01

We discuss search, minimal path and minimal spanning tree algorithms and their applications to disordered systems. Greedy algorithms solve these problems exactly, and are related to extremal dynamics in physics. Minimal cost path (Dijkstra) and minimal cost spanning tree (Prim) algorithms provide extremal dynamics for a polymer in a random medium (the KPZ universality class) and invasion percolation (without trapping) respectively.

Toward Evidence-Based Transport of Evidence-Based Treatments: MST as an Example

ERIC Educational Resources Information Center

Schoenwald, Sonja K.

2008-01-01

This article describes the journey toward evidence-based transport and implementation in usual care settings of Multisystemic Therapy (MST) for youth with drug abuse and behavioral problems (Henggeler, Schoenwald, Borduin, Rowland, & Cunningham, 1998). Research and experience informing the design of the MST transport strategy, progress in…

1. VIEW OF SOUTHEAST CORNER OF MOBILE SERVICE TOWER (MST). ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. VIEW OF SOUTHEAST CORNER OF MOBILE SERVICE TOWER (MST). CABLE TRAY SHED IN FOREGROUND. MICROWAVE ANTENNAS AND AIR-CONDITIONING PORCH ON EAST SIDE OF MST. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Middle Atmosphere Program. Handbook for MAP, volume 28

NASA Technical Reports Server (NTRS)

Liu, C. H. (Editor); Edwards, Belva (Editor)

1989-01-01

Extended abstracts from the fourth workshop on the technical and scientific aspects of MST (mesosphere stratosphere troposphere) radar are presented. Individual sessions addressed the following topics: meteorological applications of MST and ST radars, networks, and campaigns; dynamics of the equatorial middle atmosphere; interpretation of radar returns from clear air; techniques for studying gravity waves and turbulence; intercomparison and calibration of wind and wave measurements at various frequencies; progress in existing and planned MST and ST radars; hardware design for MST and ST radars and boundary layer/lower troposphere profilers; signal processing; and data management.

Materials science tetrahedron--a useful tool for pharmaceutical research and development.

PubMed

Sun, Changquan Calvin

2009-05-01

The concept of materials science tetrahedron (MST) concisely depicts the inter-dependent relationship among the structure, properties, performance, and processing of a drug. Similar to its role in traditional materials science, MST encompasses the development in the emerging field of pharmaceutical materials science and forms a scientific foundation to the design and development of new drug products. Examples are given to demonstrate the applicability of MST to both pharmaceutical research and product development. It is proposed that a systematic implementation of MST can expedite the transformation of pharmaceutical product development from an art to a science. By following the principle of MST, integration of research among different laboratories can be attained. The pharmaceutical science community as a whole can conduct more efficient, collaborative, and coherent research.

Plant interactions alter the predictions of metabolic scaling theory.

PubMed

Lin, Yue; Berger, Uta; Grimm, Volker; Huth, Franka; Weiner, Jacob

2013-01-01

Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive.

Electric field strength and focality in electroconvulsive therapy and magnetic seizure therapy: a finite element simulation study

NASA Astrophysics Data System (ADS)

Deng, Zhi-De; Lisanby, Sarah H.; Peterchev, Angel V.

2011-02-01

We present the first computational study comparing the electric field induced by various electroconvulsive therapy (ECT) and magnetic seizure therapy (MST) paradigms. Four ECT electrode configurations (bilateral, bifrontal, right unilateral, and focal electrically administered seizure therapy) and three MST coil configurations (circular, cap, and double cone) were modeled. The model incorporated a modality-specific neural activation threshold. ECT (0.3 ms pulse width) and MST induced the maximum electric field of 2.1-2.5 V cm-1 and 1.1-2.2 V cm-1 in the brain, corresponding to 6.2-7.2 times and 1.2-2.3 times the neural activation threshold, respectively. The MST electric field is more confined to the superficial cortex compared to ECT. The brain volume stimulated was much larger with ECT (up to 100%) than with MST (up to 8.2%). MST with the double-cone coil was the most focal, and bilateral ECT was the least focal. Our results suggest a possible biophysical explanation of the reduced side effects of MST compared to ECT. Our results also indicate that the conventional ECT pulse amplitude (800-900 mA) is much higher than necessary for seizure induction. Reducing the ECT pulse amplitude should be explored as a potential means of diminishing side effects.

Magnetic Seizure Therapy for Unipolar and Bipolar Depression: A Systematic Review

PubMed Central

Cretaz, Eric; Brunoni, André R.

2015-01-01

Objective. Magnetic seizure therapy (MST) is a novel, experimental therapeutic intervention, which combines therapeutic aspects of electroconvulsive therapy (ECT) and transcranial magnetic stimulation, in order to achieve the efficacy of the former with the safety of the latter. MST might prove to be a valuable tool in the treatment of mood disorders, such as major depressive disorder (MDD) and bipolar disorder. Our aim is to review current literature on MST. Methods. OVID and MEDLINE databases were used to systematically search for clinical studies on MST. The terms “magnetic seizure therapy,” “depression,” and “bipolar” were employed. Results. Out of 74 studies, 8 met eligibility criteria. There was considerable variability in the methods employed and samples sizes were small, limiting the generalization of the results. All studies focused on depressive episodes, but few included patients with bipolar disorder. The studies found reported significant antidepressant effects, with remission rates ranging from 30% to 40%. No significant cognitive side effects related to MST were found, with a better cognitive profile when compared to ECT. Conclusion. MST was effective in reducing depressive symptoms in mood disorders, with generally less side effects than ECT. No study focused on comparing MST to ECT on bipolar depression specifically. PMID:26075100

Preliminary data suggest rates of male military sexual trauma may be higher than previously reported.

PubMed

Sheppard, Sean C; Hickling, Edward J; Earleywine, Mitch; Hoyt, Tim; Russo, Amanda R; Donati, Matthew R; Kip, Kevin E

2015-11-01

Stigma associated with disclosing military sexual trauma (MST) makes estimating an accurate base rate difficult. Anonymous assessment may help alleviate stigma. Although anonymous research has found higher rates of male MST, no study has evaluated whether providing anonymity sufficiently mitigates the impact of stigma on accurate reporting. This study used the unmatched count technique (UCT), a form of randomized response techniques, to gain information about the accuracy of base rate estimates of male MST derived via anonymous assessment of Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) combat veterans. A cross-sectional convenience sample of 180 OEF/OIF male combat veterans, recruited via online websites for military populations, provided data about history of MST via traditional anonymous self-report and the UCT. The UCT revealed a rate of male MST more than 15 times higher than the rate derived via traditional anonymous assessment (1.1% vs. 17.2%). These data suggest that anonymity does not adequately mitigate the impact of stigma on disclosure of male MST. Results, though preliminary, suggest that published rates of male MST may substantially underestimate the true rate of this problem. The UCT has significant potential to improve base rate estimation of sensitive behaviors in the military. (c) 2015 APA, all rights reserved).

Newly Isolated Paenibacillus tyrfis sp. nov., from Malaysian Tropical Peat Swamp Soil with Broad Spectrum Antimicrobial Activity

PubMed Central

Aw, Yoong-Kit; Ong, Kuan-Shion; Lee, Learn-Han; Cheow, Yuen-Lin; Yule, Catherine M.; Lee, Sui-Mae

2016-01-01

Emergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1T that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1T belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17T (99.5%). Whole genome comparison between strain MSt1T with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1T with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1T with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1T contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1T were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1T was 51.5 mol%. The extract from strain MSt1T exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1T when compared to its closely related type species, we propose that strain MSt1T represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708T = MCCC 1K01247T) is proposed. PMID:26973605

The Telomerase Inhibitor MST-312 Interferes with Multiple Steps in the Herpes Simplex Virus Life Cycle.

PubMed

Haberichter, Jarod; Roberts, Scott; Abbasi, Imran; Dedthanou, Phonphanh; Pradhan, Prajakta; Nguyen, Marie L

2015-10-01

The life cycle of herpes simplex virus (HSV) has the potential to be further manipulated to yield novel, more effective therapeutic treatments. Recent research has demonstrated that HSV-1 can increase telomerase activity and that expression of the catalytic component of telomerase, telomerase reverse transcriptase (TERT), alters sensitivity to HSV-dependent apoptosis. Telomerase is a cellular enzyme that synthesizes nucleotide repeats at the ends of chromosomes (telomeres), which prevents shortening of the 3' ends of DNA with each cell division. Once telomeres reach a critical length, cells undergo senescence and apoptosis. Here, we used a cell-permeable, reversible inhibitor of the telomerase enzyme, MST-312, to investigate telomerase activity during HSV infection. Human mammary epithelial cells immortalized through TERT expression and human carcinoma HEp-2 cells were infected with the KOS1.1 strain of HSV-1 in the presence of MST-312. MST-312 treatment reduced the number of cells displaying a cytopathic effect and the accumulation of immediate early and late viral proteins. Moreover, the presence of 20 μM to 100 μM MST-312 during infection led to a 2.5- to 5.5-log10 decrease in viral titers. MST-312 also inhibited the replication of HSV-2 and a recent clinical isolate of HSV-1. Additionally, we determined that MST-312 has the largest impact on viral events that take place prior to 5 h postinfection (hpi). Furthermore, MST-312 treatment inhibited virus replication, as measured by adsorption assays and quantification of genome replication. Together, these findings demonstrate that MST-312 interferes with the HSV life cycle. Further investigation into the mechanism for MST-312 is warranted and may provide novel targets for HSV therapies. Herpes simplex virus (HSV) infections can lead to cold sores, blindness, and brain damage. Identification of host factors that are important for the virus life cycle may provide novel targets for HSV antivirals. One such factor, telomerase, is the cellular enzyme that synthesizes DNA repeats at the ends of chromosomes during replication to prevent DNA shortening. In this study, we investigate role of telomerase in HSV infection. The data demonstrate that the telomerase inhibitor MST-312 suppressed HSV replication at multiple steps of viral infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A data driven approach for condition monitoring of wind turbine blade using vibration signals through best-first tree algorithm and functional trees algorithm: A comparative study.

PubMed

Joshuva, A; Sugumaran, V

2017-03-01

Wind energy is one of the important renewable energy resources available in nature. It is one of the major resources for production of energy because of its dependability due to the development of the technology and relatively low cost. Wind energy is converted into electrical energy using rotating blades. Due to environmental conditions and large structure, the blades are subjected to various vibration forces that may cause damage to the blades. This leads to a liability in energy production and turbine shutdown. The downtime can be reduced when the blades are diagnosed continuously using structural health condition monitoring. These are considered as a pattern recognition problem which consists of three phases namely, feature extraction, feature selection, and feature classification. In this study, statistical features were extracted from vibration signals, feature selection was carried out using a J48 decision tree algorithm and feature classification was performed using best-first tree algorithm and functional trees algorithm. The better algorithm is suggested for fault diagnosis of wind turbine blade. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Object-Oriented Algorithm For Evaluation Of Fault Trees

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1992-01-01

Algorithm for direct evaluation of fault trees incorporates techniques of object-oriented programming. Reduces number of calls needed to solve trees with repeated events. Provides significantly improved software environment for such computations as quantitative analyses of safety and reliability of complicated systems of equipment (e.g., spacecraft or factories).

The first new application of the mathematical theory of stochastic processes to lunar and planetary science: topography profile diagrams of Mars

NASA Astrophysics Data System (ADS)

Salamuniccar, G.

The Mathematical Statistics Theory (MST) and the Mathematical Theory of Stochastic Processes (MTSP) are different branches of the more general Mathematical Probability Theory (MPT) that represents different aspects of some physical processes we can analyze using mathematics. Each model of a stochastic process according to MTSP can provide one or more interpretations in MST domain. Large body of work on the impact crater statistics according to MST was already done many years ago, for e.g., where Cratering Chronology Diagrams (CCD) were shown in log/log scale, showing Cum. Crater Frequency [N km-2] that is the function of Age [years] for some particular crater diameter. However, all this is only one possible representation in MST domain, of the bombardment of the planetary surface modeled as stochastic process according to MTSP. The idea that other representations in MST domain of the same stochastic process from MTSP are possible was recently presented [G. Salamuniæcar, Adv. Space Res. in press]. The importance of the approach is that each such interpretation can provide large amount of new information. Topography Profile Diagrams (TPDs) are one example, that with MOLA data provide us with large amount of new information regarding history of Mars. TPDs consists of [34thLPS #1403]: (1) Topography-Profile Curve (TPC) that is representation of the planet topography, (2) Density-of-Craters Curve (DCC) that represents density of craters, (3) Filtered-DCC (FDCC) that represents DCC filtered by a low-pass filter included with the purpose of reducing the noise and (4) Level-of-Substance-Over-Time Curve (LSOTC). While definition of TPC uniquely corresponds to way we will compute it, the same is not also the case with DCC and FDCC. While DCC depends on algorithms for computing crater altitude according to the topography, center coordinates and radius of impact crater [34thLPS #1409], FDCC depends on the architecture of the custom designed low-pass filter for filtering DCC [34thLPS #1415]. However all variations of DCC and FDCC including the different input craters data-sets confirmed correlation between density of craters and topographic altitude over 70˜ 80% of the planet surface. For the assumption that ocean primarily caused noted correlation, LSOTC additionally for the first time offers mathematical approach how to compute how level of ocean was changing over time [6thMars #3187]. Accordingly, conclusion is that TPDs are the first new practical application of MTSP to the Lunar and Planetary Science (LPS).

Applications and Benefits for Big Data Sets Using Tree Distances and The T-SNE Algorithm

DTIC Science & Technology

2016-03-01

BENEFITS FOR BIG DATA SETS USING TREE DISTANCES AND THE T-SNE ALGORITHM by Suyoung Lee March 2016 Thesis Advisor: Samuel E. Buttrey...REPORT TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE APPLICATIONS AND BENEFITS FOR BIG DATA SETS USING TREE DISTANCES AND THE T-SNE...this work we use tree distance computed using Buttrey’s treeClust package in R, as discussed by Buttrey and Whitaker in 2015, to process mixed data

Wavelet compression of multichannel ECG data by enhanced set partitioning in hierarchical trees algorithm.

PubMed

Sharifahmadian, Ershad

2006-01-01

The set partitioning in hierarchical trees (SPIHT) algorithm is very effective and computationally simple technique for image and signal compression. Here the author modified the algorithm which provides even better performance than the SPIHT algorithm. The enhanced set partitioning in hierarchical trees (ESPIHT) algorithm has performance faster than the SPIHT algorithm. In addition, the proposed algorithm reduces the number of bits in a bit stream which is stored or transmitted. I applied it to compression of multichannel ECG data. Also, I presented a specific procedure based on the modified algorithm for more efficient compression of multichannel ECG data. This method employed on selected records from the MIT-BIH arrhythmia database. According to experiments, the proposed method attained the significant results regarding compression of multichannel ECG data. Furthermore, in order to compress one signal which is stored for a long time, the proposed multichannel compression method can be utilized efficiently.

Randomized controlled trial of the cognitive side-effects of magnetic seizure therapy (MST) and electroconvulsive shock (ECS).

PubMed

Moscrip, Tammy D; Terrace, Herbert S; Sackeim, Harold A; Lisanby, Sarah H

2006-02-01

Magnetic seizure therapy (MST) is under development as a means of improving the cognitive side-effect profile of electroconvulsive therapy (ECT) by inducing more spatially delimited seizures that spare cortical regions involved in memory. We tested whether MST had a cognitive side-effect profile distinct from electroconvulsive shock (ECS) in a non-human primate model, using the Columbia University Primate Cognitive Profile, which has been shown to be sensitive to the cognitive effects of ECS. Using a within-subject cross-over design, daily ECS, MST, and sham (anaesthesia-only) interventions were administered in 5-wk blocks. Rhesus macaques (n = 2) were trained on a long-term memory task, an anterograde learning and memory task, and a combined anterograde and retrograde task where learning and memory were evaluated for new and previously learned 3-item lists. Acutely following each intervention, monkeys were tested on the cognitive battery twice daily, separated by a 3-h retention interval. Overall, monkeys were least accurate following ECS (p's < 0.05) compared to sham and MST. This effect was most marked for long-term memory of a constant target, short-term memory of a variable target and recall of previously learned 3-item lists. Monkeys were slowest to complete all tasks following ECS (p's = 0.0001). Time to task completion following MST did not differ from sham. These findings suggest that MST results in a more benign acute cognitive side-effect profile than ECS in this model, consistent with initial observations with human MST.

The effect from maximal bench press strength training on work economy during wheelchair propulsion in men with spinal cord injury.

PubMed

Tørhaug, T; Brurok, B; Hoff, J; Helgerud, J; Leivseth, G

2016-10-01

To assess the effect from maximal bench press strength training (MST) on wheelchair propulsion work economy (WE). Pretest-posttest case-control group design. St Olavs Hospital, Trondheim, Norway. Seventeen male individuals with spinal cord injury (SCI) paraplegia were allocated to either MST bench press (n=11) or the control group (CG) (n=7). The MST group trained bench press three times per week, for 6 weeks, starting at 85-95% of their pretest bench press one-repetition maximum (1RM). For calculation of WE during wheelchair propulsion, oxygen uptake (VO 2 ) measurements were collected during wheelchair ergometry (WCE) at submaximal workload of 50 W. Similarly, peak oxygen uptake (VO 2peak ) and peak power output (W) were measured during WCE. Individuals in the MST regimen significantly improved WE compared with the CG by 17.3 % (mean between-group differences: 95% confidence interval) of 2.63 ml kg -1  min -1 : (-4.34, -0.91) (P=0.007). Between pretest and posttest, the increase in bench press 1RM was by 17% higher in the MST group compared with the CG. At peak testing, the MST group generated significantly higher peak power compared with the CG. All other physiological variables were comparable within and between groups. A 6-week MST bench press regimen significantly improved WE during wheelchair propulsion at 50 W workload. These preliminary data support a possible beneficial role for MST to reduce the energy cost of wheelchair propulsion for SCI individuals.

Hybrid micro/nanostructural surface offering improved stress distribution and enhanced osseointegration properties of the biomedical titanium implant.

PubMed

Hou, Ping-Jen; Ou, Keng-Liang; Wang, Chin-Chieh; Huang, Chiung-Fang; Ruslin, Muhammad; Sugiatno, Erwan; Yang, Tzu-Sen; Chou, Hsin-Hua

2018-03-01

The aim of the present study was to investigate the surface characteristic, biomechanical behavior, hemocompatibility, bone tissue response and osseointegration of the optimal micro-arc oxidation surface-treated titanium (MST-Ti) dental implant. The surface characteristic, biomechanical behavior and hemocompatibility of the MST-Ti dental implant were performed using scanning electron microscope, finite element method, blood dripping and immersion tests. The mini-pig model was utilized to evaluate the bone tissue response and osseointegration of the MST-Ti dental implant in vivo. Data were analyzed by analysis of variance using the Student's t-test (P ≤ 0.05). The hybrid volcano-like micro/nanoporous structure was formed on the surface of the MST-Ti dental implant. The hybrid volcano-like micro/nanoporous surface played an important role to improve the stress transfer between fixture, cortical bone and cancellous bone for the MST-Ti dental implant. Moreover, the MST-Ti implant was considered to have the outstanding hemocompatibility. In vivo testing results showed that the bone-to-implant contact (BIC) ratio significantly altered as the implant with micro/nanoporous surface. After 12 weeks of implantation, the MST-Ti dental implant group exhibited significantly higher BIC ratio than the untreated dental implant group. In addition, the MST-Ti dental implant group also presented an enhancing osseointegration, particularly in the early stages of bone healing. It can be concluded that the micro-arc oxidation approach induced the formation of micro/nanoporous surface is a promising and reliable alternative surface modification for Ti dental implant applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Time course of motor gains induced by music-supported therapy after stroke: An exploratory case study.

PubMed

Grau-Sánchez, Jennifer; Ramos, Neus; Duarte, Esther; Särkämö, Teppo; Rodríguez-Fornells, Antoni

2017-09-01

Previous studies have shown that Music-Supported Therapy (MST) can improve the motor function and promote functional neuroplastic changes in motor areas; however, the time course of motor gains across MST sessions and treatment periods remain unknown. The aim of this study was to explore the progression of the rehabilitation of motor deficits in a chronic stroke patient for a period of 7 months. A reversal design (ABAB) was implemented in a chronic stroke patient where no treatment was provided in the A periods and MST was applied in the B periods. Each period comprised of 4 weeks and an extensive evaluation of the motor function using clinical motor tests and 3D movement analysis was performed weekly. During the MST periods, a keyboard task was recorded daily. A follow-up evaluation was performed 3 months after the second MST treatment. Improvements were observed during the first sessions in the keyboard task but clinical gains were noticeable only at the end of the first treatment and during the second treatment period. These gains were maintained in the follow-up evaluation. This is the first study examining the pattern of motor recovery progression in MST, evidencing that gradual and continuous motor improvements are possible with the repeated application of MST training. Fast-acquisition in specific motor abilities was observed at the beginning of the MST training but generalization of these improvements to other motor tasks took place at the end or when another treatment period was provided. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A pilot study of the comparative efficacy of 100 Hz magnetic seizure therapy and electroconvulsive therapy in persistent depression.

PubMed

Fitzgerald, Paul B; Hoy, Kate E; Elliot, David; McQueen, Susan; Wambeek, Lenore E; Chen, Leo; Clinton, Anne Maree; Downey, Glenn; Daskalakis, Zafiris J

2018-05-01

Magnetic seizure therapy (MST) is a novel brain stimulation technique that uses a high-powered transcranial magnetic stimulation device to produce therapeutic seizures. Preliminary MST studies have found antidepressant effects in the absence of cognitive side effects but its efficacy compared to electroconvulsive therapy (ECT) remains unclear. The aim of this study was to investigate the therapeutic efficacy and cognitive profile of MST compared to standard right unilateral ECT treatment. Thirty-seven patients completed a course of at least nine ECT or MST treatments in a randomized double-blind protocol. Assessments of depression severity and cognition were performed before and after treatment. No difference in the antidepressant effectiveness between the treatments was seen across any of the clinical outcome measures, although the overall response rates in both groups were quite low. In regards to cognition, following MST there were significant improvements in tests of psychomotor speed, verbal memory, and cognitive inhibition, with no reductions in cognitive performance. Following ECT there was significant improvement in only one of the cognitive inhibition tasks. With respect to the between-group comparisons, the MST group showed a significantly greater improvement on psychomotor speed than ECT. MST showed similar efficacy to right unilateral ECT in patients with treatment-resistant depression without cognitive side effects but in a sample that was only of sufficient size to demonstrate relatively large differences in response between the two groups. Future research should aim to optimize the methods of MST administration and compare its efficacy to ECT in large randomized controlled trials. © 2018 Wiley Periodicals, Inc.

Effect of local therapy on locoregional recurrence in postmenopausal women with breast cancer in the Tamoxifen Exemestane Adjuvant Multinational (TEAM) trial.

PubMed

van Hezewijk, Marjan; Bastiaannet, Esther; Putter, Hein; Scholten, Astrid N; Liefers, Gerrit-Jan; Rea, Daniel; Hasenburg, Annette; Paridaens, Robert; Hozumi, Yasuo; Markopoulos, Christos; Seynaeve, Caroline; Jones, Stephen E; Marijnen, Corrie A M; van de Velde, Cornelis J H

2013-08-01

The TEAM trial investigated the efficacy and safety of adjuvant endocrine therapy consisting of either exemestane or the sequence of tamoxifen followed by exemestane in postmenopausal hormone-sensitive breast cancer. The present analyses explored the association between locoregional therapy and recurrence (LRR) in this population. Between 2001 and 2006, 9779 patients were randomized. Local treatment was breast conserving surgery plus radiotherapy (BCS+RT), mastectomy without radiotherapy (MST-only), or mastectomy plus radiotherapy (MST+RT). Patients with unknown data on surgery, radiotherapy, tumor or nodal stage (n=199), and patients treated by lumpectomy without radiotherapy (n=349) were excluded. After a median follow-up of 5.2 years, 270 LRRs occurred (2.9%) among 9231 patients. The 5-years actuarial incidence of LRR was 4.2% (95% CI 3.3-4.9%) for MST-only, 3.4% (95% CI 2.4-4.2%) for MST+RT and 1.9% (95% CI 1.5-2.3%) for BCS+RT. After adjustment for prognostic factors, the hazard ratio (HR, reference BCS+RT) for LRR remained significantly higher for MST-only (HR 1.53; 95% CI 1.10-2.11), not for MST+RT (HR 0.78; 95% CI 0.50-1.22). This explorative analysis showed a higher LRR risk after MST-only than after BCS+RT, even after adjustment for prognostic factors. As this effect was not seen for MST+RT versus BCS+RT, it might be explained by the beneficial effects of radiation treatment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

PubMed

Kordi, Misagh; Bansal, Mukul S

2017-01-01

Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.

The Development of MST Test Information for the Prediction of Test Performances

ERIC Educational Resources Information Center

Park, Ryoungsun; Kim, Jiseon; Chung, Hyewon; Dodd, Barbara G.

2017-01-01

The current study proposes novel methods to predict multistage testing (MST) performance without conducting simulations. This method, called MST test information, is based on analytic derivation of standard errors of ability estimates across theta levels. We compared standard errors derived analytically to the simulation results to demonstrate the…

Rare itemsets mining algorithm based on RP-Tree and spark framework

NASA Astrophysics Data System (ADS)

Liu, Sainan; Pan, Haoan

2018-05-01

For the issues of the rare itemsets mining in big data, this paper proposed a rare itemsets mining algorithm based on RP-Tree and Spark framework. Firstly, it arranged the data vertically according to the transaction identifier, in order to solve the defects of scan the entire data set, the vertical datasets are divided into frequent vertical datasets and rare vertical datasets. Then, it adopted the RP-Tree algorithm to construct the frequent pattern tree that contains rare items and generate rare 1-itemsets. After that, it calculated the support of the itemsets by scanning the two vertical data sets, finally, it used the iterative process to generate rare itemsets. The experimental show that the algorithm can effectively excavate rare itemsets and have great superiority in execution time.

MST1 is a key regulator of beta cell apoptosis and dysfunction in diabetes.

PubMed

Ardestani, Amin; Paroni, Federico; Azizi, Zahra; Kaur, Supreet; Khobragade, Vrushali; Yuan, Ting; Frogne, Thomas; Tao, Wufan; Oberholzer, Jose; Pattou, Francois; Conte, Julie Kerr; Maedler, Kathrin

2014-04-01

Apoptotic cell death is a hallmark of the loss of insulin-producing beta cells in all forms of diabetes mellitus. Current treatments fail to halt the decline in functional beta cell mass, and strategies to prevent beta cell apoptosis and dysfunction are urgently needed. Here, we identified mammalian sterile 20-like kinase-1 (MST1) as a critical regulator of apoptotic beta cell death and function. Under diabetogenic conditions, MST1 was strongly activated in beta cells in human and mouse islets and specifically induced the mitochondrial-dependent pathway of apoptosis through upregulation of the BCL-2 homology-3 (BH3)-only protein BIM. MST1 directly phosphorylated the beta cell transcription factor PDX1 at T11, resulting in the latter's ubiquitination and degradation and thus in impaired insulin secretion. MST1 deficiency completely restored normoglycemia, beta cell function and survival in vitro and in vivo. We show MST1 as a proapoptotic kinase and key mediator of apoptotic signaling and beta cell dysfunction and suggest that it may serve as target for the development of new therapies for diabetes.

The maize stripe virus major noncapsid protein messenger RNA transcripts contain heterogeneous leader sequences at their 5' termini.

PubMed

Huiet, L; Feldstein, P A; Tsai, J H; Falk, B W

1993-12-01

Primer extension analyses and a PCR-based cloning strategy were used to identify and characterize 5' nucleotide sequences on the maize stripe virus (MStV) RNA4 mRNA transcripts encoding the major noncapsid protein (NCP). Direct RNA sequence analysis by primer extension showed that the NCP mRNA transcripts had 10-15 nucleotides beyond the 5' terminus of the MStV RNA4 nucleotide sequence. MStV genomic RNAs isolated from ribonucleoprotein particles (RNPs) lacked the additional 5' nucleotides. cDNA clones representing the 5' region of the mRNA transcripts were constructed, and the nucleotide sequences of the 5' regions were determined for 16 clones. Each was found to have a distinct 10-15 nucleotide sequence immediately 5' of the MStV RNA4 sequence. Eleven of 16 clones had the correct MStV RNA4 5' nucleotide sequence, while five showed minor variations at or near the 5' most MStV RNA4 nucleotide. These characteristics show strong similarities to other viral mRNA transcripts which are synthesized by cap snatching.

Complexity Characteristics of Currency Networks

NASA Astrophysics Data System (ADS)

Gorski, A. Z.; Drozdz, S.; Kwapien, J.; Oswiecimka, P.

2006-11-01

A large set of daily FOREX time series is analyzed. The corresponding correlation matrices (CM) are constructed for USD, EUR and PLN used as the base currencies. The triangle rule is interpreted as constraints reducing the number of independent returns. The CM spectrum is computed and compared with the cases of shuffled currencies and a fictitious random currency taken as a base currency. The Minimal Spanning Tree (MST) graphs are calculated and the clustering effects for strong currencies are found. It is shown that for MSTs the node rank has power like, scale free behavior. Finally, the scaling exponents are evaluated and found in the range analogous to those identified recently for various complex networks.

Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera.

PubMed

Nguyen, Thuy Tuong; Slaughter, David C; Hanson, Bradley D; Barber, Andrew; Freitas, Amy; Robles, Daniel; Whelan, Erin

2015-07-28

This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera) and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration) required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1) an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2) a plant counting method based on projection histograms; and (3) a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images.

Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera

PubMed Central

Nguyen, Thuy Tuong; Slaughter, David C.; Hanson, Bradley D.; Barber, Andrew; Freitas, Amy; Robles, Daniel; Whelan, Erin

2015-01-01

This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera) and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration) required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1) an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2) a plant counting method based on projection histograms; and (3) a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images. PMID:26225982

Six-minute stepper test: a valid clinical exercise tolerance test for COPD patients

PubMed Central

Grosbois, JM; Riquier, C; Chehere, B; Coquart, J; Béhal, H; Bart, F; Wallaert, B; Chenivesse, C

2016-01-01

Introduction Exercise tolerance testing is an integral part of the pulmonary rehabilitation (PR) management of patients with chronic obstructive pulmonary disease (COPD). The 6-minute stepper test (6MST) is a new, well-tolerated, reproducible exercise test, which can be performed without any spatial constraints. Objective The aim of this study was to compare the results of the 6MST to those obtained during a 6-minute walk test (6MWT) and cardiopulmonary exercise testing (CPET) in a cohort of COPD patients. Methods Ninety-one COPD patients managed by outpatient PR and assessed by 6MST, 6MWT, and CPET were retrospectively included in this study. Correlations between the number of steps on the 6MST, the distance covered on the 6MWT, oxygen consumption, and power at the ventilatory threshold and at maximum effort during CPET were analyzed before starting PR, and the improvement on the 6MST and 6MWT was compared after PR. Results The number of steps on the 6MST was significantly correlated with the distance covered on the 6MWT (r=0.56; P<0.0001), the power at maximum effort (r=0.46; P<0.0001), and oxygen consumption at maximum effort (r=0.39; P<0.005). Performances on the 6MST and 6MWT were significantly improved after PR (570 vs 488 steps, P=0.001 and 448 vs 406 m, respectively; P<0.0001). Improvements of the 6MST and 6MWT after PR were significantly correlated (r=0.34; P=0.03). Conclusion The results of this study show that the 6MST is a valid test to evaluate exercise tolerance in COPD patients. The use of this test in clinical practice appears to be particularly relevant for the assessment of patients managed by home PR. PMID:27099483

Maximal strength training improves work economy, rate of force development and maximal strength more than conventional strength training.

PubMed

Heggelund, Jørn; Fimland, Marius S; Helgerud, Jan; Hoff, Jan

2013-06-01

This study compared maximal strength training (MST) with equal training volume (kg × sets × repetitions) of conventional strength training (CON) primarily with regard to work economy, and second one repetition maximum (1RM) and rate of force development (RFD) of single leg knee extension. In an intra-individual design, one leg was randomized to knee-extension MST (4 or 5RM) and the other leg to CON (3 × 10RM) three times per week for 8 weeks. MST was performed with maximal concentric mobilization of force while CON was performed with moderate velocity. Eight untrained or moderately trained men (26 ± 1 years) completed the study. The improvement in gross work economy was -0.10 ± 0.08 L min(-1) larger after MST (P = 0.011, between groups). From pre- to post-test the MST and CON improved net work economy with 31 % (P < 0.001) and 18 % (P = 0.01), respectively. Compared with CON, the improvement in 1RM and dynamic RFD was 13.7 ± 8.4 kg (P = 0.002) and 587 ± 679 N s(-1) (P = 0.044) larger after MST, whereas isometric RFD was of borderline significance 3,028 ± 3,674 N s(-1) (P = 0.053). From pre- to post-test, MST improved 1RM and isometric RFD with 50 % (P < 0.001) and 155 % (P < 0.001), respectively whereas CON improved 1RM and isometric RFD with 35 % (P < 0.001) and 83 % (P = 0.028), respectively. Anthropometric measures of quadriceps femoris muscle mass and peak oxygen uptake did not change. In conclusion, 8 weeks of MST was more effective than CON for improving work economy, 1RM and RFD in untrained and moderately trained men. The advantageous effect of MST to improve work economy could be due to larger improvements in 1RM and RFD.

Hippo/Yap signaling controls epithelial progenitor cell proliferation and differentiation in the embryonic and adult lung

PubMed Central

Lange, Alexander W.; Sridharan, Anusha; Xu, Yan; Stripp, Barry R.; Perl, Anne-Karina; Whitsett, Jeffrey A.

2015-01-01

The Hippo/Yap pathway is a well-conserved signaling cascade that regulates cell proliferation and differentiation to control organ size and stem/progenitor cell behavior. Following airway injury, Yap was dynamically regulated in regenerating airway epithelial cells. To determine the role of Hippo signaling in the lung, the mammalian Hippo kinases, Mst1 and Mst2, were deleted in epithelial cells of the embryonic and mature mouse lung. Mst1/2 deletion in the fetal lung enhanced proliferation and inhibited sacculation and epithelial cell differentiation. The transcriptional inhibition of cell proliferation and activation of differentiation during normal perinatal lung maturation were inversely regulated following embryonic Mst1/2 deletion. Ablation of Mst1/2 from bronchiolar epithelial cells in the adult lung caused airway hyperplasia and altered differentiation. Inhibitory Yap phosphorylation was decreased and Yap nuclear localization and transcriptional targets were increased after Mst1/2 deletion, consistent with canonical Hippo/Yap signaling. YAP potentiated cell proliferation and inhibited differentiation of human bronchial epithelial cells in vitro. Loss of Mst1/2 and expression of YAP regulated transcriptional targets controlling cell proliferation and differentiation, including Ajuba LIM protein. Ajuba was required for the effects of YAP on cell proliferation in vitro. Hippo/Yap signaling regulates Ajuba and controls proliferation and differentiation of lung epithelial progenitor cells. PMID:25480985

Hydrogen sulfide ameliorates subarachnoid hemorrhage-induced neuronal apoptosis via the ROS-MST1 pathway

PubMed Central

Shi, Ligen; Lei, Jianwei; Xu, Hangzhe; Zheng, Jingwei; Wang, Yan; Peng, Yucong; Yu, Jun; Zhang, Jianmin

2017-01-01

Background Hydrogen sulfide (H2S) has shown a neuroprotective role in several cerebrovascular diseases. This study aimed to explore the underlying mechanisms of H2S in early brain injury after subarachnoid hemorrhage (SAH). Methods One hundred seventy-seven male Sprague-Dawley rats were employed in this study. Sodium hydrosulfide (NaHS), a donor of H2S, was injected intraperitoneally at 60 min after SAH was induced by endovascular perforation. Western blot analysis determined the expression of several proteins of interest, and an immunofluorescence assay was used to examine neuronal apoptosis. Results Exogenous NaHS markedly improved neurological scores, attenuated brain edema, and ameliorated neuronal apoptosis at 24 h after SAH induction. The underlying mechanisms of H2S in ameliorating neuronal apoptosis might be executed through inhibition of the activity of mammalian sterile 20-like kinase 1 (MST1) protein. Western blot analysis demonstrated that exogenous NaHS decreased cleaved MST1 (cl-MST1) while increasing full-length MST1 expression. This anti-apoptotic effect of H2S could be reversed by chelerythrine, which could activate MST1 via caspase-dependent cleavage. Conclusions Exogenous NaHS, as a donor of H2S, could ameliorate early brain injury after SAH by inhibiting neuronal apoptosis by reducing the activity of the MST1 protein. PMID:29088725

Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide

PubMed Central

Hanaoka, Kenjiro; Sasakura, Kiyoshi; Suwanai, Yusuke; Toma-Fukai, Sachiko; Shimamoto, Kazuhito; Takano, Yoko; Shibuya, Norihiro; Terai, Takuya; Komatsu, Toru; Ueno, Tasuku; Ogasawara, Yuki; Tsuchiya, Yukihiro; Watanabe, Yasuo; Kimura, Hideo; Wang, Chao; Uchiyama, Masanobu; Kojima, Hirotatsu; Okabe, Takayoshi; Urano, Yasuteru; Shimizu, Toshiyuki; Nagano, Tetsuo

2017-01-01

Very recent studies indicate that sulfur atoms with oxidation state 0 or −1, called sulfane sulfurs, are the actual mediators of some physiological processes previously considered to be regulated by hydrogen sulfide (H2S). 3-Mercaptopyruvate sulfurtransferase (3MST), one of three H2S-producing enzymes, was also recently shown to produce sulfane sulfur (H2Sn). Here, we report the discovery of several potent 3MST inhibitors by means of high-throughput screening (HTS) of a large chemical library (174,118 compounds) with our H2S-selective fluorescent probe, HSip-1. Most of the identified inhibitors had similar aromatic ring-carbonyl-S-pyrimidone structures. Among them, compound 3 showed very high selectivity for 3MST over other H2S/sulfane sulfur-producing enzymes and rhodanese. The X-ray crystal structures of 3MST complexes with two of the inhibitors revealed that their target is a persulfurated cysteine residue located in the active site of 3MST. Precise theoretical calculations indicated the presence of a strong long-range electrostatic interaction between the persulfur anion of the persulfurated cysteine residue and the positively charged carbonyl carbon of the pyrimidone moiety of the inhibitor. Our results also provide the experimental support for the idea that the 3MST-catalyzed reaction with 3-mercaptopyruvate proceeds via a ping-pong mechanism. PMID:28079151

Electric field strength and focality in electroconvulsive therapy and magnetic seizure therapy: A finite element simulation study

PubMed Central

Deng, Zhi-De; Lisanby, Sarah H.; Peterchev, Angel V.

2014-01-01

We present the first computational study comparing the electric field induced by various electroconvulsive therapy (ECT) and magnetic seizure therapy (MST) paradigms. Four ECT electrode configurations (bilateral, bifrontal, right unilateral, and focal electrically administered seizure therapy) and three MST coil configurations (circular, cap, and double cone) were modeled. The model incorporated a modality-specific neural activation threshold. ECT (0.3 ms pulse width) and MST induced maximum electric field in the brain of 2.1–2.5 V/cm and 1.1–2.2 V/cm, corresponding to 6.2–7.2 times and 1.2–2.3 times the neural activation threshold, respectively. The MST electric field is more confined to the superficial cortex compared to ECT. The brain volume stimulated was much higher with ECT (up to 100%) than MST (up to 8.2%). MST with the double cone coil was the most focal and bilateral ECT was the least focal. Our results suggest a possible biophysical explanation of the reduced side effects of MST compared to ECT. Our results also indicate that the conventional ECT pulse amplitude (800–900 mA) is much higher than necessary for seizure induction. Reducing the ECT pulse amplitude should be explored as a potential means of diminishing side effects. PMID:21248385

Block-Based Connected-Component Labeling Algorithm Using Binary Decision Trees

PubMed Central

Chang, Wan-Yu; Chiu, Chung-Cheng; Yang, Jia-Horng

2015-01-01

In this paper, we propose a fast labeling algorithm based on block-based concepts. Because the number of memory access points directly affects the time consumption of the labeling algorithms, the aim of the proposed algorithm is to minimize neighborhood operations. Our algorithm utilizes a block-based view and correlates a raster scan to select the necessary pixels generated by a block-based scan mask. We analyze the advantages of a sequential raster scan for the block-based scan mask, and integrate the block-connected relationships using two different procedures with binary decision trees to reduce unnecessary memory access. This greatly simplifies the pixel locations of the block-based scan mask. Furthermore, our algorithm significantly reduces the number of leaf nodes and depth levels required in the binary decision tree. We analyze the labeling performance of the proposed algorithm alongside that of other labeling algorithms using high-resolution images and foreground images. The experimental results from synthetic and real image datasets demonstrate that the proposed algorithm is faster than other methods. PMID:26393597

An Investigation on Computer-Adaptive Multistage Testing Panels for Multidimensional Assessment

ERIC Educational Resources Information Center

Wang, Xinrui

2013-01-01

The computer-adaptive multistage testing (ca-MST) has been developed as an alternative to computerized adaptive testing (CAT), and been increasingly adopted in large-scale assessments. Current research and practice only focus on ca-MST panels for credentialing purposes. The ca-MST test mode, therefore, is designed to gauge a single scale. The…

29. DETAIL OF OUTLET DUCTS FOR MST AIRCONDITIONING SYSTEM IN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

29. DETAIL OF OUTLET DUCTS FOR MST AIR-CONDITIONING SYSTEM IN NORTHWEST CORNER OF SLC-3W MST STATION 70.5 (LOWEST PAYLOAD SERVICE STATION). NOTE RING ATTACHMENT FOR PERSONNEL SAFETY HARNESS IN LEFT FOREGROUND. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Propaganda, Collective Participation and the "War of Position" in the Brazilian Landless Workers' Movement

ERIC Educational Resources Information Center

Meek, David

2011-01-01

The Landless Workers' Movement (MST) is recognized as Brazil's most successful social movement. Although its goal is agrarian reform, the MST has been the subject of significant educational scholarship due to the emphasis it places on education reform, and formal and informal education. The MST's pedagogy has been extensively analysed. However,…

Changes in Maternal Depression Are Associated with MST Outcomes for Adolescents with Co-Occurring Externalizing and Internalizing Problems

ERIC Educational Resources Information Center

Grimbos, Teresa; Granic, Isabela

2009-01-01

The efficacy of Multisystemic therapy (MST) in treating adolescent aggression has been established, however, not all youth and their families benefit from MST. One reason for this treatment variability could be the failure to distinguish between different aggressive subtypes with different risk factors, developmental prognoses and treatment needs.…

A Comparison of IRT Proficiency Estimation Methods under Adaptive Multistage Testing

ERIC Educational Resources Information Center

Kim, Sooyeon; Moses, Tim; Yoo, Hanwook

2015-01-01

This inquiry is an investigation of item response theory (IRT) proficiency estimators' accuracy under multistage testing (MST). We chose a two-stage MST design that includes four modules (one at Stage 1, three at Stage 2) and three difficulty paths (low, middle, high). We assembled various two-stage MST panels (i.e., forms) by manipulating two…

14. VIEW OF MST, FACING SOUTHEAST, AND LAUNCH PAD TAKEN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. VIEW OF MST, FACING SOUTHEAST, AND LAUNCH PAD TAKEN FROM NORTHEAST PHOTO TOWER WITH WINDOW OPEN. FEATURES LEFT TO RIGHT: SOUTH TELEVISION CAMERA TOWER, SOUTHWEST PHOTO TOWER, LAUNCHER, UMBILICAL MAST, MST, AND OXIDIZER APRON. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Faster Bit-Parallel Algorithms for Unordered Pseudo-tree Matching and Tree Homeomorphism

NASA Astrophysics Data System (ADS)

Kaneta, Yusaku; Arimura, Hiroki

In this paper, we consider the unordered pseudo-tree matching problem, which is a problem of, given two unordered labeled trees P and T, finding all occurrences of P in T via such many-one embeddings that preserve node labels and parent-child relationship. This problem is closely related to tree pattern matching problem for XPath queries with child axis only. If m > w , we present an efficient algorithm that solves the problem in O(nm log(w)/w) time using O(hm/w + mlog(w)/w) space and O(m log(w)) preprocessing on a unit-cost arithmetic RAM model with addition, where m is the number of nodes in P, n is the number of nodes in T, h is the height of T, and w is the word length. We also discuss a modification of our algorithm for the unordered tree homeomorphism problem, which corresponds to a tree pattern matching problem for XPath queries with descendant axis only.

Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting

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

Azad, Ariful; Buluc, Aydn; Pothen, Alex

It is difficult to obtain high performance when computing matchings on parallel processors because matching algorithms explicitly or implicitly search for paths in the graph, and when these paths become long, there is little concurrency. In spite of this limitation, we present a new algorithm and its shared-memory parallelization that achieves good performance and scalability in computing maximum cardinality matchings in bipartite graphs. This algorithm searches for augmenting paths via specialized breadth-first searches (BFS) from multiple source vertices, hence creating more parallelism than single source algorithms. Algorithms that employ multiple-source searches cannot discard a search tree once no augmenting pathmore » is discovered from the tree, unlike algorithms that rely on single-source searches. We describe a novel tree-grafting method that eliminates most of the redundant edge traversals resulting from this property of multiple-source searches. We also employ the recent direction-optimizing BFS algorithm as a subroutine to discover augmenting paths faster. Our algorithm compares favorably with the current best algorithms in terms of the number of edges traversed, the average augmenting path length, and the number of iterations. Here, we provide a proof of correctness for our algorithm. Our NUMA-aware implementation is scalable to 80 threads of an Intel multiprocessor and to 240 threads on an Intel Knights Corner coprocessor. On average, our parallel algorithm runs an order of magnitude faster than the fastest algorithms available. The performance improvement is more significant on graphs with small matching number.« less

Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting

DOE PAGES

Azad, Ariful; Buluc, Aydn; Pothen, Alex

2016-03-24

It is difficult to obtain high performance when computing matchings on parallel processors because matching algorithms explicitly or implicitly search for paths in the graph, and when these paths become long, there is little concurrency. In spite of this limitation, we present a new algorithm and its shared-memory parallelization that achieves good performance and scalability in computing maximum cardinality matchings in bipartite graphs. This algorithm searches for augmenting paths via specialized breadth-first searches (BFS) from multiple source vertices, hence creating more parallelism than single source algorithms. Algorithms that employ multiple-source searches cannot discard a search tree once no augmenting pathmore » is discovered from the tree, unlike algorithms that rely on single-source searches. We describe a novel tree-grafting method that eliminates most of the redundant edge traversals resulting from this property of multiple-source searches. We also employ the recent direction-optimizing BFS algorithm as a subroutine to discover augmenting paths faster. Our algorithm compares favorably with the current best algorithms in terms of the number of edges traversed, the average augmenting path length, and the number of iterations. Here, we provide a proof of correctness for our algorithm. Our NUMA-aware implementation is scalable to 80 threads of an Intel multiprocessor and to 240 threads on an Intel Knights Corner coprocessor. On average, our parallel algorithm runs an order of magnitude faster than the fastest algorithms available. The performance improvement is more significant on graphs with small matching number.« less

A new algorithm to construct phylogenetic networks from trees.

PubMed

Wang, J

2014-03-06

Developing appropriate methods for constructing phylogenetic networks from tree sets is an important problem, and much research is currently being undertaken in this area. BIMLR is an algorithm that constructs phylogenetic networks from tree sets. The algorithm can construct a much simpler network than other available methods. Here, we introduce an improved version of the BIMLR algorithm, QuickCass. QuickCass changes the selection strategy of the labels of leaves below the reticulate nodes, i.e., the nodes with an indegree of at least 2 in BIMLR. We show that QuickCass can construct simpler phylogenetic networks than BIMLR. Furthermore, we show that QuickCass is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary.

The effect of epoch length on estimated EEG functional connectivity and brain network organisation

NASA Astrophysics Data System (ADS)

Fraschini, Matteo; Demuru, Matteo; Crobe, Alessandra; Marrosu, Francesco; Stam, Cornelis J.; Hillebrand, Arjan

2016-06-01

Objective. Graph theory and network science tools have revealed fundamental mechanisms of functional brain organization in resting-state M/EEG analysis. Nevertheless, it is still not clearly understood how several methodological aspects may bias the topology of the reconstructed functional networks. In this context, the literature shows inconsistency in the chosen length of the selected epochs, impeding a meaningful comparison between results from different studies. Approach. The aim of this study was to provide a network approach insensitive to the effects that epoch length has on functional connectivity and network reconstruction. Two different measures, the phase lag index (PLI) and the amplitude envelope correlation (AEC) were applied to EEG resting-state recordings for a group of 18 healthy volunteers using non-overlapping epochs with variable length (1, 2, 4, 6, 8, 10, 12, 14 and 16 s). Weighted clustering coefficient (CCw), weighted characteristic path length (L w) and minimum spanning tree (MST) parameters were computed to evaluate the network topology. The analysis was performed on both scalp and source-space data. Main results. Results from scalp analysis show a decrease in both mean PLI and AEC values with an increase in epoch length, with a tendency to stabilize at a length of 12 s for PLI and 6 s for AEC. Moreover, CCw and L w show very similar behaviour, with metrics based on AEC more reliable in terms of stability. In general, MST parameters stabilize at short epoch lengths, particularly for MSTs based on PLI (1-6 s versus 4-8 s for AEC). At the source-level the results were even more reliable, with stability already at 1 s duration for PLI-based MSTs. Significance. The present work suggests that both PLI and AEC depend on epoch length and that this has an impact on the reconstructed network topology, particularly at the scalp-level. Source-level MST topology is less sensitive to differences in epoch length, therefore enabling the comparison of brain network topology between different studies.

Efficient algorithms for a class of partitioning problems

NASA Technical Reports Server (NTRS)

Iqbal, M. Ashraf; Bokhari, Shahid H.

1990-01-01

The problem of optimally partitioning the modules of chain- or tree-like tasks over chain-structured or host-satellite multiple computer systems is addressed. This important class of problems includes many signal processing and industrial control applications. Prior research has resulted in a succession of faster exact and approximate algorithms for these problems. Polynomial exact and approximate algorithms are described for this class that are better than any of the previously reported algorithms. The approach is based on a preprocessing step that condenses the given chain or tree structured task into a monotonic chain or tree. The partitioning of this monotonic take can then be carried out using fast search techniques.

LEACHING OF TITANIUM FROM MONOSODIUM TITANATE AND MODIFIED MST

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

Taylor-Pashow, K.; Fondeur, F.; Fink, S.

2012-08-01

Analysis of a fouled coalescer and pre-filters from Actinide Removal Process/Modular Caustic Side Solvent Extraction Unit (ARP/MCU) operations showed evidence of Ti containing solids. Based on these results a series of tests were planned to examine the extent of Ti leaching from monosodium titanate (MST) and modified monosodium titanate (mMST) in various solutions. The solutions tested included a series of salt solutions with varying free hydroxide concentrations, two sodium hydroxide concentrations, 9 wt % and 15 wt %, nitric and oxalic acid solutions. Overall, the amount of Ti leached from the MST and mMST was much greater in the acidmore » solutions compared to the sodium hydroxide or salt solutions, which is consistent with the expected trend. The leaching data also showed that increasing hydroxide concentration, whether pure NaOH solution used for filter cleaning in ARP or the waste salt solution, increased the amount of Ti leached from both the MST and mMST. For the respective nominal contact times with the MST solids - for filter cleaning or the normal filter operation, the dissolved Ti concentrations are comparable suggesting either cause may contribute to the increased Ti fouling on the MCU coalescers. Tests showed that Ti containing solids could be precipitated from solution after the addition of scrub acid and a decrease in temperature similar to expected in MCU operations. FTIR analysis of these solids showed some similarity to the solids observed on the fouled coalescer and pre-filters. Although only a cursory study, this information suggests that the practice of increasing free hydroxide in feed solutions to MCU as a mitigation to aluminosilicate formation may be offset by the impact of formation of Ti solids in the overall process. Additional consideration of this finding from MCU and SWPF operation is warranted.« less

Prevalence and Mental Health Correlates of Insomnia in First-Encounter Veterans with and without Military Sexual Trauma.

PubMed

Jenkins, Melissa M; Colvonen, Peter J; Norman, Sonya B; Afari, Niloofar; Allard, Carolyn B; Drummond, Sean P A

2015-10-01

There is limited information about prevalence of insomnia in general populations of veterans of recent wars in Iraq and Afghanistan. No studies have examined insomnia in veterans with military sexual trauma (MST). We assess prevalence of insomnia, identify types of services sought by veterans with insomnia, and examine correlates of insomnia in veterans with and without MST. A cross-sectional study of first-encounter veterans registering to establish care. Veteran Affairs San Diego Healthcare System. Nine hundred seventeen veterans completed questionnaires assessing insomnia, MST, service needs, traumatic brain injury, resilience, and symptoms of depression, posttraumatic stress disorder (PTSD), pain, alcohol misuse, and hypomania. N/A. 53.1% of veterans without MST and 60.8% of veterans with MST had clinically significant insomnia symptoms, with the MST subsample reporting more severe symptoms, P < 0.05. Insomnia was more prevalent than depression, hypomania, PTSD, and substance misuse. Veterans with insomnia were more likely to seek care for physical health problems and primary care versus mental health concerns, P < 0.001. For the veteran sample without MST, age, combat service, traumatic brain injury, pain, and depression were associated with worse insomnia, P < 0.001. For the MST subsample, employment status, pain, and depression were associated with worse insomnia, P < 0.001. Study findings indicate a higher rate of insomnia in veterans compared to what has been found in the general population. Insomnia is more prevalent, and more severe, in veterans with military sexual trauma. Routine insomnia assessments and referrals to providers who can provide evidence-based treatment are crucial. © 2015 Associated Professional Sleep Societies, LLC.

Is nectar reabsorption restricted by the stalk cells of floral and extrafloral nectary trichomes?

PubMed

Cardoso-Gustavson, P; Davis, A R

2015-01-01

Reabsorption is a phase of nectar dynamics that occurs concurrently with secretion; it has been described in floral nectaries that exude nectar through stomata or unicellular trichomes, but has not yet been recorded in extrafloral glands. Apparently, nectar reabsorption does not occur in multicellular secretory trichomes (MST) due to the presence of lipophilic impregnations - which resemble Casparian strips - in the anticlinal walls of the stalk cells. It has been assumed that these impregnations restrict solute movement within MST to occur unidirectionally and exclusively by the symplast, thereby preventing nectar reflux toward the underlying nectary tissues. We hypothesised that reabsorption is absent in nectaries possessing MST. The fluorochrome lucifer yellow (LYCH) was applied to standing nectar of two floral and extrafloral glands of distantly related species, and then emission spectra from nectary sections were systematically analysed using confocal microscopy. Passive uptake of LYCH via the stalk cells to the nectary tissues occurred in all MST examined. Moreover, we present evidence of nectar reabsorption in extrafloral nectaries, demonstrating that LYCH passed the stalk cells of MST, although it did not reach the deepest nectary tissues. Identical (control) experiments performed with neutral red (NR) demonstrated no uptake of this stain by actively secreting MST, whereas diffusion of NR did occur in plasmolysed MST of floral nectaries at the post-secretory phase, indicating that nectar reabsorption by MST is governed by stalk cell physiology. Interestingly, non-secretory trichomes failed to reabsorb nectar. The role of various nectary components is discussed in relation to the control of nectar reabsorption by secretory trichomes. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Manual suction versus femtosecond laser trephination for penetrating keratoplasty: intraocular pressure, endothelial cell damage, incision geometry, and wound healing responses.

PubMed

Angunawela, Romesh I; Riau, Andri; Chaurasia, Shyam S; Tan, Donald T; Mehta, Jodhbir S

2012-05-04

To measure real-time intraocular pressure (IOP) during trephination with a manual suction trephine (MST) and the femtosecond laser (FSL), and to assess endothelial cell damage, incision geometry, and wound healing response with these procedures. IOP was monitored with an intracameral sensor. Eight rabbits underwent manual suction trephination. Eight rabbits had FSL trephination (FSL-T). Slit lamp photography, confocal microscopy, and anterior segment optical coherence tomography (AS-OCT) were performed at baseline and postoperatively. Animals were sacrificed at 4 hours and 3 days. Tissue was examined with scanning electron microscopy (SEM) and immunohistochemistry for an array of wound-healing markers. Separately, 6 human corneas had MST (3) and FSL-T (3). Incision geometry was imaged with high resolution Optovue AS-OCT. The average IOP during MST and FSL-T was similar (37 mm Hg). There was wider IOP fluctuation during the MST cutting phase (60 mm Hg maximum). There were 1-2 rows of endothelial loss on either side of the incision for FSL-T and 2-5 rows deep for MST. Immune cell responses at 4 hours (CD11b) were comparable, greater apoptosis with FSL-T (TUNEL) occurred at 4 hours, and there was increased keratocyte proliferation at 3 days (Ki67) with FSL-T. There was significantly greater undercutting of the cornea with MST (46.86 degrees versus 16.72 degrees). There is more IOP variation during MST. Average IOP is 37 mm Hg for both techniques. More endothelial damage and undercutting of the cornea occurs with MST. The wound healing response to FSL-T appears greater at 3 days.

The influence of military sexual trauma on returning OEF/OIF male veterans.

PubMed

Mondragon, Sasha A; Wang, David; Pritchett, Lonique; Graham, David P; Plasencia, M Leili; Teng, Ellen J

2015-11-01

Military sexual trauma (MST) encompasses experiences of sexual harassment and/or assault that occur during active duty military service. MST is associated with postdeployment mental health, interpersonal, and physical difficulties and appears to be more influential in the development of posttraumatic stress disorder (PTSD) than other active duty experiences, including combat, among women veterans. Although some literature suggests that men who experience MST also evidence significant postdeployment difficulties, research in this area is lacking. The current study evaluated a large sample of returning male veterans (N = 961) who served in Iraq and/or Afghanistan. Veterans were referred for treatment in a trauma and anxiety specialty clinic at a large VA hospital. Of this sample, 18% (n = 173) reported MST perpetrated by a member of their unit. Results indicated veterans who reported MST were younger (p = .001), less likely to be currently married (p < .001), more likely to be diagnosed with a mood disorder (p = .040), and more likely to have experienced non-MST sexual abuse either as children or adults (p < .001). Analyses revealed that MST was negatively associated with postdeployment social support (p < .001 and positively associated with postdeployment perceived emotional mistreatment (p = .004), but was not associated with postdeployment loss of romantic relationship (p = .264), job loss (p = .351), or unemployment (p = .741) after statistically controlling for other trauma exposures and current social support. Results reflect the detrimental associations of MST on male veterans and the need for more research in this area. These findings also highlight the need for treatment interventions that address social and interpersonal functioning in addition to symptoms of depressive disorders. (c) 2015 APA, all rights reserved).

Differences in Seizure Expression Between Magnetic Seizure Therapy and Electroconvulsive Shock.

PubMed

Cycowicz, Yael M; Rowny, Stefan B; Luber, Bruce; Lisanby, Sarah H

2018-06-01

Evidence suggests that magnetic seizure therapy (MST) results in fewer side effects than electroconvulsive treatment, both in humans treated with electroconvulsive therapy (ECT) as well as in the animal preclinical model that uses electroconvulsive shock (ECS). Evidence suggests that MST results in fewer cognitive side effects than ECT. Although MST offers enhanced control over seizure induction and spread, little is known about how MST and ECT seizures differ. Seizure characteristics are associated with treatment effect. This study presents quantitative analyses of electroencephalogram (EEG) power after electrical and magnetic seizure induction and anesthesia-alone sham in an animal model. The aim was to test whether differential neurophysiological characteristics of the seizures could be identified that support earlier observations that the powers of theta, alpha, and beta but not delta frequency bands were lower after MST when compared with those after ECS. In a randomized, sham-controlled trial, 24 macaca mulatte received 6 weeks of daily sessions while scalp EEG was recorded. Electroencephalogram power was quantified within delta, theta, alpha, and beta frequency bands. Magnetic seizure therapy induced lower ictal expression in the theta, alpha and beta frequencies than ECS, but MST and ECS were indistinguishable in the delta band. Magnetic seizure therapy showed less postictal suppression than ECS. Increasing electrical dosage increased ictal power, whereas increasing MST dosage had no effect on EEG expression. Magnetic seizure therapy seizures have less robust electrophysiological expression than ECS, and these differences are largest in the alpha and beta bands. The relevance of these differences in higher frequency bands to clinical outcomes deserves further exploration. Contrasting EEG in ECS and MST may lead to insights on the physiological underpinnings of seizure-induced amnesia and to finding ways to reduce cognitive side effects.

Post-translational regulation of mercaptopyruvate sulfurtransferase via a low redox potential cysteine-sulfenate in the maintenance of redox homeostasis.

PubMed

Nagahara, Noriyuki; Katayama, Akira

2005-10-14

3-Mercaptopyruvate sulfurtransferase (MST) (EC 2.8.1.2), a multifunctional enzyme, catalyzes a transsulfuration from mercaptopyruvate to pyruvate in the degradation process of cysteine. A stoichiometric concentration of hydrogen peroxide and of tetrathionate (S(4)O(6)(2-)) inhibited rat MST (k(i) = 3.3 min(-1), K(i) = 120.5 microM and k(i) = 2.5 min(-1), K(i) = 178.6 microM, respectively). The activity was completely restored by dithiothreitol or thioredoxin with a reducing system containing thioredoxin reductase and NADPH, but glutathione did not restore the activity. On the other hand, an excess molar ratio dose of hydrogen peroxide inactivated MST. Oxidation with a stoichiometric concentration of hydrogen peroxide protected the enzyme against reaction by iodoacetate, which modifies a catalytic Cys(247), suggesting that Cys(247) is a target of the oxidants. A matrix-assisted laser desorption/ionization-time-of-flight mass spectrometric analysis revealed that hydrogen peroxide- and tetrathionate-inhibited MSTs were increased in molecular mass consistent with the addition of atomic oxygen and with a thiosulfate (S(2)O(3)(-)), respectively. Treatment with dithiothreitol restored modified MST to the original mass. These findings suggested that there was no nearby cysteine with which to form a disulfide, and mild oxidation of MST resulted in formation of a sulfenate (SO(-)) at Cys(247), which exhibited exceptional stability and a lower redox potential than that of glutathione. Oxidative stress decreases MST activity so as to increase the amount of cysteine, a precursor of thioredoxin or glutathione, and furthermore, these cellular reductants restore the activity. Thus the redox state regulates MST activity at the enzymatic level, and on the other hand, MST controls redox to maintain cellular redox homeostasis.

The use of ECT and MST in treating depression.

PubMed

Allan, Charlotte L; Ebmeier, Klaus P

2011-10-01

Electroconvulsive therapy (ECT) has been used clinically since 1938. Its most common use is in the treatment of depression: first line treatment where rapid recovery is a priority, but more frequently as an effective treatment for patients who do not respond to pharmacological and psychological approaches. Whilst it is widely hailed as an effective treatment, concerns about its effect on cognition remain. The development of magnetic seizure therapy (MST) over the past decade has attempted to devise a therapy with comparable efficacy to ECT, but without the associated cognitive side effects. The rationale for this is that MST uses magnetic fields to induce seizures in the cortex, without electrical stimulation of brain structures involved with memory. MST has been used successfully in the treatment of depression, yet there is a dearth of literature in comparison with ECT. We present a systematic review of the literature on ECT (from 2009-2011) and MST (from 2001-2011).

Meta-cognitive skills training enhances computerized cognitive remediation outcomes among individuals with first-episode psychosis.

PubMed

Breitborde, Nicholas J K; Woolverton, Cindy; Dawson, Spencer C; Bismark, Andrew; Bell, Emily K; Bathgate, Christina J; Norman, Kaila

2017-06-01

Meta-cognitive skills training (MST) is a frequent component of cognitive remediation programmes for individuals with psychosis. However, no study has investigated whether incorporating such activities produces increased clinical benefits compared with computerized cognitive remediation alone. Individuals with first-episode psychosis who completed computerized cognitive remediation with concurrent meta-cognitive skills training (CCR + MST) were compared with a historical control group who received computerized cognitive remediation alone (CCR) and did not differ from the CCR + MST group with regard to pre-intervention cognition, diagnosis, age, duration of psychotic illness or sex. Participants completed assessments of cognition and real-world functioning before and after 6 months of treatment. Individual receiving CCR + MST experience greater gains in cognition and real-world functioning than individuals who received CCR. MST may be an important component within cognitive remediation programmes for first-episode psychosis. © 2015 Wiley Publishing Asia Pty Ltd.

Non-Invasive Imaging of Reactor Cores Using Cosmic Ray Muons

NASA Astrophysics Data System (ADS)

Milner, Edward

2011-10-01

Cosmic ray muons penetrate deeply in material, with some passing completely through very thick objects. This penetrating quality is the basis of two distinct, but related imaging techniques. The first measures the number of cosmic ray muons transmitted through parts of an object. Relatively fewer muons are absorbed along paths in which they encounter less material, compared to higher density paths, so the relative density of material is measured. This technique is called muon transmission imaging, and has been used to infer the density and structure of a variety of large masses, including mine overburden, volcanoes, pyramids, and buildings. In a second, more recently developed technique, the angular deflection of muons is measured by trajectory-tracking detectors placed on two opposing sides of an object. Muons are deflected more strongly by heavy nuclei, since multiple Coulomb scattering angle is approximately proportional to the nuclear charge. Therefore, a map showing regions of large deflection will identify the location of uranium in contrast to lighter nuclei. This technique is termed muon scattering tomography (MST) and has been developed to screen shipping containers for the presence of concealed nuclear material. Both techniques are a good way of non-invasively inspecting objects. A previously unexplored topic was applying MST to imaging large objects. Here we demonstrate extending the MST technique to the task of identifying relatively thick objects inside very thick shielding. We measured cosmic ray muons passing through a physical arrangement of material similar to a nuclear reactor, with thick concrete shielding and a heavy metal core. Newly developed algorithms were used to reconstruct an image of the ``mock reactor core,'' with resolution of approximately 30 cm.

Development of a novel omnidirectional magnetostrictive transducer for plate applications

NASA Astrophysics Data System (ADS)

Vinogradov, Sergey; Cobb, Adam; Bartlett, Jonathan; Udagawa, Youichi

2018-04-01

The application of guided waves for the testing of plate-type structures has been recently investigated by a number of research groups due to the ability of guided waves to detect corrosion in remote and hidden areas. Guided wave sensors for plate applications can be either directed (i.e., the waves propagate in a single direction) or omnidirectional. Each type has certain advantages and disadvantages. Omnidirectional sensors can inspect large areas from a single location, but it is challenging to define where a feature is located. Conversely, directed sensors can be used to precisely locate an indication, but have no sensitivity to flaws away from the wave propagation direction. This work describes a newly developed sensor that combines the strengths of both sensor types to create a novel omnidirectional transducer. The sensor transduction is based on a custom magnetostrictive transducer (MsT). In this new probe design, a directed, plate-application MsT with known characteristics was incorporated into an automated scanner. This scanner rotates the directed MsT for data collection at regular intervals. Coupling of the transducer to the plate is accomplished using a shear wave couplant. The array of data that is received is used for compiling B-scans and imaging, utilizing a synthetic aperture focusing algorithm (SAFT). The performance of the probe was evaluated on a 0.5-inch thick carbon steel plate mockup with a surface area of over 100 square feet. The mockup had a variety of known anomalies representing localized and distributed pitting corrosion, gradual wall thinning, and notches of different depths. Experimental data was also acquired using the new probe on a retired storage tank with known corrosion damage. The performance of the new sensor and its limitations are discussed together with general directions in technology development.

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

PubMed Central

2010-01-01

Background Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. Results We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. Conclusions GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events. PMID:20534164

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

PubMed

Thomas, Paul D

2010-06-09

Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.

Military sexual trauma among U.S. female veterans.

PubMed

Williams, Irene; Bernstein, Kunsook

2011-04-01

Sexual abuse among female veterans reportedly occurs in significant numbers in the U.S. military and has been recognized to cause posttraumatic stress disorder (PTSD). PTSD, which stems from sexual abuse, has been called military sexual trauma (MST), which has only recently been recognized by the Department of Defense. Consequently, there has been scant research on the prevalence, impact, and treatment of MST. This article explores the phenomenon of sexual aggression against female veterans in the U.S. military, risk factors for MST, PTSD as a result of MST, a conceptual framework for treating PTSD stress, and treatment strategies for PTSD. Published by Elsevier Inc.

Perceived barriers to care and provider gender preferences among veteran men who have experienced military sexual trauma: a qualitative analysis.

PubMed

Turchik, Jessica A; McLean, Caitlin; Rafie, Samantha; Hoyt, Tim; Rosen, Craig S; Kimerling, Rachel

2013-05-01

Research suggests that there may be unique barriers to accessing care among men who have experienced sexual trauma. The primary goal of the current research was to elucidate potential barriers to accessing military sexual trauma (MST)-related care for male veterans. A secondary goal was to explore whether veterans have preferences regarding the gender of clinicians providing MST-related care. Qualitative analyses were used to examine data collected from semistructured interviews conducted with 20 male veterans enrolled in Veterans Health Administration care who reported MST but who had not received any MST-related mental health care. Veterans identified a number of potential barriers, with the majority of reported barriers relating to issues of stigma and gender. Regarding provider gender preferences, veterans were mixed, with 50% preferring a female provider, 25% a male provider, and 25% reporting no gender preference. These preliminary data suggest that stigma, gender, and knowledge-related barriers may exist for men regarding seeking MST-related care. Interventions to address potential barriers, such as outreach interventions and providing gender-specific psychoeducation, may increase access to care for male veterans who report MST. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Test of “Facilitation” vs. “Proximal Process” Moderator Models for the Effects of Multisystemic Therapy on Adolescents with Severe Conduct Problem

PubMed Central

Weiss, Bahr; Han, Susan S.; Tran, Nam T.; Gallop, Robert; Ngo, Victoria K.

2014-01-01

The present study identified moderators of Multisystemic Therapy’s (MST) effects on adolescent conduct problems, considering “facilitation” and “proximal process” moderation models. The sample included 164 adolescents (mean age=14.6 years; 83% male) randomly assigned to receive MST or services as usual; parent, youth, and teacher reports of adolescent functioning were obtained. A number of significant moderators were identified. Proximal process moderation patterns were identified (e.g., families with parents with lower levels of adaptive child discipline skills gained more from MST), but the majority of significant interactions showed a facilitation moderation pattern with, for instance, higher levels of adaptive functioning in families and parents appearing to facilitate MST (i.e., greater benefits from MST were found for these families). This facilitation pattern may reflect such families being more capable of and/or more motivated to use the resources provided by MST. It is suggested that factors consistently identified as facilitation moderators may serve as useful foci for MST’s strength-based levers of change approach. Other implications of these findings for individualized treatment also are discussed. PMID:25387903

Hippo/Yap signaling controls epithelial progenitor cell proliferation and differentiation in the embryonic and adult lung.

PubMed

Lange, Alexander W; Sridharan, Anusha; Xu, Yan; Stripp, Barry R; Perl, Anne-Karina; Whitsett, Jeffrey A

2015-02-01

The Hippo/Yap pathway is a well-conserved signaling cascade that regulates cell proliferation and differentiation to control organ size and stem/progenitor cell behavior. Following airway injury, Yap was dynamically regulated in regenerating airway epithelial cells. To determine the role of Hippo signaling in the lung, the mammalian Hippo kinases, Mst1 and Mst2, were deleted in epithelial cells of the embryonic and mature mouse lung. Mst1/2 deletion in the fetal lung enhanced proliferation and inhibited sacculation and epithelial cell differentiation. The transcriptional inhibition of cell proliferation and activation of differentiation during normal perinatal lung maturation were inversely regulated following embryonic Mst1/2 deletion. Ablation of Mst1/2 from bronchiolar epithelial cells in the adult lung caused airway hyperplasia and altered differentiation. Inhibitory Yap phosphorylation was decreased and Yap nuclear localization and transcriptional targets were increased after Mst1/2 deletion, consistent with canonical Hippo/Yap signaling. YAP potentiated cell proliferation and inhibited differentiation of human bronchial epithelial cells in vitro. Loss of Mst1/2 and expression of YAP regulated transcriptional targets controlling cell proliferation and differentiation, including Ajuba LIM protein. Ajuba was required for the effects of YAP on cell proliferation in vitro. Hippo/Yap signaling regulates Ajuba and controls proliferation and differentiation of lung epithelial progenitor cells. © The Author (2014). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS. All rights reserved.

Emulating the Visual Receptive Field Properties of MST Neurons with a Template Model of Heading Estimation

NASA Technical Reports Server (NTRS)

Perrone, John A.; Stone, Leland S.

1997-01-01

We have previously proposed a computational neural-network model by which the complex patterns of retinal image motion generated during locomotion (optic flow) can be processed by specialized detectors acting as templates for specific instances of self-motion. The detectors in this template model respond to global optic flow by sampling image motion over a large portion of the visual field through networks of local motion sensors with properties similar to neurons found in the middle temporal (MT) area of primate extrastriate visual cortex. The model detectors were designed to extract self-translation (heading), self-rotation, as well as the scene layout (relative distances) ahead of a moving observer, and are arranged in cortical-like heading maps to perform this function. Heading estimation from optic flow has been postulated by some to be implemented within the medial superior temporal (MST) area. Others have questioned whether MST neurons can fulfill this role because some of their receptive-field properties appear inconsistent with a role in heading estimation. To resolve this issue, we systematically compared MST single-unit responses with the outputs of model detectors under matched stimulus conditions. We found that the basic physiological properties of MST neurons can be explained by the template model. We conclude that MST neurons are well suited to support heading estimation and that the template model provides an explicit set of testable hypotheses which can guide future exploration of MST and adjacent areas within the primate superior temporal sulcus.

New algorithm for lossless hyper-spectral image compression with mixing transform to eliminate redundancy

NASA Astrophysics Data System (ADS)

Xie, ChengJun; Xu, Lin

2008-03-01

This paper presents a new algorithm based on mixing transform to eliminate redundancy, SHIRCT and subtraction mixing transform is used to eliminate spectral redundancy, 2D-CDF(2,2)DWT to eliminate spatial redundancy, This transform has priority in hardware realization convenience, since it can be fully implemented by add and shift operation. Its redundancy elimination effect is better than (1D+2D)CDF(2,2)DWT. Here improved SPIHT+CABAC mixing compression coding algorithm is used to implement compression coding. The experiment results show that in lossless image compression applications the effect of this method is a little better than the result acquired using (1D+2D)CDF(2,2)DWT+improved SPIHT+CABAC, still it is much better than the results acquired by JPEG-LS, WinZip, ARJ, DPCM, the research achievements of a research team of Chinese Academy of Sciences, NMST and MST. Using hyper-spectral image Canal of American JPL laboratory as the data set for lossless compression test, on the average the compression ratio of this algorithm exceeds the above algorithms by 42%,37%,35%,30%,16%,13%,11% respectively.

iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure.

PubMed

Limpiti, Tulaya; Amornbunchornvej, Chainarong; Intarapanich, Apichart; Assawamakin, Anunchai; Tongsima, Sissades

2014-01-01

Understanding genetic differences among populations is one of the most important issues in population genetics. Genetic variations, e.g., single nucleotide polymorphisms, are used to characterize commonality and difference of individuals from various populations. This paper presents an efficient graph-based clustering framework which operates iteratively on the Neighbor-Joining (NJ) tree called the iNJclust algorithm. The framework uses well-known genetic measurements, namely the allele-sharing distance, the neighbor-joining tree, and the fixation index. The behavior of the fixation index is utilized in the algorithm's stopping criterion. The algorithm provides an estimated number of populations, individual assignments, and relationships between populations as outputs. The clustering result is reported in the form of a binary tree, whose terminal nodes represent the final inferred populations and the tree structure preserves the genetic relationships among them. The clustering performance and the robustness of the proposed algorithm are tested extensively using simulated and real data sets from bovine, sheep, and human populations. The result indicates that the number of populations within each data set is reasonably estimated, the individual assignment is robust, and the structure of the inferred population tree corresponds to the intrinsic relationships among populations within the data.

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

PubMed Central

Chen, Shaoping; Tu, Yi-Cheng; Xia, Yuni

2011-01-01

Many scientific and engineering fields produce large volume of spatiotemporal data. The storage, retrieval, and analysis of such data impose great challenges to database systems design. Analysis of scientific spatiotemporal data often involves computing functions of all point-to-point interactions. One such analytics, the Spatial Distance Histogram (SDH), is of vital importance to scientific discovery. Recently, algorithms for efficient SDH processing in large-scale scientific databases have been proposed. These algorithms adopt a recursive tree-traversing strategy to process point-to-point distances in the visited tree nodes in batches, thus require less time when compared to the brute-force approach where all pairwise distances have to be computed. Despite the promising experimental results, the complexity of such algorithms has not been thoroughly studied. In this paper, we present an analysis of such algorithms based on a geometric modeling approach. The main technique is to transform the analysis of point counts into a problem of quantifying the area of regions where pairwise distances can be processed in batches by the algorithm. From the analysis, we conclude that the number of pairwise distances that are left to be processed decreases exponentially with more levels of the tree visited. This leads to the proof of a time complexity lower than the quadratic time needed for a brute-force algorithm and builds the foundation for a constant-time approximate algorithm. Our model is also general in that it works for a wide range of point spatial distributions, histogram types, and space-partitioning options in building the tree. PMID:21804753

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

PubMed

Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

2017-04-01

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

PubMed Central

Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

2009-01-01

Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

An algorithm to count the number of repeated patient data entries with B tree.

PubMed

Okada, M; Okada, M

1985-04-01

An algorithm to obtain the number of different values that appear a specified number of times in a given data field of a given data file is presented. Basically, a well-known B-tree structure is employed in this study. Some modifications were made to the basic B-tree algorithm. The first step of the modifications is to allow a data item whose values are not necessary distinct from one record to another to be used as a primary key. When a key value is inserted, the number of previous appearances is counted. At the end of all the insertions, the number of key values which are unique in the tree, the number of key values which appear twice, three times, and so forth are obtained. This algorithm is especially powerful for a large size file in disk storage.

Wavelet tree structure based speckle noise removal for optical coherence tomography

NASA Astrophysics Data System (ADS)

Yuan, Xin; Liu, Xuan; Liu, Yang

2018-02-01

We report a new speckle noise removal algorithm in optical coherence tomography (OCT). Though wavelet domain thresholding algorithms have demonstrated superior advantages in suppressing noise magnitude and preserving image sharpness in OCT, the wavelet tree structure has not been investigated in previous applications. In this work, we propose an adaptive wavelet thresholding algorithm via exploiting the tree structure in wavelet coefficients to remove the speckle noise in OCT images. The threshold for each wavelet band is adaptively selected following a special rule to retain the structure of the image across different wavelet layers. Our results demonstrate that the proposed algorithm outperforms conventional wavelet thresholding, with significant advantages in preserving image features.

Using trees to compute approximate solutions to ordinary differential equations exactly

NASA Technical Reports Server (NTRS)

Grossman, Robert

1991-01-01

Some recent work is reviewed which relates families of trees to symbolic algorithms for the exact computation of series which approximate solutions of ordinary differential equations. It turns out that the vector space whose basis is the set of finite, rooted trees carries a natural multiplication related to the composition of differential operators, making the space of trees an algebra. This algebraic structure can be exploited to yield a variety of algorithms for manipulating vector fields and the series and algebras they generate.

Therapeutic effects of maximal strength training on walking efficiency in patients with schizophrenia - a pilot study.

PubMed

Heggelund, Jørn; Morken, Gunnar; Helgerud, Jan; Nilsberg, Geir E; Hoff, Jan

2012-07-03

Patients with schizophrenia frequently have disabling gait deficits. The net mechanical efficiency of walking (ϵnet) is an accurate measure often used to evaluate walking performance. Patients with gait deficits have a reduced ϵnet with excessive energy expenditure during sub-maximal walking. Maximal strength training (MST) improves ϵnet in healthy individuals and is associated with reduced risk of mortality. The aim of this study was to investigate whether MST improves ϵnet in patients with schizophrenia. Patients (ICD-10 schizophrenia, schizotypal or delusional disorders (F20-F29)) were included in a non-randomized trial. Patients were assigned to one of two groups: 1) MST consisting of 4x4 repetitions at 85-90% one repetition maximum (1RM) performed in a leg press apparatus or 2) playing computer games (CG). Both groups carried out their activity three days per week for eight weeks. 1RM, ϵnet at 60 watt walking, peak oxygen uptake (VO2peak), the Positive and Negative Syndrome Scale (PANSS) and the 36-items short form (SF-36) were measured pre and post intervention. The baseline ϵnet was 17.3 ± 1.2% and 19.4 ± 3.0% in the MST (n = 6) and CG groups (n = 7), respectively, which is categorized as mechanical inefficiency. The MST group improved 1RM by 79 kg (p = 0.006) and ϵnet by 3.4% (p = 0.046) more than the CG group. The MST group improved 1RM and ϵnet, by a mean of 83 kg (p = 0.028) and 3.4% (p = 0.028), respectively. VO2peak at baseline was 34.2 ± 10.2 and 38.3 ± 9.8 ml·kg-1·min-1 in the MST and CG groups, respectively, and did not change (p > 0.05). No change was observed in PANSS or SF-36 (p > 0.05). MST improves 1RM and ϵnet in patients with schizophrenia. MST could be used as a therapeutic intervention for patients with schizophrenia to normalize their reduced ϵnet.

Local applications of myostatin-siRNA with atelocollagen increase skeletal muscle mass and recovery of muscle function.

PubMed

Kawakami, Emi; Kawai, Nobuhiko; Kinouchi, Nao; Mori, Hiroyo; Ohsawa, Yutaka; Ishimaru, Naozumi; Sunada, Yoshihide; Noji, Sumihare; Tanaka, Eiji

2013-01-01

Growing evidence suggests that small-interfering RNA (siRNA) can promote gene silencing in mammalian cells without induction of interferon synthesis or nonspecific gene suppression. Recently, a number of highly specific siRNAs targeted against disease-causing or disease-promoting genes have been developed. In this study, we evaluate the effectiveness of atelocollagen (ATCOL)-mediated application of siRNA targeting myostatin (Mst), a negative regulator of skeletal muscle growth, into skeletal muscles of muscular dystrophy model mice. We injected a nanoparticle complex containing myostatin-siRNA and ATCOL (Mst-siRNA/ATCOL) into the masseter muscles of mutant caveolin-3 transgenic (mCAV-3Tg) mice, an animal model for muscular dystrophy. Scrambled (scr) -siRNA/ATCOL complex was injected into the contralateral muscles as a control. Two weeks after injection, the masseter muscles were dissected for histometric analyses. To investigate changes in masseter muscle activity by local administration of Mst-siRNA/ATCOL complex, mouse masseter electromyography (EMG) was measured throughout the experimental period via telemetry. After local application of the Mst-siRNA/ATCOL complex, masseter muscles were enlarged, while no significant change was observed on the contralateral side. Histological analysis showed that myofibrils of masseter muscles treated with the Mst-siRNA/ATCOL complex were significantly larger than those of the control side. Real-time PCR analysis revealed a significant downregulation of Mst expression in the treated masseters of mCAV-3Tg mice. In addition, expression of myogenic transcription factors was upregulated in the Mst-siRNA-treated masseter muscle, while expression of adipogenic transcription factors was significantly downregulated. EMG results indicate that masseter muscle activity in mCAV-3Tg mice was increased by local administration of the Mst-siRNA/ATCOL complex. These data suggest local administration of Mst-siRNA/ATCOL complex could lead to skeletal muscle hypertrophy and recovery of motor disability in mCAV-3Tg mice. Therefore, ATCOL-mediated application of siRNA is a potential tool for therapeutic use in muscular atrophy diseases.

Improved quantum backtracking algorithms using effective resistance estimates

NASA Astrophysics Data System (ADS)

Jarret, Michael; Wan, Kianna

2018-02-01

We investigate quantum backtracking algorithms of the type introduced by Montanaro (Montanaro, arXiv:1509.02374). These algorithms explore trees of unknown structure and in certain settings exponentially outperform their classical counterparts. Some of the previous work focused on obtaining a quantum advantage for trees in which a unique marked vertex is promised to exist. We remove this restriction by recharacterizing the problem in terms of the effective resistance of the search space. In this paper, we present a generalization of one of Montanaro's algorithms to trees containing k marked vertices, where k is not necessarily known a priori. Our approach involves using amplitude estimation to determine a near-optimal weighting of a diffusion operator, which can then be applied to prepare a superposition state with support only on marked vertices and ancestors thereof. By repeatedly sampling this state and updating the input vertex, a marked vertex is reached in a logarithmic number of steps. The algorithm thereby achieves the conjectured bound of O ˜(√{T Rmax }) for finding a single marked vertex and O ˜(k √{T Rmax }) for finding all k marked vertices, where T is an upper bound on the tree size and Rmax is the maximum effective resistance encountered by the algorithm. This constitutes a speedup over Montanaro's original procedure in both the case of finding one and the case of finding multiple marked vertices in an arbitrary tree.

Handbook for MAP, volume 32. Part 1: MAP summary. Part 2: MAPSC minutes, reading, August 1989. MAP summaries from nations. Part 3: MAP data catalogue

NASA Technical Reports Server (NTRS)

Vincent, R. A. (Editor); Edwards, B. (Editor); Hirota, I. (Editor)

1991-01-01

Extended abstracts from the fourth workshop on the technical and scientific aspects of mesosphere stratosphere troposphere (MST) radar are presented. Individual sessions addressed the following topics: meteorological applications of MST and ST radars, networks, and campaigns; the dynamics of the equatorial middle atmosphere; interpretation of radar returns from clear air; techniques for studying gravity waves and turbulence, intercomparison and calibration of wind and wave measurements at various frequencies; progress in existing and planned MST and ST radars; hardware design for MST and ST radars and boundary layer/lower troposphere profilers; signal processing; and data management.

Hierarchical structures of correlations networks among Turkey’s exports and imports by currencies

NASA Astrophysics Data System (ADS)

Kocakaplan, Yusuf; Deviren, Bayram; Keskin, Mustafa

2012-12-01

We have examined the hierarchical structures of correlations networks among Turkey’s exports and imports by currencies for the 1996-2010 periods, using the concept of a minimal spanning tree (MST) and hierarchical tree (HT) which depend on the concept of ultrametricity. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial markets. We derived a hierarchical organization and build the MSTs and HTs during the 1996-2001 and 2002-2010 periods. The reason for studying two different sub-periods, namely 1996-2001 and 2002-2010, is that the Euro (EUR) came into use in 2001, and some countries have made their exports and imports with Turkey via the EUR since 2002, and in order to test various time-windows and observe temporal evolution. We have carried out bootstrap analysis to associate a value of the statistical reliability to the links of the MSTs and HTs. We have also used the average linkage cluster analysis (ALCA) to observe the cluster structure more clearly. Moreover, we have obtained the bidimensional minimal spanning tree (BMST) due to economic trade being a bidimensional problem. From the structural topologies of these trees, we have identified different clusters of currencies according to their proximity and economic ties. Our results show that some currencies are more important within the network, due to a tighter connection with other currencies. We have also found that the obtained currencies play a key role for Turkey’s exports and imports and have important implications for the design of portfolio and investment strategies.

Uncertain decision tree inductive inference

NASA Astrophysics Data System (ADS)

Zarban, L.; Jafari, S.; Fakhrahmad, S. M.

2011-10-01

Induction is the process of reasoning in which general rules are formulated based on limited observations of recurring phenomenal patterns. Decision tree learning is one of the most widely used and practical inductive methods, which represents the results in a tree scheme. Various decision tree algorithms have already been proposed such as CLS, ID3, Assistant C4.5, REPTree and Random Tree. These algorithms suffer from some major shortcomings. In this article, after discussing the main limitations of the existing methods, we introduce a new decision tree induction algorithm, which overcomes all the problems existing in its counterparts. The new method uses bit strings and maintains important information on them. This use of bit strings and logical operation on them causes high speed during the induction process. Therefore, it has several important features: it deals with inconsistencies in data, avoids overfitting and handles uncertainty. We also illustrate more advantages and the new features of the proposed method. The experimental results show the effectiveness of the method in comparison with other methods existing in the literature.

Hierarchical Learning of Tree Classifiers for Large-Scale Plant Species Identification.

PubMed

Fan, Jianping; Zhou, Ning; Peng, Jinye; Gao, Ling

2015-11-01

In this paper, a hierarchical multi-task structural learning algorithm is developed to support large-scale plant species identification, where a visual tree is constructed for organizing large numbers of plant species in a coarse-to-fine fashion and determining the inter-related learning tasks automatically. For a given parent node on the visual tree, it contains a set of sibling coarse-grained categories of plant species or sibling fine-grained plant species, and a multi-task structural learning algorithm is developed to train their inter-related classifiers jointly for enhancing their discrimination power. The inter-level relationship constraint, e.g., a plant image must first be assigned to a parent node (high-level non-leaf node) correctly if it can further be assigned to the most relevant child node (low-level non-leaf node or leaf node) on the visual tree, is formally defined and leveraged to learn more discriminative tree classifiers over the visual tree. Our experimental results have demonstrated the effectiveness of our hierarchical multi-task structural learning algorithm on training more discriminative tree classifiers for large-scale plant species identification.

A fast bottom-up algorithm for computing the cut sets of noncoherent fault trees

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

Corynen, G.C.

1987-11-01

An efficient procedure for finding the cut sets of large fault trees has been developed. Designed to address coherent or noncoherent systems, dependent events, shared or common-cause events, the method - called SHORTCUT - is based on a fast algorithm for transforming a noncoherent tree into a quasi-coherent tree (COHERE), and on a new algorithm for reducing cut sets (SUBSET). To assure sufficient clarity and precision, the procedure is discussed in the language of simple sets, which is also developed in this report. Although the new method has not yet been fully implemented on the computer, we report theoretical worst-casemore » estimates of its computational complexity. 12 refs., 10 figs.« less

Learning Extended Finite State Machines

NASA Technical Reports Server (NTRS)

Cassel, Sofia; Howar, Falk; Jonsson, Bengt; Steffen, Bernhard

2014-01-01

We present an active learning algorithm for inferring extended finite state machines (EFSM)s, combining data flow and control behavior. Key to our learning technique is a novel learning model based on so-called tree queries. The learning algorithm uses the tree queries to infer symbolic data constraints on parameters, e.g., sequence numbers, time stamps, identifiers, or even simple arithmetic. We describe sufficient conditions for the properties that the symbolic constraints provided by a tree query in general must have to be usable in our learning model. We have evaluated our algorithm in a black-box scenario, where tree queries are realized through (black-box) testing. Our case studies include connection establishment in TCP and a priority queue from the Java Class Library.

RS-Forest: A Rapid Density Estimator for Streaming Anomaly Detection.

PubMed

Wu, Ke; Zhang, Kun; Fan, Wei; Edwards, Andrea; Yu, Philip S

Anomaly detection in streaming data is of high interest in numerous application domains. In this paper, we propose a novel one-class semi-supervised algorithm to detect anomalies in streaming data. Underlying the algorithm is a fast and accurate density estimator implemented by multiple fully randomized space trees (RS-Trees), named RS-Forest. The piecewise constant density estimate of each RS-tree is defined on the tree node into which an instance falls. Each incoming instance in a data stream is scored by the density estimates averaged over all trees in the forest. Two strategies, statistical attribute range estimation of high probability guarantee and dual node profiles for rapid model update, are seamlessly integrated into RS-Forest to systematically address the ever-evolving nature of data streams. We derive the theoretical upper bound for the proposed algorithm and analyze its asymptotic properties via bias-variance decomposition. Empirical comparisons to the state-of-the-art methods on multiple benchmark datasets demonstrate that the proposed method features high detection rate, fast response, and insensitivity to most of the parameter settings. Algorithm implementations and datasets are available upon request.

RS-Forest: A Rapid Density Estimator for Streaming Anomaly Detection

PubMed Central

Wu, Ke; Zhang, Kun; Fan, Wei; Edwards, Andrea; Yu, Philip S.

2015-01-01

Anomaly detection in streaming data is of high interest in numerous application domains. In this paper, we propose a novel one-class semi-supervised algorithm to detect anomalies in streaming data. Underlying the algorithm is a fast and accurate density estimator implemented by multiple fully randomized space trees (RS-Trees), named RS-Forest. The piecewise constant density estimate of each RS-tree is defined on the tree node into which an instance falls. Each incoming instance in a data stream is scored by the density estimates averaged over all trees in the forest. Two strategies, statistical attribute range estimation of high probability guarantee and dual node profiles for rapid model update, are seamlessly integrated into RS-Forest to systematically address the ever-evolving nature of data streams. We derive the theoretical upper bound for the proposed algorithm and analyze its asymptotic properties via bias-variance decomposition. Empirical comparisons to the state-of-the-art methods on multiple benchmark datasets demonstrate that the proposed method features high detection rate, fast response, and insensitivity to most of the parameter settings. Algorithm implementations and datasets are available upon request. PMID:25685112

GRAPE-6A: A Single-Card GRAPE-6 for Parallel PC-GRAPE Cluster Systems

NASA Astrophysics Data System (ADS)

Fukushige, Toshiyuki; Makino, Junichiro; Kawai, Atsushi

2005-12-01

In this paper, we describe the design and performance of GRAPE-6A, a special-purpose computer for gravitational many-body simulations. It was designed to be used with a PC cluster, in which each node has one GRAPE-6A. Such a configuration is particularly cost-effective in running parallel tree algorithms. Though the use of parallel tree algorithms was possible with the original GRAPE-6 hardware, it was not very cost-effective since a single GRAPE-6 board was still too fast and too expensive. Therefore, we designed GRAPE-6A as a single PCI card to minimize the reproduction cost and to optimize the computing speed. The peak performance is 130 Gflops for one GRAPE-6A board and 3.1 Tflops for our 24 node cluster. We describe the implementation of the tree, TreePM and individual timestep algorithms on both a single GRAPE-6A system and GRAPE-6A cluster. Using the tree algorithm on our 16-node GRAPE-6A system, we can complete a collisionless simulation with 100 million particles (8000 steps) within 10 days.

An Extension of CART's Pruning Algorithm. Program Statistics Research Technical Report No. 91-11.

ERIC Educational Resources Information Center

Kim, Sung-Ho

Among the computer-based methods used for the construction of trees such as AID, THAID, CART, and FACT, the only one that uses an algorithm that first grows a tree and then prunes the tree is CART. The pruning component of CART is analogous in spirit to the backward elimination approach in regression analysis. This idea provides a tool in…

CE: Military Sexual Trauma in Male Service Members.

PubMed

Eckerlin, Denise M; Kovalesky, Andrea; Jakupcak, Matthew

2016-09-01

: The experience of military sexual trauma (MST), which can result from assault, battery, or harassment of a sexual nature, may jeopardize the mental health of service members as well as that of their family members, colleagues, and community members. Although a greater proportion of female than male service members are subjected to MST, the Department of Defense estimates that the absolute numbers of affected men and women, across all ranks and branches of military service, are nearly equal because roughly 85% of military members are men. Little research has explored the effects of MST on men. This article discusses the unique ways in which men may experience MST, and examines how social stereotypes of masculinity, myths surrounding sexual assault, and military culture and structure often influence a man's interpretation of an attack and his likelihood of reporting the incident or seeking treatment. It describes current treatments for MST-related mental health conditions and addresses implications for nurses and other health care professionals.

Automatic creation of object hierarchies for ray tracing

NASA Technical Reports Server (NTRS)

Goldsmith, Jeffrey; Salmon, John

1987-01-01

Various methods for evaluating generated trees are proposed. The use of the hierarchical extent method of Rubin and Whitted (1980) to find the objects that will be hit by a ray is examined. This method employs tree searching; the construction of a tree of bounding volumes in order to determine the number of objects that will be hit by a ray is discussed. A tree generation algorithm, which uses a heuristic tree search strategy, is described. The effects of shuffling and sorting on the input data are investigated. The cost of inserting an object into the hierarchy during the construction of a tree algorithm is estimated. The steps involved in estimating the number of intersection calculations are presented.

Integrated Network Decompositions and Dynamic Programming for Graph Optimization (INDDGO)

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

The INDDGO software package offers a set of tools for finding exact solutions to graph optimization problems via tree decompositions and dynamic programming algorithms. Currently the framework offers serial and parallel (distributed memory) algorithms for finding tree decompositions and solving the maximum weighted independent set problem. The parallel dynamic programming algorithm is implemented on top of the MADNESS task-based runtime.

Learning accurate very fast decision trees from uncertain data streams

NASA Astrophysics Data System (ADS)

Liang, Chunquan; Zhang, Yang; Shi, Peng; Hu, Zhengguo

2015-12-01

Most existing works on data stream classification assume the streaming data is precise and definite. Such assumption, however, does not always hold in practice, since data uncertainty is ubiquitous in data stream applications due to imprecise measurement, missing values, privacy protection, etc. The goal of this paper is to learn accurate decision tree models from uncertain data streams for classification analysis. On the basis of very fast decision tree (VFDT) algorithms, we proposed an algorithm for constructing an uncertain VFDT tree with classifiers at tree leaves (uVFDTc). The uVFDTc algorithm can exploit uncertain information effectively and efficiently in both the learning and the classification phases. In the learning phase, it uses Hoeffding bound theory to learn from uncertain data streams and yield fast and reasonable decision trees. In the classification phase, at tree leaves it uses uncertain naive Bayes (UNB) classifiers to improve the classification performance. Experimental results on both synthetic and real-life datasets demonstrate the strong ability of uVFDTc to classify uncertain data streams. The use of UNB at tree leaves has improved the performance of uVFDTc, especially the any-time property, the benefit of exploiting uncertain information, and the robustness against uncertainty.

Application of electrically invisible antennas to the Modulated Scatterer Technique

DOE PAGES

Crocker, Dylan A.; Donnell, Kristen M.

2015-09-16

The modulated scatterer technique (MST) has shown promise for applications in microwave imaging, electric field mapping, and materials characterization. Traditionally, MST scatterers are dipoles centrally loaded with an element capable of modulation (e.g., a p-i-n diode). By modulating the load element, signals scattered from the MST scatterer are also modulated. However, due to the small size of such scatterers, it can be difficult to reliably detect the modulated signal. Increasing the modulation depth (MD; a parameter related to how well the scatterer modulates the scattered signal) may improve the detectability of the scattered signal. In an effort to improve themore » MD, the concept of electrically invisible antennas is applied to the design of MST scatterers. Our paper presents simulations and measurements of MST scatterers that have been designed to be electrically invisible during the reverse bias state of the modulated element (a p-i-n diode in this case), while producing detectable scattering during the forward bias state (i.e., operate in an electrically visible state). Furthermore, the results using the new design show significant improvement to the MD of the scattered signal as compared with a traditional MST scatterer (i.e., dipole centrally loaded with a p-i-n diode).« less

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

PubMed

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Enumeration of spanning trees in planar unclustered networks

NASA Astrophysics Data System (ADS)

Xiao, Yuzhi; Zhao, Haixing; Hu, Guona; Ma, Xiujuan

2014-07-01

Among a variety of subgraphs, spanning trees are one of the most important and fundamental categories. They are relevant to diverse aspects of networks, including reliability, transport, self-organized criticality, loop-erased random walks and so on. In this paper, we introduce a family of modular, self-similar planar networks with zero clustering. Relevant properties of this family are comparable to those networks associated with technological systems having low clustering, like power grids, some electronic circuits, the Internet and some biological systems. So, it is very significant to research on spanning trees of planar networks. However, for a large network, evaluating the relevant determinant is intractable. In this paper, we propose a fairly generic linear algorithm for counting the number of spanning trees of a planar network. Using the algorithm, we derive analytically the exact numbers of spanning trees in planar networks. Our result shows that the computational complexity is O(t) , which is better than that of the matrix tree theorem with O(m2t2) , where t is the number of steps and m is the girth of the planar network. We also obtain the entropy for the spanning trees of a given planar network. We find that the entropy of spanning trees in the studied network is small, which is in sharp contrast to the previous result for planar networks with the same average degree. We also determine an upper bound and a lower bound for the numbers of spanning trees in the family of planar networks by the algorithm. As another application of the algorithm, we give a formula for the number of spanning trees in an outerplanar network with small-world features.

Effects of electroconvulsive therapy and magnetic seizure therapy on acute memory retrieval.

PubMed

Polster, Julia D; Kayser, Sarah; Bewernick, Bettina H; Hurlemann, René; Schlaepfer, Thomas E

2015-03-01

Electroconvulsive therapy (ECT) is currently the most effective treatment for severe depression. However, it is frequently associated with negative cognitive side effects. Magnetic seizure therapy (MST) depicts an alternative, although experimental, convulsive treatment for major depression. Initial results suggest comparable antidepressant effects accompanied by a better side effect profile. However, no studies up to now have addressed acute retrieval disruption after MST in comparison to ECT. Therefore, we intended to broaden insight into the side effect profile of MST compared to ECT by examining the disruption of acute verbal memory processes after treatment. Twenty depressed patients were randomly assigned to either MST (10 patients) or ECT (10 patients) treatment. On 2 treatment days and 2 treatment-free days, the patients memorized words using a controlled learning paradigm derived from the Batchelder and Riefer storage retrieval model. Four hours after memorization, the patients were asked to retrieve words freely (delayed recall) and a second time with the help of an additional cue constructed out of a hypernymic category (cued recall). By comparing memory performance on treatment days to control days, treatment-induced memory disruption was evaluated. After ECT, delayed recall was disturbed, whereas after MST, it was not. However, this difference in performance was no longer apparent upon cue application (cued recall). This study demonstrates that ECT-induced acute memory disruption measured by delayed recall is absent after MST, confirming its superior side effect profile. We hope that confirming advantages of MST over ECT will improve therapy options for patients with severe depression.

Associations of military sexual trauma, combat exposure, and number of deployments with physical and mental health indicators in Iraq and Afghanistan veterans.

PubMed

Godfrey, Kathryn M; Mostoufi, Sheeva; Rodgers, Carie; Backhaus, Autumn; Floto, Elizabeth; Pittman, James; Afari, Niloofar

2015-11-01

Trauma exposure (TE) and numerous deployments have been associated with negative health outcomes in veterans, many of whom have military sexual trauma (MST) and combat exposure (CE). The aims of this study were to examine the relationships between physical and mental health symptoms with MST and CE and number of deployments. Iraq and Afghanistan veterans at the Veterans Affairs San Diego Healthcare System completed self-report measures for MST, CE, number of deployments, posttraumatic stress disorder (PTSD) symptoms, depression symptoms, alcohol use, somatic symptoms, health functioning, and body mass index (BMI). Regression analyses examined main and interaction effects of CE and MST and the linear and quadratic trends of number of deployments. The sample (N = 1,294) had a mean age of 31 and was 85% male. The MST by CE interaction on BMI was significant (p = .005), such that MST was associated with lower BMI in veterans with CE and with higher BMI in veterans without CE. MST and CE were associated with higher somatic, PTSD, and depression symptoms and with lower mental health functioning (ps < .001 to .002). CE was associated with lower physical health functioning and higher alcohol use (ps < .001 to .025). Number of deployments was linearly related to higher BMI (p = .004) and had a quadratic association with alcohol use (p = .008). Findings highlight the relationship between TE and poor health outcomes and the need to further study the mechanisms of TE on physical and mental health. (c) 2015 APA, all rights reserved).

Effect of Maxing Shigan Tang on H1N1 Influenza A Virus-Associated Acute Lung Injury in Mice.

PubMed

Zhong, Yanchun; Zhou, Jie; Liang, Ning; Liu, Bihao; Lu, Ruirui; He, Yu; Liang, Chunlin; Wu, Junbiao; Zhou, Yuan; Hu, Miaomiao; Zhou, Jiuyao

2016-01-01

This study is aimed at examining the effects of Maxing Shigan Tang (MST) treatment on H1N1-associated acute lung injury (ALI) and exploring the possible mechanism. Mice were randomly divided into a control group, model group, peroxisomal proliferator activator receptor γ (PPARγ) inhibition group (PPARγ-), PPARγ activation group (PPARγ+), and MST group. Influenza A (H1N1) virus of the Fort Monmouth 1 (FM1) strain was used to induce an ALI mice model. Hematoxylin and eosin staining was performed to investigate the effect of MST treatment on H1N1-associated ALI. Cell apoptosis of lung tissues of each group were conducted through transferase-mediated dUTP nick end-labeling methods. Moreover, the expression level of caspase 3, activity of caspase 3, and serum level of tumor necrosis factor (TNF)-α of each group were also analyzed. Finally, quantitative real-time polymerase chain reaction and Western blotting analysis were carried out to detect angiopoietin-like 4 (ANGPTL4) expression level. We found that mice infected with the FM1 strain of H1N1 influenza A virus developed severe ALI, and MST could improve H1N1-induced ALI. Moreover, MST decreased lung cell apoptosis and reduced the serum content of TNF-α. In addition, MST significantly induced the ANGPTL4 expression in H1N1-induced ALI. MST improves H1N1-associated ALI maybe through targeting ANGPTL4 in mice. © 2017 S. Karger AG, Basel.

Multisystemic Therapy and Functional Family Therapy Compared on their Effectiveness Using the Propensity Score Method.

PubMed

Eeren, Hester V; Goossens, Lucas M A; Scholte, Ron H J; Busschbach, Jan J V; van der Rijken, Rachel E A

2018-01-09

Multisystemic Therapy (MST) and Functional Family Therapy (FFT) have overlapping target populations and treatment goals. In this study, these interventions were compared on their effectiveness using a quasi-experimental design. Between October, 2009 and June, 2014, outcome data were collected from 697 adolescents (mean age 15.3 (SD 1.48), 61.9% male) assigned to either MST or FFT (422 MST; 275 FFT). Data were gathered during Routine Outcome Monitoring. The primary outcome was externalizing problem behavior (Child Behavior Checklist and Youth Self Report). Secondary outcomes were the proportion of adolescents living at home, engaged in school or work, and who lacked police contact during treatment. Because of the non-random assignment, a propensity score method was used to control for observed pre-treatment differences. Because the risk-need-responsivity (RNR) model guided treatment assignment, effectiveness was also estimated in youth with and without a court order as an indicator of their risk level. Looking at the whole sample, no difference in effect was found with regard to externalizing problems. For adolescents without a court order, effects on externalizing problems were larger after MST. Because many more adolescents with a court order were assigned to MST compared to FFT, the propensity score method could not balance the treatment groups in this subsample. In conclusion, few differences between MST and FFT were found. In line with the RNR model, higher risk adolescents were assigned to the more intensive treatment, namely MST. In the group with lower risk adolescents, this more intensive treatment was more effective in reducing externalizing problems.

Emulating the visual receptive-field properties of MST neurons with a template model of heading estimation

NASA Technical Reports Server (NTRS)

Perrone, J. A.; Stone, L. S.

1998-01-01

We have proposed previously a computational neural-network model by which the complex patterns of retinal image motion generated during locomotion (optic flow) can be processed by specialized detectors acting as templates for specific instances of self-motion. The detectors in this template model respond to global optic flow by sampling image motion over a large portion of the visual field through networks of local motion sensors with properties similar to those of neurons found in the middle temporal (MT) area of primate extrastriate visual cortex. These detectors, arranged within cortical-like maps, were designed to extract self-translation (heading) and self-rotation, as well as the scene layout (relative distances) ahead of a moving observer. We then postulated that heading from optic flow is directly encoded by individual neurons acting as heading detectors within the medial superior temporal (MST) area. Others have questioned whether individual MST neurons can perform this function because some of their receptive-field properties seem inconsistent with this role. To resolve this issue, we systematically compared MST responses with those of detectors from two different configurations of the model under matched stimulus conditions. We found that the characteristic physiological properties of MST neurons can be explained by the template model. We conclude that MST neurons are well suited to support self-motion estimation via a direct encoding of heading and that the template model provides an explicit set of testable hypotheses that can guide future exploration of MST and adjacent areas within the superior temporal sulcus.

Is military sexual trauma associated with trading sex among women veterans seeking outpatient mental health care?

PubMed

Strauss, Jennifer L; Marx, Christine E; Weitlauf, Julie C; Stechuchak, Karen M; Straits-Troster, Kristy; Worjoloh, Ayaba W; Sherrod, Christina B; Olsen, Maren K; Butterfield, Marian I; Calhoun, Patrick S

2011-01-01

A robust association between sexual trauma and trading sex has been documented in civilian samples but has not been examined in veterans. Women veterans experience high rates of sexual victimization across the lifespan, including during military service (military sexual trauma [MST]). Associations between MST and trading sex were examined in 200 women enrolled in a crosssectional study of HIV risks and seroprevalence among women receiving outpatient mental health care at a Veterans Affairs (VA) medical center. Each woman completed an assessment interview composed of validated measures that queried childhood sexual trauma; substance use; and risk behaviors, including trading sex for money, drugs, shelter, food, or other things. History of MST was derived from mandated VA screening results and chart notes. Overall, 19.7% reported a history of trading sex. Those who reported trading sex had a higher rate of MST than those who did not report trading sex (87.2% vs. 62.9%, respectively). A multivariable logistic regression model examined the relationship between trading sex and MST, controlling a priori for substance abuse and childhood sexual trauma (both associated with trading sex in civilian samples) and education, which was associated with trading sex in our sample. In this adjusted model, MST was associated with trading sex: odds ratio = 3.26, p = .025, 95% confidence interval = [1.16, 9.18]. To our knowledge, this is the 1st report of an association between MST and trading sex. Results extend previously observed associations between sexual trauma and trading sex in civilian cohorts and underscore the pernicious influence of sexual victimization across the lifespan.

Implementation of Data Mining to Analyze Drug Cases Using C4.5 Decision Tree

NASA Astrophysics Data System (ADS)

Wahyuni, Sri

2018-03-01

Data mining was the process of finding useful information from a large set of databases. One of the existing techniques in data mining was classification. The method used was decision tree method and algorithm used was C4.5 algorithm. The decision tree method was a method that transformed a very large fact into a decision tree which was presenting the rules. Decision tree method was useful for exploring data, as well as finding a hidden relationship between a number of potential input variables with a target variable. The decision tree of the C4.5 algorithm was constructed with several stages including the selection of attributes as roots, created a branch for each value and divided the case into the branch. These stages would be repeated for each branch until all the cases on the branch had the same class. From the solution of the decision tree there would be some rules of a case. In this case the researcher classified the data of prisoners at Labuhan Deli prison to know the factors of detainees committing criminal acts of drugs. By applying this C4.5 algorithm, then the knowledge was obtained as information to minimize the criminal acts of drugs. From the findings of the research, it was found that the most influential factor of the detainee committed the criminal act of drugs was from the address variable.

Differential Risk for Homelessness Among US Male and Female Veterans With a Positive Screen for Military Sexual Trauma.

PubMed

Brignone, Emily; Gundlapalli, Adi V; Blais, Rebecca K; Carter, Marjorie E; Suo, Ying; Samore, Matthew H; Kimerling, Rachel; Fargo, Jamison D

2016-06-01

Military sexual trauma (MST) is associated with adverse physical and mental health outcomes following military separation. Recent research suggests that MST may be a determinant in several factors associated with postdeployment homelessness. To evaluate MST as an independent risk factor for homelessness and to determine whether risk varies by sex. A retrospective cohort study of US veterans who used Veterans Health Administration (VHA) services between fiscal years 2004 and 2013 was conducted using administrative data from the Department of Defense and VHA. Included in the study were 601 892 US veterans deployed in Iraq or Afghanistan who separated from the military between fiscal years 2001 and 2011 and subsequently used VHA services. Positive response to screen for MST administered in VHA facilities. Administrative evidence of homelessness within 30 days, 1 year, and 5 years following the first VHA encounter after last deployment. The mean (SD) age of the 601 892 participants was 38.9 (9.4) years, 527 874 (87.7%) were male, 310 854 (51.6%) were white, and 382 361 (63.5%) were enlisted in the Army. Among veterans with a positive screen for MST, rates of homelessness were 1.6% within 30 days, 4.4% within 1 year, and 9.6% within 5 years, more than double the rates of veterans with a negative MST screen (0.7%, 1.8%, and 4.3%, respectively). A positive screen for MST was significantly and independently associated with postdeployment homelessness. In regression models adjusted for demographic and military service characteristics, odds of experiencing homelessness were higher among those who screened positive for MST compared with those who screened negative (30-day: adjusted odds ratio [AOR], 1.89; 95% CI, 1.58-2.24; 1-year: AOR, 2.27; 95% CI, 2.04-2.53; and 5-year: AOR, 2.63; 95% CI, 2.36-2.93). Military sexual trauma screen status remained independently associated with homelessness after adjusting for co-occurring mental health and substance abuse diagnoses in follow-up regression models (30-day: AOR, 1.62; 95% CI, 1.36-1.93; 1-year: AOR, 1.49; 95% CI, 1.33-1.66; and 5-year: AOR, 1.39; 95% CI, 1.24-1.55). In the fully adjusted models, the interaction between MST status and sex was significant in the 30-day and 1-year cohorts (30-day: AOR, 1.54; 95% CI, 1.18-2.02; and 1-year: AOR, 1.46; 95% CI, 1.23-1.74), denoting higher risk for homelessness among males with a positive screen for MST. A positive screen for MST was independently associated with postdeployment homelessness, with male veterans at greater risk than female veterans. These results underscore the importance of the MST screen as a clinically important marker of reintegration outcomes among veterans. These findings demonstrate significant long-term negative effects and inform our understanding of the public health implications of sexual abuse and harassment.

Live phylogeny with polytomies: Finding the most compact parsimonious trees.

PubMed

Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

2017-08-01

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Blooming Trees: Substructures and Surrounding Groups of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Yu, Heng; Diaferio, Antonaldo; Serra, Ana Laura; Baldi, Marco

2018-06-01

We develop the Blooming Tree Algorithm, a new technique that uses spectroscopic redshift data alone to identify the substructures and the surrounding groups of galaxy clusters, along with their member galaxies. Based on the estimated binding energy of galaxy pairs, the algorithm builds a binary tree that hierarchically arranges all of the galaxies in the field of view. The algorithm searches for buds, corresponding to gravitational potential minima on the binary tree branches; for each bud, the algorithm combines the number of galaxies, their velocity dispersion, and their average pairwise distance into a parameter that discriminates between the buds that do not correspond to any substructure or group, and thus eventually die, and the buds that correspond to substructures and groups, and thus bloom into the identified structures. We test our new algorithm with a sample of 300 mock redshift surveys of clusters in different dynamical states; the clusters are extracted from a large cosmological N-body simulation of a ΛCDM model. We limit our analysis to substructures and surrounding groups identified in the simulation with mass larger than 1013 h ‑1 M ⊙. With mock redshift surveys with 200 galaxies within 6 h ‑1 Mpc from the cluster center, the technique recovers 80% of the real substructures and 60% of the surrounding groups; in 57% of the identified structures, at least 60% of the member galaxies of the substructures and groups belong to the same real structure. These results improve by roughly a factor of two the performance of the best substructure identification algorithm currently available, the σ plateau algorithm, and suggest that our Blooming Tree Algorithm can be an invaluable tool for detecting substructures of galaxy clusters and investigating their complex dynamics.

Adversarial search by evolutionary computation.

PubMed

Hong, T P; Huang, K Y; Lin, W Y

2001-01-01

In this paper, we consider the problem of finding good next moves in two-player games. Traditional search algorithms, such as minimax and alpha-beta pruning, suffer great temporal and spatial expansion when exploring deeply into search trees to find better next moves. The evolution of genetic algorithms with the ability to find global or near global optima in limited time seems promising, but they are inept at finding compound optima, such as the minimax in a game-search tree. We thus propose a new genetic algorithm-based approach that can find a good next move by reserving the board evaluation values of new offspring in a partial game-search tree. Experiments show that solution accuracy and search speed are greatly improved by our algorithm.

Using laser altimetry-based segmentation to refine automated tree identification in managed forests of the Black Hills, South Dakota

Treesearch

Eric Rowell; Carl Selelstad; Lee Vierling; Lloyd Queen; Wayne Sheppard

2006-01-01

The success of a local maximum (LM) tree detection algorithm for detecting individual trees from lidar data depends on stand conditions that are often highly variable. A laser height variance and percent canopy cover (PCC) classification is used to segment the landscape by stand condition prior to stem detection. We test the performance of the LM algorithm using canopy...

3D Forest: An application for descriptions of three-dimensional forest structures using terrestrial LiDAR

PubMed Central

Krůček, Martin; Vrška, Tomáš; Král, Kamil

2017-01-01

Terrestrial laser scanning is a powerful technology for capturing the three-dimensional structure of forests with a high level of detail and accuracy. Over the last decade, many algorithms have been developed to extract various tree parameters from terrestrial laser scanning data. Here we present 3D Forest, an open-source non-platform-specific software application with an easy-to-use graphical user interface with the compilation of algorithms focused on the forest environment and extraction of tree parameters. The current version (0.42) extracts important parameters of forest structure from the terrestrial laser scanning data, such as stem positions (X, Y, Z), tree heights, diameters at breast height (DBH), as well as more advanced parameters such as tree planar projections, stem profiles or detailed crown parameters including convex and concave crown surface and volume. Moreover, 3D Forest provides quantitative measures of between-crown interactions and their real arrangement in 3D space. 3D Forest also includes an original algorithm of automatic tree segmentation and crown segmentation. Comparison with field data measurements showed no significant difference in measuring DBH or tree height using 3D Forest, although for DBH only the Randomized Hough Transform algorithm proved to be sufficiently resistant to noise and provided results comparable to traditional field measurements. PMID:28472167

EDNA: Expert fault digraph analysis using CLIPS

NASA Technical Reports Server (NTRS)

Dixit, Vishweshwar V.

1990-01-01

Traditionally fault models are represented by trees. Recently, digraph models have been proposed (Sack). Digraph models closely imitate the real system dependencies and hence are easy to develop, validate and maintain. However, they can also contain directed cycles and analysis algorithms are hard to find. Available algorithms tend to be complicated and slow. On the other hand, the tree analysis (VGRH, Tayl) is well understood and rooted in vast research effort and analytical techniques. The tree analysis algorithms are sophisticated and orders of magnitude faster. Transformation of a digraph (cyclic) into trees (CLP, LP) is a viable approach to blend the advantages of the representations. Neither the digraphs nor the trees provide the ability to handle heuristic knowledge. An expert system, to capture the engineering knowledge, is essential. We propose an approach here, namely, expert network analysis. We combine the digraph representation and tree algorithms. The models are augmented by probabilistic and heuristic knowledge. CLIPS, an expert system shell from NASA-JSC will be used to develop a tool. The technique provides the ability to handle probabilities and heuristic knowledge. Mixed analysis, some nodes with probabilities, is possible. The tool provides graphics interface for input, query, and update. With the combined approach it is expected to be a valuable tool in the design process as well in the capture of final design knowledge.

Applying Data Mining Techniques to Extract Hidden Patterns about Breast Cancer Survival in an Iranian Cohort Study.

PubMed

Khalkhali, Hamid Reza; Lotfnezhad Afshar, Hadi; Esnaashari, Omid; Jabbari, Nasrollah

2016-01-01

Breast cancer survival has been analyzed by many standard data mining algorithms. A group of these algorithms belonged to the decision tree category. Ability of the decision tree algorithms in terms of visualizing and formulating of hidden patterns among study variables were main reasons to apply an algorithm from the decision tree category in the current study that has not studied already. The classification and regression trees (CART) was applied to a breast cancer database contained information on 569 patients in 2007-2010. The measurement of Gini impurity used for categorical target variables was utilized. The classification error that is a function of tree size was measured by 10-fold cross-validation experiments. The performance of created model was evaluated by the criteria as accuracy, sensitivity and specificity. The CART model produced a decision tree with 17 nodes, 9 of which were associated with a set of rules. The rules were meaningful clinically. They showed in the if-then format that Stage was the most important variable for predicting breast cancer survival. The scores of accuracy, sensitivity and specificity were: 80.3%, 93.5% and 53%, respectively. The current study model as the first one created by the CART was able to extract useful hidden rules from a relatively small size dataset.

Creating ensembles of oblique decision trees with evolutionary algorithms and sampling

DOEpatents

Cantu-Paz, Erick [Oakland, CA; Kamath, Chandrika [Tracy, CA

2006-06-13

A decision tree system that is part of a parallel object-oriented pattern recognition system, which in turn is part of an object oriented data mining system. A decision tree process includes the step of reading the data. If necessary, the data is sorted. A potential split of the data is evaluated according to some criterion. An initial split of the data is determined. The final split of the data is determined using evolutionary algorithms and statistical sampling techniques. The data is split. Multiple decision trees are combined in ensembles.

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm.

PubMed

Majumdar, Satya N

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm

NASA Astrophysics Data System (ADS)

Majumdar, Satya N.

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

A Semi-Automated Machine Learning Algorithm for Tree Cover Delineation from 1-m Naip Imagery Using a High Performance Computing Architecture

NASA Astrophysics Data System (ADS)

Basu, S.; Ganguly, S.; Nemani, R. R.; Mukhopadhyay, S.; Milesi, C.; Votava, P.; Michaelis, A.; Zhang, G.; Cook, B. D.; Saatchi, S. S.; Boyda, E.

2014-12-01

Accurate tree cover delineation is a useful instrument in the derivation of Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) satellite imagery data. Numerous algorithms have been designed to perform tree cover delineation in high to coarse resolution satellite imagery, but most of them do not scale to terabytes of data, typical in these VHR datasets. In this paper, we present an automated probabilistic framework for the segmentation and classification of 1-m VHR data as obtained from the National Agriculture Imagery Program (NAIP) for deriving tree cover estimates for the whole of Continental United States, using a High Performance Computing Architecture. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field (CRF), which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by incorporating expert knowledge through the relabeling of misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the state of California, which covers a total of 11,095 NAIP tiles and spans a total geographical area of 163,696 sq. miles. Our framework produced correct detection rates of around 85% for fragmented forests and 70% for urban tree cover areas, with false positive rates lower than 3% for both regions. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR high-resolution canopy height model shows the effectiveness of our algorithm in generating accurate high-resolution tree cover maps.

The efficacy of prospective memory rehabilitation plus metacognitive skills training for adults with traumatic brain injury: study protocol for a randomized controlled trial.

PubMed

Fleming, Jennifer; Ownsworth, Tamara; Doig, Emmah; Hutton, Lauren; Griffin, Janelle; Kendall, Melissa; Shum, David H K

2017-01-05

Impairment of prospective memory (PM) is common following traumatic brain injury (TBI) and negatively impacts on independent living. Compensatory approaches to PM rehabilitation have been found to minimize the impact of PM impairment in adults with TBI; however, poor self-awareness after TBI poses a major barrier to the generalization of compensatory strategies in daily life. Metacognitive skills training (MST) is a cognitive rehabilitation approach that aims to facilitate the development of self-awareness in adults with TBI. This paper describes the protocol of a study that aims to evaluate the efficacy of a MST approach to compensatory PM rehabilitation for improving everyday PM performance and psychosocial outcomes after TBI. This randomized controlled trial has three treatment groups: compensatory training plus metacognitive skills training (COMP-MST), compensatory training only (COMP), and waitlist control. Participants in the COMP-MST and COMP groups will complete a 6-week intervention consisting of six 2-h weekly training sessions. Each 1.5-h session will involve compensatory strategy training and 0.5 h will incorporate either MST (COMP-MST group) or filler activity as an active control (COMP group). Participants in the waitlist group receive care as usual for 6 weeks, followed by the COMP-MST intervention. Based on the sample size estimate, 90 participants with moderate to severe TBI will be randomized into the three groups using a stratified sampling approach. The primary outcomes include measures of PM performance in everyday life and level of psychosocial reintegration. Secondary outcomes include measures of PM function on psychometric testing, strategy use, self-awareness, and level of support needs following TBI. Blinded assessments will be conducted pre and post intervention, and at 3-month and 6-month follow-ups. This study seeks to determine the efficacy of COMP-MST for improving and maintaining everyday PM performance and level of psychosocial integration in adults with moderate to severe TBI. The findings will advance theoretical understanding of the role of self-awareness in compensatory PM rehabilitation and skills generalization. COMP-MST has the potential to reduce the cost of rehabilitation and lifestyle support following TBI because the intervention could enhance generalization success and lifelong application of PM compensatory strategies. New Zealand Clinical Trials Registry, ACTRN12615000996561 . Registered on 23 September 2015; retrospectively registered 2 months after commencement.

Multisystemic Therapy for social, emotional, and behavioral problems in youth aged 10-17.

PubMed

Littell, J H; Popa, M; Forsythe, B

2005-10-19

Multisystemic Therapy (MST) is an intensive, home-based intervention for families of youth with social, emotional, and behavioral problems. Masters-level therapists engage family members in identifying and changing individual, family, and environmental factors thought to contribute to problem behavior. Intervention may include efforts to improve communication, parenting skills, peer relations, school performance, and social networks. Most MST trials were conducted by program developers in the USA; results of one independent trial are available and others are in progress. To provide unbiased estimates of the impacts of MST on restrictive out-of-home living arrangements, crime and delinquency, and other behavioral and psychosocial outcomes for youth and families. Electronic searches were made of bibliographic databases (including the Cochrane Library, C2-SPECTR, PsycINFO, Science Direct and Sociological Abstracts) as well as government and professional websites, from 1985 to January 2003. Reference lists of articles were examined, and experts were contacted. Studies where youth (age 10-17) with social, emotional, and/or behavioral problems were randomised to licensed MST programs or other conditions (usual services or alternative treatments). Two reviewers independently reviewed 266 titles and abstracts; 95 full-text reports were retrieved, and 35 unique studies were identified. Two reviewers independently read all study reports for inclusion. Eight studies were eligible for inclusion. Two reviewers independently assessed study quality and extracted data from these studies. Significant heterogeneity among studies was identified (assessed using Chi-square and I(2)), hence random effects models were used to pool data across studies. Odds ratios were used in analyses of dichotomous outcomes; standardised mean differences were used with continuous outcomes. Adjustments were made for small sample sizes (using Hedges g). Pooled estimates were weighted with inverse variance methods, and 95% confidence intervals were used. The most rigorous (intent-to-treat) analysis found no significant differences between MST and usual services in restrictive out-of-home placements and arrests or convictions. Pooled results that include studies with data of varying quality tend to favor MST, but these relative effects are not significantly different from zero. The study sample size is small and effects are not consistent across studies; hence, it is not clear whether MST has clinically significant advantages over other services. There is inconclusive evidence of the effectiveness of MST compared with other interventions with youth. There is no evidence that MST has harmful effects.

Use of low density lipoprotein particle number levels as an aid in statin treatment decisions for intermediate risk patients: a cost-effectiveness analysis.

PubMed

Shiffman, Dov; Arellano, Andre R; Caulfield, Michael P; Louie, Judy Z; Bare, Lance A; Devlin, James J; Melander, Olle

2016-12-07

The 2013 ACC/AHA guideline recommended either no statin therapy or moderate-intensity statin therapy (MST) for intermediate risk patients-those with 5-7.5% 10-year risk and without cardiovascular disease (CVD), hypercholesterolemia or diabetes. The guideline further suggested that the therapy choice be based on patient-clinician discussions of risks and benefits. Since low-density lipoprotein particle (LDL-P) levels were reported to be associated with CVD independently of traditional risk factors in intermediate and low risk patients, we investigated the cost-effectiveness of using LDL-P levels to identify intermediate risk patients likely to benefit from initiating or intensifying statin therapy. We evaluated 5 care strategies for intermediate risk patients. These included the strategies suggested by the guideline: no-statin therapy and MST. We compared each of these strategies to a related strategy that incorporated LDL-P testing. No-statin therapy was compared with the strategy of MST for those with high LDL-P levels and no statin therapy for all other patients (test-and-MST). MST was compared with the strategy of high-intensity statin therapy (HST) for those with high LDL-P levels and MST for all other patients (test-and-HST). We also evaluated the strategy of HST for all. Costs (payer perspective) and utilities were assessed over a 5-year time horizon in a Markov model of 100,000 hypothetical intermediate risk patients. HST dominated all other strategies, costing less and-despite causing 739 more cases of diabetes than did MST-resulting in more quality adjusted life-years (QALYs). For patient-clinician discussions that would otherwise lead to the MST strategy, we found the test-and-HST strategy reduced costs by $4.67 MM and resulted in 134 fewer CVD events and 115 additional QALYs. For patient-clinician discussions that would otherwise lead to no statin therapy, we found that the test-and-MST strategy reduced costs by $3.25 MM, resulted in 97 fewer CVD events and 44 additional QALYs. The HST strategy was cost saving and improved outcomes in intermediate risk patients. For patient and clinicians concerned about the adverse events associated with HST, using LDL-P levels to target intensified statin therapy could improve outcomes and reduce costs.

A New Algorithm Using the Non-Dominated Tree to Improve Non-Dominated Sorting.

PubMed

Gustavsson, Patrik; Syberfeldt, Anna

2018-01-01

Non-dominated sorting is a technique often used in evolutionary algorithms to determine the quality of solutions in a population. The most common algorithm is the Fast Non-dominated Sort (FNS). This algorithm, however, has the drawback that its performance deteriorates when the population size grows. The same drawback applies also to other non-dominating sorting algorithms such as the Efficient Non-dominated Sort with Binary Strategy (ENS-BS). An algorithm suggested to overcome this drawback is the Divide-and-Conquer Non-dominated Sort (DCNS) which works well on a limited number of objectives but deteriorates when the number of objectives grows. This article presents a new, more efficient algorithm called the Efficient Non-dominated Sort with Non-Dominated Tree (ENS-NDT). ENS-NDT is an extension of the ENS-BS algorithm and uses a novel Non-Dominated Tree (NDTree) to speed up the non-dominated sorting. ENS-NDT is able to handle large population sizes and a large number of objectives more efficiently than existing algorithms for non-dominated sorting. In the article, it is shown that with ENS-NDT the runtime of multi-objective optimization algorithms such as the Non-Dominated Sorting Genetic Algorithm II (NSGA-II) can be substantially reduced.

New Hybrid Algorithms for Estimating Tree Stem Diameters at Breast Height Using a Two Dimensional Terrestrial Laser Scanner

PubMed Central

Kong, Jianlei; Ding, Xiaokang; Liu, Jinhao; Yan, Lei; Wang, Jianli

2015-01-01

In this paper, a new algorithm to improve the accuracy of estimating diameter at breast height (DBH) for tree trunks in forest areas is proposed. First, the information is collected by a two-dimensional terrestrial laser scanner (2DTLS), which emits laser pulses to generate a point cloud. After extraction and filtration, the laser point clusters of the trunks are obtained, which are optimized by an arithmetic means method. Then, an algebraic circle fitting algorithm in polar form is non-linearly optimized by the Levenberg-Marquardt method to form a new hybrid algorithm, which is used to acquire the diameters and positions of the trees. Compared with previous works, this proposed method improves the accuracy of diameter estimation of trees significantly and effectively reduces the calculation time. Moreover, the experimental results indicate that this method is stable and suitable for the most challenging conditions, which has practical significance in improving the operating efficiency of forest harvester and reducing the risk of causing accidents. PMID:26147726

Efficient Delaunay Tessellation through K-D Tree Decomposition

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

Morozov, Dmitriy; Peterka, Tom

Delaunay tessellations are fundamental data structures in computational geometry. They are important in data analysis, where they can represent the geometry of a point set or approximate its density. The algorithms for computing these tessellations at scale perform poorly when the input data is unbalanced. We investigate the use of k-d trees to evenly distribute points among processes and compare two strategies for picking split points between domain regions. Because resulting point distributions no longer satisfy the assumptions of existing parallel Delaunay algorithms, we develop a new parallel algorithm that adapts to its input and prove its correctness. We evaluatemore » the new algorithm using two late-stage cosmology datasets. The new running times are up to 50 times faster using k-d tree compared with regular grid decomposition. Moreover, in the unbalanced data sets, decomposing the domain into a k-d tree is up to five times faster than decomposing it into a regular grid.« less

Recursive optimal pruning with applications to tree structured vector quantizers

NASA Technical Reports Server (NTRS)

Kiang, Shei-Zein; Baker, Richard L.; Sullivan, Gary J.; Chiu, Chung-Yen

1992-01-01

A pruning algorithm of Chou et al. (1989) for designing optimal tree structures identifies only those codebooks which lie on the convex hull of the original codebook's operational distortion rate function. The authors introduce a modified version of the original algorithm, which identifies a large number of codebooks having minimum average distortion, under the constraint that, in each step, only modes having no descendents are removed from the tree. All codebooks generated by the original algorithm are also generated by this algorithm. The new algorithm generates a much larger number of codebooks in the middle- and low-rate regions. The additional codebooks permit operation near the codebook's operational distortion rate function without time sharing by choosing from the increased number of available bit rates. Despite the statistical mismatch which occurs when coding data outside the training sequence, these pruned codebooks retain their performance advantage over full search vector quantizers (VQs) for a large range of rates.

A faster 1.375-approximation algorithm for sorting by transpositions.

PubMed

Cunha, Luís Felipe I; Kowada, Luis Antonio B; Hausen, Rodrigo de A; de Figueiredo, Celina M H

2015-11-01

Sorting by Transpositions is an NP-hard problem for which several polynomial-time approximation algorithms have been developed. Hartman and Shamir (2006) developed a 1.5-approximation [Formula: see text] algorithm, whose running time was improved to O(nlogn) by Feng and Zhu (2007) with a data structure they defined, the permutation tree. Elias and Hartman (2006) developed a 1.375-approximation O(n(2)) algorithm, and Firoz et al. (2011) claimed an improvement to the running time, from O(n(2)) to O(nlogn), by using the permutation tree. We provide counter-examples to the correctness of Firoz et al.'s strategy, showing that it is not possible to reach a component by sufficient extensions using the method proposed by them. In addition, we propose a 1.375-approximation algorithm, modifying Elias and Hartman's approach with the use of permutation trees and achieving O(nlogn) time.

A Methodology for the Integration of a Mechanistic Source Term Analysis in a Probabilistic Framework for Advanced Reactors

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

Grabaskas, Dave; Brunett, Acacia J.; Bucknor, Matthew

GE Hitachi Nuclear Energy (GEH) and Argonne National Laboratory are currently engaged in a joint effort to modernize and develop probabilistic risk assessment (PRA) techniques for advanced non-light water reactors. At a high level, the primary outcome of this project will be the development of next-generation PRA methodologies that will enable risk-informed prioritization of safety- and reliability-focused research and development, while also identifying gaps that may be resolved through additional research. A subset of this effort is the development of PRA methodologies to conduct a mechanistic source term (MST) analysis for event sequences that could result in the release ofmore » radionuclides. The MST analysis seeks to realistically model and assess the transport, retention, and release of radionuclides from the reactor to the environment. The MST methods developed during this project seek to satisfy the requirements of the Mechanistic Source Term element of the ASME/ANS Non-LWR PRA standard. The MST methodology consists of separate analysis approaches for risk-significant and non-risk significant event sequences that may result in the release of radionuclides from the reactor. For risk-significant event sequences, the methodology focuses on a detailed assessment, using mechanistic models, of radionuclide release from the fuel, transport through and release from the primary system, transport in the containment, and finally release to the environment. The analysis approach for non-risk significant event sequences examines the possibility of large radionuclide releases due to events such as re-criticality or the complete loss of radionuclide barriers. This paper provides details on the MST methodology, including the interface between the MST analysis and other elements of the PRA, and provides a simplified example MST calculation for a sodium fast reactor.« less

Six-minute Stepper Test to Set Pulmonary Rehabilitation Intensity in Patients with COPD - A Retrospective Study.

PubMed

Bonnevie, Tristan; Gravier, Francis-Edouard; Leboullenger, Marie; Médrinal, Clément; Viacroze, Catherine; Cuvelier, Antoine; Muir, Jean-François; Tardif, Catherine; Debeaumont, David

2017-06-01

Pulmonary rehabilitation (PR) improves outcomes in patients with chronic obstructive pulmonary disease (COPD). Optimal assessment includes cardiopulmonary exercise testing (CPET), but consultations are limited. Field tests could be used to individualize PR instead of CPET. The six-minute stepper test (6MST) is easy to set up and its sensitivity and reproducibility have previously been reported in patients with COPD. The aim of this study was to develop a prediction equation to set intensity in patients attending PR, based on the 6MST. The following relationships were analyzed: mean heart rate (HR) during the first (HR 1-3 ) and last (HR 4-6 ) 3 minutes of the 6MST and HR at the ventilatory threshold (HRvt) from CPET; step count at the end of the 6MST and workload at the Ventilatory threshold (VT) (Wvt); and forced expiratory volume in 1 second and step count during the 6MST. This retrospective study included patients with COPD referred for PR who underwent CPET, pulmonary function evaluations and the 6MST. Twenty-four patients were included. Prediction equations were HRvt = 0.7887 × HR 1-3 + 20.83 and HRvt = 0.6180 × HR 4-6 + 30.77. There was a strong correlation between HR 1-3 and HR 4-6 and HRvt (r = 0.69, p < 0.001 and r = 0.57, p < 0.01 respectively). A significant correlation was also found between step count and LogWvt (r = 0.63, p < 0.01). The prediction equation was LogWvt = 0.001722 × step count + 1.248. The 6MST could be used to individualize aerobic training in patients with COPD. Further prospective studies are needed to confirm these results.

Application of electrically invisible antennas to the modulated scatterer technique

NASA Astrophysics Data System (ADS)

Crocker, Dylan Andrew

The Modulated Scatterer Technique (MST) has shown promise for applications in microwave imaging, electric field mapping, and materials characterization. Traditionally, MST scatterers consist of dipole antennas centrally loaded with a lumped element capable of modulation (commonly a PIN diode). By modulating the load element, the signal scattered from the MST scatterer is also modulated. However, due to the small size of such scatterers, it can be difficult to reliably detect the modulated signal. Increasing the modulation depth (a parameter related to how well the scatterer modulates the scattered signal) may improve the detectability of the scattered signal. In an effort to improve the modulation depth of scatterers commonly used in MST, the concept of electrically invisible antennas is applied to the design of these scatterers and is the focus of this work. Electrical invisibility of linear antennas, such as loaded dipoles, can be achieved by loading a scatterer in such a way that, when illuminated by an electromagnetic wave, the integral of the current induced along the length of the scatterer (and hence the scattered field as well) approaches zero. By designing a scatterer to be capable of modulation between visible (scattering) and invisible (minimum scattering) states, the modulation depth may be improved. This thesis presents simulations and measurements of new MST scatterers that have been designed to be electrically invisible during the reverse bias state of the modulated element (i.e., a PIN diode). Further, the scattering during the forward bias state remains the same as that of a traditional MST scatterer, resulting in an increase in modulation depth. This new MST scatterer design technique may also have application in improving the performance of similar sensors such as radio frequency identification (RFID) tags.

Military sexual trauma is associated with post-deployment eating disorders among Afghanistan and Iraq veterans.

PubMed

Blais, Rebecca K; Brignone, Emily; Maguen, Shira; Carter, Marjorie E; Fargo, Jamison D; Gundlapalli, Adi V

2017-07-01

Evaluate the association of military sexual trauma (MST) screen status with eating disorder diagnoses among veterans within 1- and 5-years after initiating Veterans Health Administration (VHA) care, and whether the association varied by sex. Retrospective cohort study of US Afghanistan/Iraq veterans who used VHA services between FY 2004 and 2014 (N = 595,525). This study used VHA administrative data to assess the presence of eating disorder diagnoses in medical records within 1- and 5-years of initiating VHA care, and whether a positive screen for MST was associated with eating disorders. Three percent (n = 18,488) screened positive for MST. At 1- and 5-year follow up, 0.1% (n= 513, 74% female), and 0.2% (n = 504, 71% female) were diagnosed with an eating disorder, respectively. In regression models adjusted for demographic variables, military service, and psychiatric comorbidities, the presence of an eating disorder diagnosis was nearly two times higher among those with a positive screen for MST in the 1-year (adjusted odds ratio [AOR] = 1.94, 95% confidence interval [CI] = 1.57-2.40) and 5-year (AOR = 1.86, 95%CI = 1.49-2.32) cohorts. The increased likelihood conferred by MST for an eating disorder diagnosis was differentially stronger among male veterans than female veterans in the 1-year cohort only (AOR = 2.13, 95%CI = 1.01-4.50). Veterans with a positive screen for MST, especially male veterans, had a nearly two-fold increased likelihood of having an eating disorder diagnosis. Screening for eating disorders may be important in both male and female veterans who report MST. © 2017 Wiley Periodicals, Inc.

Nuclear criticality safety bounding analysis for the in-tank-precipitation (ITP) process, impacted by fissile isotopic weight fractions

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

Bess, C.E.

The In-Tank Precipitation process (ITP) receives High Level Waste (HLW) supernatant liquid containing radionuclides in waste processing tank 48H. Sodium tetraphenylborate, NaTPB, and monosodium titanate (MST), NaTi{sub 2}O{sub 5}H, are added for removal of radioactive Cs and Sr, respectively. In addition to removal of radio-strontium, MST will also remove plutonium and uranium. The majority of the feed solutions to ITP will come from the dissolution of supernate that had been concentrated by evaporation to a crystallized salt form, commonly referred to as saltcake. The concern for criticality safety arises from the adsorption of U and Pt onto MST. If sufficientmore » mass and optimum conditions are achieved then criticality is credible. The concentration of u and Pt from solution into the smaller volume of precipitate represents a concern for criticality. This report supplements WSRC-TR-93-171, Nuclear Criticality Safety Bounding Analysis For The In-Tank-Precipitation (ITP) Process. Criticality safety in ITP can be analyzed by two bounding conditions: (1) the minimum safe ratio of MST to fissionable material and (2) the maximum fissionable material adsorption capacity of the MST. Calculations have provided the first bounding condition and experimental analysis has established the second. This report combines these conditions with canyon facility data to evaluate the potential for criticality in the ITP process due to the adsorption of the fissionable material from solution. In addition, this report analyzes the potential impact of increased U loading onto MST. Results of this analysis demonstrate a greater safety margin for ITP operations than the previous analysis. This report further demonstrates that the potential for criticality in the ITP process due to adsorption of fissionable material by MST is not credible.« less

Contraceptive Provision in the VA Healthcare System to Women Who Report Military Sexual Trauma

PubMed Central

Mattocks, Kristin; Schwarz, Eleanor Bimla; Borrero, Sonya; Skanderson, Melissa; Zephyrin, Laurie; Brandt, Cynthia; Haskell, Sally

2014-01-01

Abstract Background: Women Veterans who suffered military sexual trauma (MST) may be at high risk for unintended pregnancy and benefit from contraceptive services. The objective of this study is to compare documented provision of contraceptives to women Veterans using the Department of Veterans Affairs (VA) health system who report or deny MST. Methods: This retrospective cohort study included women Veterans aged 18–45 years who served in Operation Enduring or Iraqi Freedom and had at least one visit to a VA medical center between 2002 and 2010. Data were obtained from VA administrative and clinical databases. Chi-squared tests and logistic regression were conducted to evaluate the association between MST, ascertained by routine clinical screening, and first documented receipt of hormonal or long-acting contraception. Results: Of 68,466 women Veterans, 13% reported, 59% denied and 28% had missing data for the MST screen. Among the entire study cohort, 30% of women had documented receipt of a contraceptive method. Women reporting MST were significantly more likely than those denying MST to receive a method of contraception (adjusted odds ratio [aOR] 1.12, 95% confidence interval [CI] 1.07–1.18) including an intrauterine device (odds ratio [OR] 1.29, 95% CI 1.17–1.41) or contraceptive injection (OR 1.17, 95% CI 1.05–1.29). Women who were younger, unmarried, seen at a women's health clinic, or who had more than one visit were more likely to receive contraception. Conclusions: A minority of women Veterans of reproductive age receive contraceptive services from the VA. Women Veterans who report MST, and particularly those who seek care at VA women's health clinics, are more likely to receive contraception. PMID:24787680

Improvement of 10-km time-trial cycling with motivational self-talk compared with neutral self-talk.

PubMed

Barwood, Martin J; Corbett, Jo; Wagstaff, Christopher R D; McVeigh, Dan; Thelwell, Richard C

2015-03-01

Unpleasant physical sensations during maximal exercise may manifest themselves as negative cognitions that impair performance, alter pacing, and are linked to increased rating of perceived exertion (RPE). This study examined whether motivational self-talk (M-ST) could reduce RPE and change pacing strategy, thereby enhancing 10-km time-trial (TT) cycling performance in contrast to neutral self-talk (N-ST). Fourteen men undertook 4 TTs, TT1-TT4. After TT2, participants were matched into groups based on TT2 completion time and underwent M-ST (n=7) or N-ST (n=7) after TT3. Performance, power output, RPE, and oxygen uptake (VO2) were compared across 1-km segments using ANOVA. Confidence intervals (95%CI) were calculated for performance data. After TT3 (ie, before intervention), completion times were not different between groups (M-ST, 1120±113 s; N-ST, 1150±110 s). After M-ST, TT4 completion time was faster (1078±96 s); the N-ST remained similar (1165±111 s). The M-ST group achieved this through a higher power output and VO2 in TT4 (6th-10th km). RPE was unchanged. CI data indicated the likely true performance effect lay between 13- and 71-s improvement (TT4 vs TT3). M-ST improved endurance performance and enabled a higher power output, whereas N-ST induced no change. The VO2 response matched the increase in power output, yet RPE was unchanged, thereby inferring a perceptual benefit through M-ST. The valence and content of self-talk are important determinants of the efficacy of this intervention. These findings are primarily discussed in the context of the psychobiological model of pacing.

Application of the pessimistic pruning to increase the accuracy of C4.5 algorithm in diagnosing chronic kidney disease

NASA Astrophysics Data System (ADS)

Muslim, M. A.; Herowati, A. J.; Sugiharti, E.; Prasetiyo, B.

2018-03-01

A technique to dig valuable information buried or hidden in data collection which is so big to be found an interesting patterns that was previously unknown is called data mining. Data mining has been applied in the healthcare industry. One technique used data mining is classification. The decision tree included in the classification of data mining and algorithm developed by decision tree is C4.5 algorithm. A classifier is designed using applying pessimistic pruning in C4.5 algorithm in diagnosing chronic kidney disease. Pessimistic pruning use to identify and remove branches that are not needed, this is done to avoid overfitting the decision tree generated by the C4.5 algorithm. In this paper, the result obtained using these classifiers are presented and discussed. Using pessimistic pruning shows increase accuracy of C4.5 algorithm of 1.5% from 95% to 96.5% in diagnosing of chronic kidney disease.

Disentangling neural processes of egocentric and allocentric mental spatial transformations using whole-body photos of self and other.

PubMed

Ganesh, Shanti; van Schie, Hein T; Cross, Emily S; de Lange, Floris P; Wigboldus, Daniël H J

2015-08-01

Mental imagery of one's body moving through space is important for imagining changing visuospatial perspectives, as well as for determining how we might appear to other people. Previous neuroimaging research has implicated the temporoparietal junction (TPJ) in this process. It is unclear, however, how neural activity in the TPJ relates to the rotation perspectives from which mental spatial transformation (MST) of one's own body can take place, i.e. from an egocentric or an allocentric perspective. It is also unclear whether TPJ involvement in MST is self-specific or whether the TPJ may also be involved in MST of other human bodies. The aim of the current study was to disentangle neural processes involved in egocentric versus allocentric MSTs of human bodies representing self and other. We measured functional brain activity of healthy participants while they performed egocentric and allocentric MSTs in relation to whole-body photographs of themselves and a same-sex stranger. Findings indicated higher blood oxygen level-dependent (BOLD) response in bilateral TPJ during egocentric versus allocentric MST. Moreover, BOLD response in the TPJ during egocentric MST correlated positively with self-report scores indicating how awkward participants felt while viewing whole-body photos of themselves. These findings considerably advance our understanding of TPJ involvement in MST and its interplay with self-awareness. Copyright © 2015 Elsevier Inc. All rights reserved.

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

C-semiring Frameworks for Minimum Spanning Tree Problems

NASA Astrophysics Data System (ADS)

Bistarelli, Stefano; Santini, Francesco

In this paper we define general algebraic frameworks for the Minimum Spanning Tree problem based on the structure of c-semirings. We propose general algorithms that can compute such trees by following different cost criteria, which must be all specific instantiation of c-semirings. Our algorithms are extensions of well-known procedures, as Prim or Kruskal, and show the expressivity of these algebraic structures. They can deal also with partially-ordered costs on the edges.

PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at the inhibitory site

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

Jung, Sujin; Kang, Jeong Gu; Lee, Ju Hee

2014-01-24

Highlights: • PHLPP1 regulates contact inhibition by dephosphorylating Mst1 at Thr{sup 387}. • Overexpression of PHLPP1 sensitizes contact inhibition. • Tumor cells with suppressed PHLPP1 expression are refractory to apoptosis and highly proliferative. • Loss or down-regulation of PHLPP1 may drive tumor development and progression. - Abstract: Contact inhibition has been largely elusive despite that a loss of contact inhibition is a critical event for cancer development and progression. Here, we report that PHLPP1 is a binding protein for Mst1 and it modulates the Hippo pathway by dephosphorylating Mst1 at the inhibitory Thr{sup 387} of Mst1. Yap1 was localized predominantlymore » in the nucleus but marginally in the cytoplasm in HeLa cells under sparse conditions, whereas the functional protein was more directed to sequestration in the cytoplasm under dense environments. Furthermore, loss of PHLPP1 resulted in a failure of the apoptotic control. It is interesting that down-regulated expression of PHLPP1 appears to mimic the loss of contact inhibition, a hallmark of cancer.« less

Evaluating Mobile Survey Tools (MSTs) for Field-Level Monitoring and Data Collection: Development of a Novel Evaluation Framework, and Application to MSTs for Rural Water and Sanitation Monitoring

PubMed Central

Fisher, Michael B.; Mann, Benjamin H.; Cronk, Ryan D.; Shields, Katherine F.; Klug, Tori L.; Ramaswamy, Rohit

2016-01-01

Information and communications technologies (ICTs) such as mobile survey tools (MSTs) can facilitate field-level data collection to drive improvements in national and international development programs. MSTs allow users to gather and transmit field data in real time, standardize data storage and management, automate routine analyses, and visualize data. Dozens of diverse MST options are available, and users may struggle to select suitable options. We developed a systematic MST Evaluation Framework (EF), based on International Organization for Standardization/International Electrotechnical Commission (ISO/IEC) software quality modeling standards, to objectively assess MSTs and assist program implementers in identifying suitable MST options. The EF is applicable to MSTs for a broad variety of applications. We also conducted an MST user survey to elucidate needs and priorities of current MST users. Finally, the EF was used to assess seven MSTs currently used for water and sanitation monitoring, as a validation exercise. The results suggest that the EF is a promising method for evaluating MSTs. PMID:27563916

Evaluating Mobile Survey Tools (MSTs) for Field-Level Monitoring and Data Collection: Development of a Novel Evaluation Framework, and Application to MSTs for Rural Water and Sanitation Monitoring.

PubMed

Fisher, Michael B; Mann, Benjamin H; Cronk, Ryan D; Shields, Katherine F; Klug, Tori L; Ramaswamy, Rohit

2016-08-23

Information and communications technologies (ICTs) such as mobile survey tools (MSTs) can facilitate field-level data collection to drive improvements in national and international development programs. MSTs allow users to gather and transmit field data in real time, standardize data storage and management, automate routine analyses, and visualize data. Dozens of diverse MST options are available, and users may struggle to select suitable options. We developed a systematic MST Evaluation Framework (EF), based on International Organization for Standardization/International Electrotechnical Commission (ISO/IEC) software quality modeling standards, to objectively assess MSTs and assist program implementers in identifying suitable MST options. The EF is applicable to MSTs for a broad variety of applications. We also conducted an MST user survey to elucidate needs and priorities of current MST users. Finally, the EF was used to assess seven MSTs currently used for water and sanitation monitoring, as a validation exercise. The results suggest that the EF is a promising method for evaluating MSTs.

Parallel peak pruning for scalable SMP contour tree computation

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

Carr, Hamish A.; Weber, Gunther H.; Sewell, Christopher M.

As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this formmore » of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.« less

[Prediction of regional soil quality based on mutual information theory integrated with decision tree algorithm].

PubMed

Lin, Fen-Fang; Wang, Ke; Yang, Ning; Yan, Shi-Guang; Zheng, Xin-Yu

2012-02-01

In this paper, some main factors such as soil type, land use pattern, lithology type, topography, road, and industry type that affect soil quality were used to precisely obtain the spatial distribution characteristics of regional soil quality, mutual information theory was adopted to select the main environmental factors, and decision tree algorithm See 5.0 was applied to predict the grade of regional soil quality. The main factors affecting regional soil quality were soil type, land use, lithology type, distance to town, distance to water area, altitude, distance to road, and distance to industrial land. The prediction accuracy of the decision tree model with the variables selected by mutual information was obviously higher than that of the model with all variables, and, for the former model, whether of decision tree or of decision rule, its prediction accuracy was all higher than 80%. Based on the continuous and categorical data, the method of mutual information theory integrated with decision tree could not only reduce the number of input parameters for decision tree algorithm, but also predict and assess regional soil quality effectively.

Anti-proliferative effects, cell cycle G2/M phase arrest and blocking of chromosome segregation by probimane and MST-16 in human tumor cell lines

PubMed Central

Lu, Da Yong; Huang, Min; Xu, Cheng Hui; Yang, Wei Yi; Hu, Chao Xin; Lin, Li Ping; Tong, Lin Jiang; Li, Mei Hong; Lu, Wei; Zhang, Xiong Wen; Ding, Jian

2005-01-01

Background Anticancer bisdioxopiperazines, including ICRF-154, razoxane (Raz, ICRF-159) and ICRF-193, are a family of anticancer agents developed in the UK, especially targeting metastases of neoplasms. Two other bisdioxopiperazine derivatives, probimane (Pro) and MST-16, were synthesized at the Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. Cytotoxic activities and mechanisms of Raz (+)-steroisomer (ICRF-187, dexrazoxane), Pro and MST-16 against tumor cells were evaluated by MTT colorimetry, flow cytometry and karyotyping. Results Pro was cytotoxic to human tumor cell lines in vitro (IC50<50 μM for 48 h). Four human tumor cell lines (SCG-7901, K562, A549 and HL60) were susceptible to Pro at low inhibitory concentrations (IC50 values < 10 μM for 48 h). Although the IC50 against HeLa cell line of vincristine (VCR, 4.56 μM), doxorubicin (Dox, 1.12 μM) and 5-fluoruouracil (5-Fu, 0.232 μM) are lower than Pro (5.12 μM), ICRF-187 (129 μM) and MST-16 (26.4 μM), VCR, Dox and 5-Fu shows a low dose-related – high cytotoxic activity. Time-response studies showed that the cytotoxic effects of Pro are increased for 3 days in human tumor cells, whereas VCR, Dox and 5-Fu showed decreased cytotoxic action after 24 h. Cell cycle G2/M phase arrest and chromosome segregation blocking by Pro and MST-16 were noted. Although there was similar effects of Pro and MST-16 on chromosome segregation blocking action and cell cycle G2/M phase arrest at 1- 4 μM, cytotoxicity of Pro against tumor cells was higher than that of MST-16 in vitro by a factor of 3- 10 folds. Our data show that Pro may be more effective against lung cancer and leukemia while ICRF-187 and MST-16 shows similar IC50 values only against leukemia. Conclusion It suggests that Pro has a wider spectrum of cytotoxic effects against human tumor cells than other bisdioxopiperazines, especially against solid tumors, and with a single cytotoxic pathway of Pro and MST-16 affecting chromosome segregation and leading also to cell G2/ M phase arrests, which finally reduces cell division rates. Pro may be more potent than MST-16 in cytotoxicity. High dose- and time- responses of Pro, when compared with VCR, 5-Fu and Dox, were seen that suggest a selectivity of Pro against tumor growth. Compounds of bisdioxopiperazines family may keep up their cytotoxic effects longer than many other anticancer drugs. PMID:15963241

MST radar data-base management

NASA Technical Reports Server (NTRS)

Wickwar, V. B.

1983-01-01

Data management for Mesospheric-Stratospheric-Tropospheric, (MST) radars is addressed. An incoherent-scatter radar data base is discussed in terms of purpose, centralization, scope, and nature of the data base management system.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

28. VIEW SOUTH FROM SLC3W MST STATION 63. FOREGROUND LEFT: ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

28. VIEW SOUTH FROM SLC-3W MST STATION 63. FOREGROUND LEFT: THEODOLITE SHELTER (BLDG. 786) CENTER LEFT TO RIGHT: GLOBAL POSITIONING SYSTEM AZIMUTH STATION (BLDG. 775), PYROTECHNIC SHED (BLDG. 757), PORTABLE GUARD SHED, METEOROLOGICAL SHED (BLDG. 756), METEOROLOGICAL TOWER. BACKGROUND CENTER TO RIGHT: STORAGE SHED (BLDG. 776), LIQUID OXYGEN APRON, SLC-3E MST, TOP OF SLC-3E FUEL STORAGE TANK. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Exploiting the wavelet structure in compressed sensing MRI.

PubMed

Chen, Chen; Huang, Junzhou

2014-12-01

Sparsity has been widely utilized in magnetic resonance imaging (MRI) to reduce k-space sampling. According to structured sparsity theories, fewer measurements are required for tree sparse data than the data only with standard sparsity. Intuitively, more accurate image reconstruction can be achieved with the same number of measurements by exploiting the wavelet tree structure in MRI. A novel algorithm is proposed in this article to reconstruct MR images from undersampled k-space data. In contrast to conventional compressed sensing MRI (CS-MRI) that only relies on the sparsity of MR images in wavelet or gradient domain, we exploit the wavelet tree structure to improve CS-MRI. This tree-based CS-MRI problem is decomposed into three simpler subproblems then each of the subproblems can be efficiently solved by an iterative scheme. Simulations and in vivo experiments demonstrate the significant improvement of the proposed method compared to conventional CS-MRI algorithms, and the feasibleness on MR data compared to existing tree-based imaging algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

Data mining for multiagent rules, strategies, and fuzzy decision tree structure

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D., II; Fisher, Kristin

2002-03-01

A fuzzy logic based resource manager (RM) has been developed that automatically allocates electronic attack resources in real-time over many dissimilar platforms. Two different data mining algorithms have been developed to determine rules, strategies, and fuzzy decision tree structure. The first data mining algorithm uses a genetic algorithm as a data mining function and is called from an electronic game. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge. It calls a data mining function, a genetic algorithm, for data mining of the database as required and allows easy evaluation of the information mined in the second step. The criterion for re- optimization is discussed as well as experimental results. Then a second data mining algorithm that uses a genetic program as a data mining function is introduced to automatically discover fuzzy decision tree structures. Finally, a fuzzy decision tree generated through this process is discussed.

Determining Geometric Parameters of Agricultural Trees from Laser Scanning Data Obtained with Unmanned Aerial Vehicle

NASA Astrophysics Data System (ADS)

Hadas, E.; Jozkow, G.; Walicka, A.; Borkowski, A.

2018-05-01

The estimation of dendrometric parameters has become an important issue for agriculture planning and for the efficient management of orchards. Airborne Laser Scanning (ALS) data is widely used in forestry and many algorithms for automatic estimation of dendrometric parameters of individual forest trees were developed. Unfortunately, due to significant differences between forest and fruit trees, some contradictions exist against adopting the achievements of forestry science to agricultural studies indiscriminately. In this study we present the methodology to identify individual trees in apple orchard and estimate heights of individual trees, using high-density LiDAR data (3200 points/m2) obtained with Unmanned Aerial Vehicle (UAV) equipped with Velodyne HDL32-E sensor. The processing strategy combines the alpha-shape algorithm, principal component analysis (PCA) and detection of local minima. The alpha-shape algorithm is used to separate tree rows. In order to separate trees in a single row, we detect local minima on the canopy profile and slice polygons from alpha-shape results. We successfully separated 92 % of trees in the test area. 6 % of trees in orchard were not separated from each other and 2 % were sliced into two polygons. The RMSE of tree heights determined from the point clouds compared to field measurements was equal to 0.09 m, and the correlation coefficient was equal to 0.96. The results confirm the usefulness of LiDAR data from UAV platform in orchard inventory.

Method for estimating potential tree-grade distributions for northeastern forest species

Treesearch

Daniel A. Yaussy; Daniel A. Yaussy

1993-01-01

Generalized logistic regression was used to distribute trees into four potential tree grades for 20 northeastern species groups. The potential tree grade is defined as the tree grade based on the length and amount of clear cuttings and defects only, disregarding minimum grading diameter. The algorithms described use site index and tree diameter as the predictive...

Integrated Approach To Design And Analysis Of Systems

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Iverson, David L.

1993-01-01

Object-oriented fault-tree representation unifies evaluation of reliability and diagnosis of faults. Programming/fault tree described more fully in "Object-Oriented Algorithm For Evaluation Of Fault Trees" (ARC-12731). Augmented fault tree object contains more information than fault tree object used in quantitative analysis of reliability. Additional information needed to diagnose faults in system represented by fault tree.

Automatic classification of 6-month-old infants at familial risk for language-based learning disorder using a support vector machine.

PubMed

Zare, Marzieh; Rezvani, Zahra; Benasich, April A

2016-07-01

This study assesses the ability of a novel, "automatic classification" approach to facilitate identification of infants at highest familial risk for language-learning disorders (LLD) and to provide converging assessments to enable earlier detection of developmental disorders that disrupt language acquisition. Network connectivity measures derived from 62-channel electroencephalogram (EEG) recording were used to identify selected features within two infant groups who differed on LLD risk: infants with a family history of LLD (FH+) and typically-developing infants without such a history (FH-). A support vector machine was deployed; global efficiency and global and local clustering coefficients were computed. A novel minimum spanning tree (MST) approach was also applied. Cross-validation was employed to assess the resultant classification. Infants were classified with about 80% accuracy into FH+ and FH- groups with 89% specificity and precision of 92%. Clustering patterns differed by risk group and MST network analysis suggests that FH+ infants' EEG complexity patterns were significantly different from FH- infants. The automatic classification techniques used here were shown to be both robust and reliable and should provide valuable information when applied to early identification of risk or clinical groups. The ability to identify infants at highest risk for LLD using "automatic classification" strategies is a novel convergent approach that may facilitate earlier diagnosis and remediation. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Intermediate Templates Guided Groupwise Registration of Diffusion Tensor Images

PubMed Central

Jia, Hongjun; Yap, Pew-Thian; Wu, Guorong; Wang, Qian; Shen, Dinggang

2010-01-01

Registration of a population of diffusion tensor images (DTIs) is one of the key steps in medical image analysis, and it plays an important role in the statistical analysis of white matter related neurological diseases. However, pairwise registration with respect to a pre-selected template may not give precise results if the selected template deviates significantly from the distribution of images. To cater for more accurate and consistent registration, a novel framework is proposed for groupwise registration with the guidance from one or more intermediate templates determined from the population of images. Specifically, we first use a Euclidean distance, defined as a combinative measure based on the FA map and ADC map, for gauging the similarity of each pair of DTIs. A fully connected graph is then built with each node denoting an image and each edge denoting the distance between a pair of images. The root template image is determined automatically as the image with the overall shortest path length to all other images on the minimum spanning tree (MST) of the graph. Finally, a sequence of registration steps is applied to progressively warping each image towards the root template image with the help of intermediate templates distributed along its path to the root node on the MST. Extensive experimental results using diffusion tensor images of real subjects indicate that registration accuracy and fiber tract alignment are significantly improved, compared with the direct registration from each image to the root template image. PMID:20851197

Antidepressant effects, of magnetic seizure therapy and electroconvulsive therapy, in treatment-resistant depression.

PubMed

Kayser, Sarah; Bewernick, Bettina H; Grubert, Christiane; Hadrysiewicz, Barbara L; Axmacher, Nikolai; Schlaepfer, Thomas E

2011-05-01

Major depression is a common mental health problem and associated with significant morbidity and mortality, including impaired social and physical functioning and increased risk for suicide. Electroconvulsive therapy (ECT) is highly efficacious in treatment-resistant depressive disorders, but cognitive side effects are frequently associated with the treatment. Magnetic seizure therapy (MST) is a form of convulsive therapy, using magnetic fields in order to induce therapeutic seizures. First studies suggested that cognitive side effects of MST, including postictal recovery time, are more benign than those resulting from ECT treatment. In this open-label study we tested the hypothesis that MST is associated with clinically significant antidepressant effects in treatment-resistant depression (TRD) as an add-on therapy to a controlled pharmacotherapy. Twenty patients suffering from TRD were randomly assigned to receive either MST or ECT starting from July 2006 until November 2008. Primary outcome measure was antidepressant response assessed by Montgomery Åsberg Depression Scale. Secondary outcome measures included Hamilton Depression Rating Scale, Hamilton Anxiety Scale, Beck Depression Inventory and 90-Item Symptom Checklist. Antidepressant response (improvement of 50% in MADRS ratings) was statistically significant and of similar size in both treatment groups. Cognitive side effects were observed in neither group. Characteristics in MST- and ECT-induced seizures were comparable, especially regarding ictal activity and postictal suppression. Thus, MST may be a potential alternative to ECT if efficacy and safety are validated in larger clinical trials. Copyright © 2010 Elsevier Ltd. All rights reserved.

Maximizing MST's inductive capability with a Bp programmable power supply

NASA Astrophysics Data System (ADS)

Chapman, B. E.; Holly, D. J.; Jacobson, C. M.; McCollam, K. J.; Morin, J. C.; Sarff, J. S.; Squitieri, A.

2016-10-01

A major goal of the MST program is the advancement of inductive control for the development of both the RFP's fusion potential and, synergistically, the predictive capability of fusion science. This entails programmable power supplies (PPS's) for the Bt and Bp circuits. A Bt PPS is already in place, allowing advanced RFP operation and the production of tokamak plasmas, and a Bp PPS prototype is under construction. To explore some of the new capabilities to be provided by the Bp PPS, the existing Bt PPS has been temporarily connected to the Bp circuit. One key result is new-found access to very low Ip (20 kA) and very low Lundquist number, S (104). At this low S, simulation of RFP plasmas with the MHD code NIMROD is readily achievable, and work toward validation of extended MHD models using NIMROD is underway with direct comparisons to these MST plasmas. The full Bp PPS will also provide higher Ip and S than presently possible, allowing MST to produce plasmas with S spanning as much as five orders of magnitude, a dramatic extension of MST's capability. In these initial tests, the PPS has also increased five-fold MST's Ip flattop duration, to about 100 ms. This, coupled with the recently demonstrated PPS ability to drive large-amplitude sinusoidal oscillations in Ip, will allow tests of extended-duration oscillating field current drive, the goal of which is ac sustainment of a quasi-dc plasma current. Work supported by US DOE.

MDTS: automatic complex materials design using Monte Carlo tree search.

PubMed

M Dieb, Thaer; Ju, Shenghong; Yoshizoe, Kazuki; Hou, Zhufeng; Shiomi, Junichiro; Tsuda, Koji

2017-01-01

Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability. We succeeded in designing large Silicon-Germanium (Si-Ge) alloy structures that Bayesian optimization could not deal with due to excessive computational cost. MDTS is available at https://github.com/tsudalab/MDTS.

MDTS: automatic complex materials design using Monte Carlo tree search

NASA Astrophysics Data System (ADS)

Dieb, Thaer M.; Ju, Shenghong; Yoshizoe, Kazuki; Hou, Zhufeng; Shiomi, Junichiro; Tsuda, Koji

2017-12-01

Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability. We succeeded in designing large Silicon-Germanium (Si-Ge) alloy structures that Bayesian optimization could not deal with due to excessive computational cost. MDTS is available at https://github.com/tsudalab/MDTS.

A fast algorithm for identifying friends-of-friends halos

NASA Astrophysics Data System (ADS)

Feng, Y.; Modi, C.

2017-07-01

We describe a simple and fast algorithm for identifying friends-of-friends features and prove its correctness. The algorithm avoids unnecessary expensive neighbor queries, uses minimal memory overhead, and rejects slowdown in high over-density regions. We define our algorithm formally based on pair enumeration, a problem that has been heavily studied in fast 2-point correlation codes and our reference implementation employs a dual KD-tree correlation function code. We construct features in a hierarchical tree structure, and use a splay operation to reduce the average cost of identifying the root of a feature from O [ log L ] to O [ 1 ] (L is the size of a feature) without additional memory costs. This reduces the overall time complexity of merging trees from O [ L log L ] to O [ L ] , reducing the number of operations per splay by orders of magnitude. We next introduce a pruning operation that skips merge operations between two fully self-connected KD-tree nodes. This improves the robustness of the algorithm, reducing the number of merge operations in high density peaks from O [δ2 ] to O [ δ ] . We show that for cosmological data set the algorithm eliminates more than half of merge operations for typically used linking lengths b ∼ 0 . 2 (relative to mean separation). Furthermore, our algorithm is extremely simple and easy to implement on top of an existing pair enumeration code, reusing the optimization effort that has been invested in fast correlation function codes.

Over-reporting bias and the modified Stroop effect in Operation Enduring and Iraqi Freedom veterans with and without PTSD.

PubMed

Constans, Joseph I; Kimbrell, Timothy A; Nanney, John T; Marx, Brian P; Jegley, Susan; Pyne, Jeffrey M

2014-02-01

The current study investigated in a sample of Operation Enduring and Iraqi Freedom (OEF/OIF) veterans how a symptom overreporting response style might influence the association between PTSD diagnostic status and color-naming response latency for trauma-related stimuli during the Modified Stroop Task (i.e., the Modified Stroop Task effect, MST effect). It was hypothesized that, if an overreporting response style reflected feigning or exaggerating PTSD symptoms, an attenuated MST effect would be expected in overreporters with PTSD as compared with PTSD-diagnosed veterans without an overreporting style. If, however, overreporting stemmed from high levels of distress, the MST effect might be greater in overreporters compared with those with a neutral response style. The results showed that veterans with PTSD and an overreporting response style demonstrated an augmented MST effect in comparison with those with a more neutral style of response. Overreporters also reported greater levels of psychopathology, including markedly elevated reports of dissociative experiences. We suggest that dissociation-prone overreporters may misattribute emotional distress to combat experiences leading to the enhanced MST effect. Other possible explanations for these results are also discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Over-reporting bias and the Modified Stroop Effect in OEF/OIF Veterans with and without PTSD

PubMed Central

Constans, Joseph I.; Kimbrell, Timothy A.; Nanney, John. T.; Marx, Brian P.; Jegley, Susan; Pyne, Jeffrey M.

2014-01-01

The current study investigated in a sample of OEF/OIF Veterans how a symptom over-reporting response style might influence the association between PTSD diagnostic status and color-naming response latency for trauma-related stimuli during the Modified Stroop Task (i.e., the Modified Stroop Task effect, MST effect). It was hypothesized that, if an over-reporting response style reflected feigning or exaggerating PTSD symptoms, an attenuated MST effect would be expected in over-reporters with PTSD as compared with PTSD-diagnosed Veterans without an over-reporting style. If, however, over-reporting stemmed from high levels of distress, the MST effect might be greater in over-reporters compared to those with a neutral response style. The results showed that Veterans with PTSD and an over-reporting response style demonstrated an augmented MST effect in comparison to those with a more neutral style of response. Over-reporters also reported greater levels of psychopathology, including markedly elevated reports of dissociative experiences. We suggest that dissociation-prone over-reporters may misattribute emotional distress to combat experiences leading to the enhanced MST effect. Other possible explanations for these results are also discussed. PMID:24274375

Cutaneous leishmaniasis in the Peruvian Andes: an epidemiological study of infection and immunity.

PubMed Central

Davies, C. R.; Llanos-Cuentas, E. A.; Pyke, S. D.; Dye, C.

1995-01-01

A prospective longitudinal survey of cutaneous leishmaniasis (Leishmania peruviana) was carried out in Peru on a study population of 4716 persons living in 38 villages (Departments of Lima, Ancash and Piura). Demographic and clinical data were collected from all individuals, and a Montenegro skin test (MST) was carried out on 72% (3418) of the study population. Each household was revisited at 3-monthly intervals for up to 2 years to detect new leishmaniasis cases; 497 people received a second MST at the end of the study. Analysis of the epidemiological data indicated that (i) 17% (16/94) of all infections were subclinical, (ii) this percentage increased significantly with age, (iii) clinical infections led to 73.9% protective immunity (95% C.I. 53.0-85.5%) and relatively permanent MST responsiveness (recovery rate = 0.0098/year; 95% C.I. 0.000-0.020/year), (iv) sub-clinical infections led to protective immunity, which was positively correlated with their MST induration size (increasing by 17.9% per mm; P < 0.0001), and a mean MST recovery rate of 0.114/year (4/421 man-months), and (v) recurrent leishmaniasis was dominated by reactivations, not by reinfections. PMID:7705493

Tree-based solvers for adaptive mesh refinement code FLASH - I: gravity and optical depths

NASA Astrophysics Data System (ADS)

Wünsch, R.; Walch, S.; Dinnbier, F.; Whitworth, A.

2018-04-01

We describe an OctTree algorithm for the MPI parallel, adaptive mesh refinement code FLASH, which can be used to calculate the gas self-gravity, and also the angle-averaged local optical depth, for treating ambient diffuse radiation. The algorithm communicates to the different processors only those parts of the tree that are needed to perform the tree-walk locally. The advantage of this approach is a relatively low memory requirement, important in particular for the optical depth calculation, which needs to process information from many different directions. This feature also enables a general tree-based radiation transport algorithm that will be described in a subsequent paper, and delivers excellent scaling up to at least 1500 cores. Boundary conditions for gravity can be either isolated or periodic, and they can be specified in each direction independently, using a newly developed generalization of the Ewald method. The gravity calculation can be accelerated with the adaptive block update technique by partially re-using the solution from the previous time-step. Comparison with the FLASH internal multigrid gravity solver shows that tree-based methods provide a competitive alternative, particularly for problems with isolated or mixed boundary conditions. We evaluate several multipole acceptance criteria (MACs) and identify a relatively simple approximate partial error MAC which provides high accuracy at low computational cost. The optical depth estimates are found to agree very well with those of the RADMC-3D radiation transport code, with the tree-solver being much faster. Our algorithm is available in the standard release of the FLASH code in version 4.0 and later.

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

PubMed Central

2010-01-01

Background The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations. PMID:20525185

OCTGRAV: Sparse Octree Gravitational N-body Code on Graphics Processing Units

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-10-01

Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of heta approx 0.5. To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second. The code has a convenient user interface and is freely available for use.

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

PubMed

Zaccaria, Simone; El-Kebir, Mohammed; Klau, Gunnar W; Raphael, Benjamin J

2018-04-16

Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.

Multi-hop path tracing of mobile robot with multi-range image

NASA Astrophysics Data System (ADS)

Choudhury, Ramakanta; Samal, Chandrakanta; Choudhury, Umakanta

2010-02-01

It is well known that image processing depends heavily upon image representation technique . This paper intends to find out the optimal path of mobile robots for a specified area where obstacles are predefined as well as modified. Here the optimal path is represented by using the Quad tree method. Since there has been rising interest in the use of quad tree, we have tried to use the successive subdivision of images into quadrants from which the quad tree is developed. In the quad tree, obstacles-free area and the partial filled area are represented with different notations. After development of quad tree the algorithm is used to find the optimal path by employing neighbor finding technique, with a view to move the robot from the source to destination. The algorithm, here , permeates through the entire tree, and tries to locate the common ancestor for computation. The computation and the algorithm, aim at easing the ability of the robot to trace the optimal path with the help of adjacencies between the neighboring nodes as well as determining such adjacencies in the horizontal, vertical and diagonal directions. In this paper efforts have been made to determine the movement of the adjacent block in the quad tree and to detect the transition between the blocks equal size and finally generate the result.

A hybrid 3D spatial access method based on quadtrees and R-trees for globe data

NASA Astrophysics Data System (ADS)

Gong, Jun; Ke, Shengnan; Li, Xiaomin; Qi, Shuhua

2009-10-01

3D spatial access method for globe data is very crucial technique for virtual earth. This paper presents a brand-new maintenance method to index 3d objects distributed on the whole surface of the earth, which integrates the 1:1,000,000- scale topographic map tiles, Quad-tree and R-tree. Furthermore, when traditional methods are extended into 3d space, the performance of spatial index deteriorates badly, for example 3D R-tree. In order to effectively solve this difficult problem, a new algorithm of dynamic R-tree is put forward, which includes two sub-procedures, namely node-choosing and node-split. In the node-choosing algorithm, a new strategy is adopted, not like the traditional mode which is from top to bottom, but firstly from bottom to top then from top to bottom. This strategy can effectively solve the negative influence of node overlap. In the node-split algorithm, 2-to-3 split mode substitutes the traditional 1-to-2 mode, which can better concern the shape and size of nodes. Because of the rational tree shape, this R-tree method can easily integrate the concept of LOD. Therefore, it will be later implemented in commercial DBMS and adopted in time-crucial 3d GIS system.

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.

PubMed

Cannistraci, Carlo Vittorio; Ravasi, Timothy; Montevecchi, Franco Maria; Ideker, Trey; Alessio, Massimo

2010-09-15

Nonlinear small datasets, which are characterized by low numbers of samples and very high numbers of measures, occur frequently in computational biology, and pose problems in their investigation. Unsupervised hybrid-two-phase (H2P) procedures-specifically dimension reduction (DR), coupled with clustering-provide valuable assistance, not only for unsupervised data classification, but also for visualization of the patterns hidden in high-dimensional feature space. 'Minimum Curvilinearity' (MC) is a principle that-for small datasets-suggests the approximation of curvilinear sample distances in the feature space by pair-wise distances over their minimum spanning tree (MST), and thus avoids the introduction of any tuning parameter. MC is used to design two novel forms of nonlinear machine learning (NML): Minimum Curvilinear embedding (MCE) for DR, and Minimum Curvilinear affinity propagation (MCAP) for clustering. Compared with several other unsupervised and supervised algorithms, MCE and MCAP, whether individually or combined in H2P, overcome the limits of classical approaches. High performance was attained in the visualization and classification of: (i) pain patients (proteomic measurements) in peripheral neuropathy; (ii) human organ tissues (genomic transcription factor measurements) on the basis of their embryological origin. MC provides a valuable framework to estimate nonlinear distances in small datasets. Its extension to large datasets is prefigured for novel NMLs. Classification of neuropathic pain by proteomic profiles offers new insights for future molecular and systems biology characterization of pain. Improvements in tissue embryological classification refine results obtained in an earlier study, and suggest a possible reinterpretation of skin attribution as mesodermal. https://sites.google.com/site/carlovittoriocannistraci/home.

Reconciliation of Decision-Making Heuristics Based on Decision Trees Topologies and Incomplete Fuzzy Probabilities Sets

PubMed Central

Doubravsky, Karel; Dohnal, Mirko

2015-01-01

Complex decision making tasks of different natures, e.g. economics, safety engineering, ecology and biology, are based on vague, sparse, partially inconsistent and subjective knowledge. Moreover, decision making economists / engineers are usually not willing to invest too much time into study of complex formal theories. They require such decisions which can be (re)checked by human like common sense reasoning. One important problem related to realistic decision making tasks are incomplete data sets required by the chosen decision making algorithm. This paper presents a relatively simple algorithm how some missing III (input information items) can be generated using mainly decision tree topologies and integrated into incomplete data sets. The algorithm is based on an easy to understand heuristics, e.g. a longer decision tree sub-path is less probable. This heuristic can solve decision problems under total ignorance, i.e. the decision tree topology is the only information available. But in a practice, isolated information items e.g. some vaguely known probabilities (e.g. fuzzy probabilities) are usually available. It means that a realistic problem is analysed under partial ignorance. The proposed algorithm reconciles topology related heuristics and additional fuzzy sets using fuzzy linear programming. The case study, represented by a tree with six lotteries and one fuzzy probability, is presented in details. PMID:26158662

Reconciliation of Decision-Making Heuristics Based on Decision Trees Topologies and Incomplete Fuzzy Probabilities Sets.

PubMed

Doubravsky, Karel; Dohnal, Mirko

2015-01-01

Complex decision making tasks of different natures, e.g. economics, safety engineering, ecology and biology, are based on vague, sparse, partially inconsistent and subjective knowledge. Moreover, decision making economists / engineers are usually not willing to invest too much time into study of complex formal theories. They require such decisions which can be (re)checked by human like common sense reasoning. One important problem related to realistic decision making tasks are incomplete data sets required by the chosen decision making algorithm. This paper presents a relatively simple algorithm how some missing III (input information items) can be generated using mainly decision tree topologies and integrated into incomplete data sets. The algorithm is based on an easy to understand heuristics, e.g. a longer decision tree sub-path is less probable. This heuristic can solve decision problems under total ignorance, i.e. the decision tree topology is the only information available. But in a practice, isolated information items e.g. some vaguely known probabilities (e.g. fuzzy probabilities) are usually available. It means that a realistic problem is analysed under partial ignorance. The proposed algorithm reconciles topology related heuristics and additional fuzzy sets using fuzzy linear programming. The case study, represented by a tree with six lotteries and one fuzzy probability, is presented in details.

Computing all hybridization networks for multiple binary phylogenetic input trees.

PubMed

Albrecht, Benjamin

2015-07-30

The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

System aspects of the Indian MST radar facility

NASA Technical Reports Server (NTRS)

Viswanathan, G.

1986-01-01

One of the major objectives of the Indian Middle Atmosphere Program is to investigate the motions of the middle atmosphere on temporal and spatial scales and the interaction between the three height regions of the middle atmosphere. Realizing the fact that radar technique has proven to be a very powerful tool for the study of Earth atmosphere, the Indian Middle Atmosphere Program has recommended establishing a mesosphere-stratosphere-troposphere (MST) radar as a national facility for atmospheric research. The major landmarks in this attempt to setup the MST radar as a national facility are described.

Continuous-time quantum search on balanced trees

NASA Astrophysics Data System (ADS)

Philipp, Pascal; Tarrataca, Luís; Boettcher, Stefan

2016-03-01

We examine the effect of network heterogeneity on the performance of quantum search algorithms. To this end, we study quantum search on a tree for the oracle Hamiltonian formulation employed by continuous-time quantum walks. We use analytical and numerical arguments to show that the exponent of the asymptotic running time ˜Nβ changes uniformly from β =0.5 to β =1 as the searched-for site is moved from the root of the tree towards the leaves. These results imply that the time complexity of the quantum search algorithm on a balanced tree is closely correlated with certain path-based centrality measures of the searched-for site.

Application of a fast skyline computation algorithm for serendipitous searching problems

NASA Astrophysics Data System (ADS)

Koizumi, Kenichi; Hiraki, Kei; Inaba, Mary

2018-02-01

Skyline computation is a method of extracting interesting entries from a large population with multiple attributes. These entries, called skyline or Pareto optimal entries, are known to have extreme characteristics that cannot be found by outlier detection methods. Skyline computation is an important task for characterizing large amounts of data and selecting interesting entries with extreme features. When the population changes dynamically, the task of calculating a sequence of skyline sets is called continuous skyline computation. This task is known to be difficult to perform for the following reasons: (1) information of non-skyline entries must be stored since they may join the skyline in the future; (2) the appearance or disappearance of even a single entry can change the skyline drastically; (3) it is difficult to adopt a geometric acceleration algorithm for skyline computation tasks with high-dimensional datasets. Our new algorithm called jointed rooted-tree (JR-tree) manages entries using a rooted tree structure. JR-tree delays extend the tree to deep levels to accelerate tree construction and traversal. In this study, we presented the difficulties in extracting entries tagged with a rare label in high-dimensional space and the potential of fast skyline computation in low-latency cell identification technology.

Implementation of Tree and Butterfly Barriers with Optimistic Time Management Algorithms for Discrete Event Simulation

NASA Astrophysics Data System (ADS)

Rizvi, Syed S.; Shah, Dipali; Riasat, Aasia

The Time Wrap algorithm [3] offers a run time recovery mechanism that deals with the causality errors. These run time recovery mechanisms consists of rollback, anti-message, and Global Virtual Time (GVT) techniques. For rollback, there is a need to compute GVT which is used in discrete-event simulation to reclaim the memory, commit the output, detect the termination, and handle the errors. However, the computation of GVT requires dealing with transient message problem and the simultaneous reporting problem. These problems can be dealt in an efficient manner by the Samadi's algorithm [8] which works fine in the presence of causality errors. However, the performance of both Time Wrap and Samadi's algorithms depends on the latency involve in GVT computation. Both algorithms give poor latency for large simulation systems especially in the presence of causality errors. To improve the latency and reduce the processor ideal time, we implement tree and butterflies barriers with the optimistic algorithm. Our analysis shows that the use of synchronous barriers such as tree and butterfly with the optimistic algorithm not only minimizes the GVT latency but also minimizes the processor idle time.

Fish to meat intake ratio and cooking oils are associated with hepatitis C virus carriers with persistently normal alanine aminotransferase levels.

PubMed

Otsuka, Momoka; Uchida, Yuki; Kawaguchi, Takumi; Taniguchi, Eitaro; Kawaguchi, Atsushi; Kitani, Shingo; Itou, Minoru; Oriishi, Tetsuharu; Kakuma, Tatsuyuki; Tanaka, Suiko; Yagi, Minoru; Sata, Michio

2012-10-01

  Dietary habits are involved in the development of chronic inflammation; however, the impact of dietary profiles of hepatitis C virus carriers with persistently normal alanine transaminase levels (HCV-PNALT) remains unclear. The decision-tree algorithm is a data-mining statistical technique, which uncovers meaningful profiles of factors from a data collection. We aimed to investigate dietary profiles associated with HCV-PNALT using a decision-tree algorithm.   Twenty-seven HCV-PNALT and 41 patients with chronic hepatitis C were enrolled in this study. Dietary habit was assessed using a validated semiquantitative food frequency questionnaire. A decision-tree algorithm was created by dietary variables, and was evaluated by area under the receiver operating characteristic curve analysis (AUROC).   In multivariate analysis, fish to meat ratio, dairy product and cooking oils were identified as independent variables associated with HCV-PNALT. The decision-tree algorithm was created with two variables: a fish to meat ratio and cooking oils/ideal bodyweight. When subjects showed a fish to meat ratio of 1.24 or more, 68.8% of the subjects were HCV-PNALT. On the other hand, 11.5% of the subjects were HCV-PNALT when subjects showed a fish to meat ratio of less than 1.24 and cooking oil/ideal bodyweight of less than 0.23 g/kg. The difference in the proportion of HCV-PNALT between these groups are significant (odds ratio 16.87, 95% CI 3.40-83.67, P = 0.0005). Fivefold cross-validation of the decision-tree algorithm showed an AUROC of 0.6947 (95% CI 0.5656-0.8238, P = 0.0067).   The decision-tree algorithm disclosed that fish to meat ratio and cooking oil/ideal bodyweight were associated with HCV-PNALT. © 2012 The Japan Society of Hepatology.

Assessment of performing an MST strike in Tank 21H

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

Poirier, Michael R.

2014-09-29

Previous Savannah River National Laboratory (SRNL) tank mixing studies performed for the Small Column Ion Exchange (SCIX) project have shown that 3 Submersible Mixer Pumps (SMPs) installed in Tank 41 are sufficient to support actinide removal by MST sorption as well as subsequent resuspension and removal of settled solids. Savannah River Remediation (SRR) is pursuing MST addition into Tank 21 as part of the Large Tank Strike (LTS) project. The preliminary scope for LTS involves the use of three standard slurry pumps (installed in N, SE, and SW risers) in a Type IV tank. Due to the differences in tankmore » size, internal interferences, and pump design, a separate mixing evaluation is required to determine if the proposed configuration will allow for MST suspension and strontium and actinide sorption. The author performed the analysis by reviewing drawings for Tank 21 [W231023] and determining the required cleaning radius or zone of influence for the pumps. This requirement was compared with previous pilot-scale MST suspension data collected for SCIX that determined the cleaning radius, or zone of influence, as a function of pump operating parameters. The author also reviewed a previous Tank 50 mixing analysis that examined the ability of standard slurry pumps to suspend sludge particles. Based on a review of the pilot-scale SCIX mixing tests and Tank 50 pump operating experience, three standard slurry pumps should be able to suspend sludge and MST to effectively sorb strontium and actinides onto the MST. Using the SCIX data requires an assumption about the impact of cooling coils on slurry pump mixing. The basis for this assumption is described in this report. Using the Tank 50 operating experience shows three standard slurry pumps should be able to suspend solids if the shear strength of the settled solids is less than 160 Pa. Because Tank 21 does not contain cooling coils, the shear strength could be larger.« less

Prediction of Cardiorespiratory Fitness by the Six-Minute Step Test and Its Association with Muscle Strength and Power in Sedentary Obese and Lean Young Women: A Cross-Sectional Study

PubMed Central

Bonjorno Junior, José Carlos; de Oliveira, Cláudio Ricardo; Luporini, Rafael Luís; Mendes, Renata Gonçalves; Zangrando, Katiany Thais Lopes; Trimer, Renata; Arena, Ross

2015-01-01

Impaired cardiorespiratory fitness (CRF) is a hallmark characteristic in obese and lean sedentary young women. Peak oxygen consumption (VO2peak) prediction from the six-minute step test (6MST) has not been established for sedentary females. It is recognized that lower-limb muscle strength and power play a key role during functional activities. The aim of this study was to investigate cardiorespiratory responses during the 6MST and CPX and to develop a predictive equation to estimate VO2peak in both lean and obese subjects. Additionally we aim to investigate how muscle function impacts functional performance. Lean (LN = 13) and obese (OB = 18) women, aged 20–45, underwent a CPX, two 6MSTs, and isokinetic and isometric knee extensor strength and power evaluations. Regression analysis assessed the ability to predict VO2peak from the 6MST, age and body mass index (BMI). CPX and 6MST main outcomes were compared between LN and OB and correlated with strength and power variables. CRF, functional capacity, and muscle strength and power were lower in the OB compared to LN (<0.05). During the 6MST, LN and OB reached ~90% of predicted maximal heart rate and ~80% of the VO2peak obtained during CPX. BMI, age and number of step cycles (NSC) explained 83% of the total variance in VO2peak. Moderate to strong correlations between VO2peak at CPX and VO2peak at 6MST (r = 0.86), VO2peak at CPX and NSC (r = 0.80), as well as between VO2peak, NSC and muscle strength and power variables were found (p<0.05). These findings indicate the 6MST, BMI and age accurately predict VO2peak in both lean and obese young sedentary women. Muscle strength and power were related to measures of aerobic and functional performance. PMID:26717568

Association between split selection instability and predictive error in survival trees.

PubMed

Radespiel-Tröger, M; Gefeller, O; Rabenstein, T; Hothorn, T

2006-01-01

To evaluate split selection instability in six survival tree algorithms and its relationship with predictive error by means of a bootstrap study. We study the following algorithms: logrank statistic with multivariate p-value adjustment without pruning (LR), Kaplan-Meier distance of survival curves (KM), martingale residuals (MR), Poisson regression for censored data (PR), within-node impurity (WI), and exponential log-likelihood loss (XL). With the exception of LR, initial trees are pruned by using split-complexity, and final trees are selected by means of cross-validation. We employ a real dataset from a clinical study of patients with gallbladder stones. The predictive error is evaluated using the integrated Brier score for censored data. The relationship between split selection instability and predictive error is evaluated by means of box-percentile plots, covariate and cutpoint selection entropy, and cutpoint selection coefficients of variation, respectively, in the root node. We found a positive association between covariate selection instability and predictive error in the root node. LR yields the lowest predictive error, while KM and MR yield the highest predictive error. The predictive error of survival trees is related to split selection instability. Based on the low predictive error of LR, we recommend the use of this algorithm for the construction of survival trees. Unpruned survival trees with multivariate p-value adjustment can perform equally well compared to pruned trees. The analysis of split selection instability can be used to communicate the results of tree-based analyses to clinicians and to support the application of survival trees.

Medical simulation technology: educational overview, industry leaders, and what's missing.

PubMed

Spooner, Nicholas; Hurst, Stephen; Khadra, Mohamed

2012-01-01

Modern medical simulation technology (MST) debuted in 1960 with the development of Resusci Annie (Laerdal 2007), which assisted students in the acquisition of proper ventilation and compression techniques used during basic life support. Following a steady stream of subsequent technological advances and innovations, MST manufacturers are now able to offer training aids capable of facilitating innovative learning in such diverse areas as human patient simulators, simulated clinical environments, virtual procedure stations, virtual medical environments, electronic tutors, and performance recording. The authors list a number of the most popular MSTs presently available while citing evaluative efforts undertaken to date regarding the efficacy of MST to the medical profession. They conclude by proposing a variety of simulation innovations of prospective interest to both medical and technology personnel while offering healthcare administrators a series of recommended considerations when planning to integrate MST into existing medical systems.

Vibrational relaxation of I2 in complexing solvents: The role of solvent-solute attractive forces

NASA Astrophysics Data System (ADS)

Shiang, Joseph J.; Liu, Hongjun; Sension, Roseanne J.

1998-12-01

Femtosecond transient absorption studies of I2-arene complexes, with arene=hexamethylbenzene (HMB), mesitylene (MST), or m-xylene (mX), are used to investigate the effect of solvent-solute attractive forces upon the rate of vibrational relaxation in solution. Comparison of measurements on I2-MST complexes in neat mesitylene and I2-MST complexes diluted in carbontetrachloride demonstrate that binary solvent-solute attractive forces control the rate of vibrational relaxation in this prototypical model of diatomic vibrational relaxation. The data obtained for different arenes demonstrate that the rate of I2 relaxation increases with the magnitude of the I2-arene attractive interaction. I2-HMB relaxes much faster than I2 in MST or mX. The results of these experiments are discussed in terms of both isolated binary collision and instantaneous normal mode models for vibrational relaxation.

Encountering women veterans with military sexual trauma.

PubMed

Conard, Patricia L; Young, Cathy; Hogan, LaMicha; Armstrong, Myrna L

2014-10-01

As women veterans (WVs) are returning from Operation Iraqi Freedom and Operation Enduring Freedom with military sexual trauma (MST), the purpose of this article is twofold. First, important exploratory questions that can assist with a thorough assessment and history are presented as well as the applicable treatment for any new, recurrent, or unresolved symptoms that involve MST. Review of multiple literary materials, as well as a clinical situation. WVs will be encountered in a variety of military or civilian primary and community care healthcare settings. Every woman (and man) in the civilian sector should be asked, "Have you ever served in the military?" Recognition, acknowledgment, and applicable interventions for MST and associated comorbidities, especially post-traumatic stress disorder, are presented as currently 80-90% of MST experiences have gone unreported. Immediate treatment and follow-up are critical for the well-being of the WVs. © 2014 Wiley Periodicals, Inc.

Extensions and applications of ensemble-of-trees methods in machine learning

NASA Astrophysics Data System (ADS)

Bleich, Justin

Ensemble-of-trees algorithms have emerged to the forefront of machine learning due to their ability to generate high forecasting accuracy for a wide array of regression and classification problems. Classic ensemble methodologies such as random forests (RF) and stochastic gradient boosting (SGB) rely on algorithmic procedures to generate fits to data. In contrast, more recent ensemble techniques such as Bayesian Additive Regression Trees (BART) and Dynamic Trees (DT) focus on an underlying Bayesian probability model to generate the fits. These new probability model-based approaches show much promise versus their algorithmic counterparts, but also offer substantial room for improvement. The first part of this thesis focuses on methodological advances for ensemble-of-trees techniques with an emphasis on the more recent Bayesian approaches. In particular, we focus on extensions of BART in four distinct ways. First, we develop a more robust implementation of BART for both research and application. We then develop a principled approach to variable selection for BART as well as the ability to naturally incorporate prior information on important covariates into the algorithm. Next, we propose a method for handling missing data that relies on the recursive structure of decision trees and does not require imputation. Last, we relax the assumption of homoskedasticity in the BART model to allow for parametric modeling of heteroskedasticity. The second part of this thesis returns to the classic algorithmic approaches in the context of classification problems with asymmetric costs of forecasting errors. First we consider the performance of RF and SGB more broadly and demonstrate its superiority to logistic regression for applications in criminology with asymmetric costs. Next, we use RF to forecast unplanned hospital readmissions upon patient discharge with asymmetric costs taken into account. Finally, we explore the construction of stable decision trees for forecasts of violence during probation hearings in court systems.

ATLAAS: an automatic decision tree-based learning algorithm for advanced image segmentation in positron emission tomography.

PubMed

Berthon, Beatrice; Marshall, Christopher; Evans, Mererid; Spezi, Emiliano

2016-07-07

Accurate and reliable tumour delineation on positron emission tomography (PET) is crucial for radiotherapy treatment planning. PET automatic segmentation (PET-AS) eliminates intra- and interobserver variability, but there is currently no consensus on the optimal method to use, as different algorithms appear to perform better for different types of tumours. This work aimed to develop a predictive segmentation model, trained to automatically select and apply the best PET-AS method, according to the tumour characteristics. ATLAAS, the automatic decision tree-based learning algorithm for advanced segmentation is based on supervised machine learning using decision trees. The model includes nine PET-AS methods and was trained on a 100 PET scans with known true contour. A decision tree was built for each PET-AS algorithm to predict its accuracy, quantified using the Dice similarity coefficient (DSC), according to the tumour volume, tumour peak to background SUV ratio and a regional texture metric. The performance of ATLAAS was evaluated for 85 PET scans obtained from fillable and printed subresolution sandwich phantoms. ATLAAS showed excellent accuracy across a wide range of phantom data and predicted the best or near-best segmentation algorithm in 93% of cases. ATLAAS outperformed all single PET-AS methods on fillable phantom data with a DSC of 0.881, while the DSC for H&N phantom data was 0.819. DSCs higher than 0.650 were achieved in all cases. ATLAAS is an advanced automatic image segmentation algorithm based on decision tree predictive modelling, which can be trained on images with known true contour, to predict the best PET-AS method when the true contour is unknown. ATLAAS provides robust and accurate image segmentation with potential applications to radiation oncology.

ATLAAS: an automatic decision tree-based learning algorithm for advanced image segmentation in positron emission tomography

NASA Astrophysics Data System (ADS)

Berthon, Beatrice; Marshall, Christopher; Evans, Mererid; Spezi, Emiliano

2016-07-01

Accurate and reliable tumour delineation on positron emission tomography (PET) is crucial for radiotherapy treatment planning. PET automatic segmentation (PET-AS) eliminates intra- and interobserver variability, but there is currently no consensus on the optimal method to use, as different algorithms appear to perform better for different types of tumours. This work aimed to develop a predictive segmentation model, trained to automatically select and apply the best PET-AS method, according to the tumour characteristics. ATLAAS, the automatic decision tree-based learning algorithm for advanced segmentation is based on supervised machine learning using decision trees. The model includes nine PET-AS methods and was trained on a 100 PET scans with known true contour. A decision tree was built for each PET-AS algorithm to predict its accuracy, quantified using the Dice similarity coefficient (DSC), according to the tumour volume, tumour peak to background SUV ratio and a regional texture metric. The performance of ATLAAS was evaluated for 85 PET scans obtained from fillable and printed subresolution sandwich phantoms. ATLAAS showed excellent accuracy across a wide range of phantom data and predicted the best or near-best segmentation algorithm in 93% of cases. ATLAAS outperformed all single PET-AS methods on fillable phantom data with a DSC of 0.881, while the DSC for H&N phantom data was 0.819. DSCs higher than 0.650 were achieved in all cases. ATLAAS is an advanced automatic image segmentation algorithm based on decision tree predictive modelling, which can be trained on images with known true contour, to predict the best PET-AS method when the true contour is unknown. ATLAAS provides robust and accurate image segmentation with potential applications to radiation oncology.

The effect of different distance measures in detecting outliers using clustering-based algorithm for circular regression model

NASA Astrophysics Data System (ADS)

Di, Nur Faraidah Muhammad; Satari, Siti Zanariah

2017-05-01

Outlier detection in linear data sets has been done vigorously but only a small amount of work has been done for outlier detection in circular data. In this study, we proposed multiple outliers detection in circular regression models based on the clustering algorithm. Clustering technique basically utilizes distance measure to define distance between various data points. Here, we introduce the similarity distance based on Euclidean distance for circular model and obtain a cluster tree using the single linkage clustering algorithm. Then, a stopping rule for the cluster tree based on the mean direction and circular standard deviation of the tree height is proposed. We classify the cluster group that exceeds the stopping rule as potential outlier. Our aim is to demonstrate the effectiveness of proposed algorithms with the similarity distances in detecting the outliers. It is found that the proposed methods are performed well and applicable for circular regression model.

Automatic Classification of Trees from Laser Scanning Point Clouds

NASA Astrophysics Data System (ADS)

Sirmacek, B.; Lindenbergh, R.

2015-08-01

Development of laser scanning technologies has promoted tree monitoring studies to a new level, as the laser scanning point clouds enable accurate 3D measurements in a fast and environmental friendly manner. In this paper, we introduce a probability matrix computation based algorithm for automatically classifying laser scanning point clouds into 'tree' and 'non-tree' classes. Our method uses the 3D coordinates of the laser scanning points as input and generates a new point cloud which holds a label for each point indicating if it belongs to the 'tree' or 'non-tree' class. To do so, a grid surface is assigned to the lowest height level of the point cloud. The grids are filled with probability values which are calculated by checking the point density above the grid. Since the tree trunk locations appear with very high values in the probability matrix, selecting the local maxima of the grid surface help to detect the tree trunks. Further points are assigned to tree trunks if they appear in the close proximity of trunks. Since heavy mathematical computations (such as point cloud organization, detailed shape 3D detection methods, graph network generation) are not required, the proposed algorithm works very fast compared to the existing methods. The tree classification results are found reliable even on point clouds of cities containing many different objects. As the most significant weakness, false detection of light poles, traffic signs and other objects close to trees cannot be prevented. Nevertheless, the experimental results on mobile and airborne laser scanning point clouds indicate the possible usage of the algorithm as an important step for tree growth observation, tree counting and similar applications. While the laser scanning point cloud is giving opportunity to classify even very small trees, accuracy of the results is reduced in the low point density areas further away than the scanning location. These advantages and disadvantages of two laser scanning point cloud sources are discussed in detail.

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

Behroozi, Peter S.; Wechsler, Risa H.; Wu, Hao-Yi

We present a new algorithm for generating merger trees and halo catalogs which explicitly ensures consistency of halo properties (mass, position, and velocity) across time steps. Our algorithm has demonstrated the ability to improve both the completeness (through detecting and inserting otherwise missing halos) and purity (through detecting and removing spurious objects) of both merger trees and halo catalogs. In addition, our method is able to robustly measure the self-consistency of halo finders; it is the first to directly measure the uncertainties in halo positions, halo velocities, and the halo mass function for a given halo finder based on consistencymore » between snapshots in cosmological simulations. We use this algorithm to generate merger trees for two large simulations (Bolshoi and Consuelo) and evaluate two halo finders (ROCKSTAR and BDM). We find that both the ROCKSTAR and BDM halo finders track halos extremely well; in both, the number of halos which do not have physically consistent progenitors is at the 1%-2% level across all halo masses. Our code is publicly available at http://code.google.com/p/consistent-trees. Our trees and catalogs are publicly available at http://hipacc.ucsc.edu/Bolshoi/.« less

DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2

PubMed Central

Kwan, Julian; Sczaniecka, Anna; Heidary Arash, Emad; Nguyen, Liem; Chen, Chia-Chun; Ratkovic, Srdjana; Klezovitch, Olga; Attisano, Liliana; McNeill, Helen; Emili, Andrew; Vasioukhin, Valeri

2016-01-01

Disruption of apical–basal polarity is implicated in developmental disorders and cancer; however, the mechanisms connecting cell polarity proteins with intracellular signaling pathways are largely unknown. We determined previously that membrane-associated guanylate kinase (MAGUK) protein discs large homolog 5 (DLG5) functions in cell polarity and regulates cellular proliferation and differentiation via undefined mechanisms. We report here that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, which controls organ size through the modulation of cell proliferation and differentiation. Affinity purification/mass spectrometry revealed a critical role of DLG5 in the formation of protein assemblies containing core Hippo kinases mammalian ste20 homologs 1/2 (MST1/2) and Par-1 polarity proteins microtubule affinity-regulating kinases 1/2/3 (MARK1/2/3). Consistent with this finding, Hippo signaling is markedly hyperactive in mammalian Dlg5−/− tissues and cells in vivo and ex vivo and in Drosophila upon dlg5 knockdown. Conditional deletion of Mst1/2 fully rescued the phenotypes of brain-specific Dlg5 knockout mice. Dlg5 also interacts genetically with Hippo effectors Yap1/Taz. Mechanistically, we show that DLG5 inhibits the association between MST1/2 and large tumor suppressor homologs 1/2 (LATS1/2), uses its scaffolding function to link MST1/2 with MARK3, and inhibits MST1/2 kinase activity. These data reveal a direct connection between cell polarity proteins and Hippo, which is essential for proper development of multicellular organisms. PMID:28087714

Individualized Low-Amplitude Seizure Therapy: Minimizing Current for Electroconvulsive Therapy and Magnetic Seizure Therapy.

PubMed

Peterchev, Angel V; Krystal, Andrew D; Rosa, Moacyr A; Lisanby, Sarah H

2015-08-01

Electroconvulsive therapy (ECT) at conventional current amplitudes (800-900 mA) is highly effective but carries the risk of cognitive side effects. Lowering and individualizing the current amplitude may reduce side effects by virtue of a less intense and more focal electric field exposure in the brain, but this aspect of ECT dosing is largely unexplored. Magnetic seizure therapy (MST) induces a weaker and more focal electric field than ECT; however, the pulse amplitude is not individualized and the minimum amplitude required to induce a seizure is unknown. We titrated the amplitude of long stimulus trains (500 pulses) as a means of determining the minimum current amplitude required to induce a seizure with ECT (bilateral, right unilateral, bifrontal, and frontomedial electrode placements) and MST (round coil on vertex) in nonhuman primates. Furthermore, we investigated a novel method of predicting this amplitude-titrated seizure threshold (ST) by a non-convulsive measurement of motor threshold (MT) using single pulses delivered through the ECT electrodes or MST coil. Average STs were substantially lower than conventional pulse amplitudes (112-174 mA for ECT and 37.4% of maximum device amplitude for MST). ST was more variable in ECT than in MST. MT explained 63% of the ST variance and is hence the strongest known predictor of ST. These results indicate that seizures can be induced with less intense electric fields than conventional ECT that may be safer; efficacy and side effects should be evaluated in clinical studies. MT measurement could be a faster and safer alternative to empirical ST titration for ECT and MST.

Comparison of two nutritional screening tools to detect nutritional risk in hematologic inpatients.

PubMed

Fiol-Martínez, Lucía; Calleja-Fernández, Alicia; Pintor de la Maza, Begoña; Vidal-Casariego, Alfonso; Villar-Taibo, Rocío; Urioste-Fondo, Ana; Cuervo, Marta; Cano-Rodríguez, Isidoro; Ballesteros-Pomar, María D

2017-02-01

The aim of the study was to compare two nutritional screening tools in oncohematologic inpatients. A cross-sectional study was performed in a hematology ward from August to December 2015. Within the first 24 h of admission, the following nutritional screenings were performed: Malnutrition Universal Screening Tool (MUST), Malnutrition Screening Tool (MST), and Subjective Global Assessment (SGA). Patients who stayed in the hematologic ward were reevaluated with the three screening tools 1 and 2 wk after admission. The SGA was used as the gold standard in the detection of malnutrition. Sixty-three patients were included in the study. Of these, 61.9% were men, ages 64 y (SD = 17.9 y) with 90.5% having a diagnosis of cancer. The prevalence of patients with nutritional risk at admission was 17.5% with SGA, 16.7% at week 1, and 31.6% at week 2. According to MST, the prevalence was 41.3% at admission, 13.9% at week 1, and 15.8% at week 2. According to MUST, the prevalence was 36.5%, 25%, and 36.8%, respectively. The results of diagnostic tests on admission were an area under the curve receiver operating characteristic of 0.691 for MST and 0.830 for MUST at admission; at week 1, 0.717 for MST and 0.850 for MUST; and at week 2 of assessment, 0.506 for MST and 0.840 for MUST. MUST might be a better screening tool than MST for detecting the risk for malnutrition in oncohematological inpatients. Copyright © 2016 Elsevier Inc. All rights reserved.

Perceived Burdensomeness, Thwarted Belongingness, and Fearlessness about Death: Associations With Suicidal Ideation among Female Veterans Exposed to Military Sexual Trauma.

PubMed

Monteith, Lindsey L; Bahraini, Nazanin H; Menefee, Deleene S

2017-12-01

Military sexual trauma (MST) is prevalent among female Veterans and is associated with increased risk for suicidal self-directed violence. Yet research examining processes which contribute to suicidal ideation and attempts among MST survivors has been sparse, focusing primarily on psychiatric symptoms or diagnoses, rather than employing a theory-driven approach. The interpersonal-psychological theory (Joiner, 2005) is a leading theory of suicide that may be particularly relevant for understanding suicidal ideation among female Veterans who have experienced MST. We examined whether constructs derived from the interpersonal-psychological theory of suicide (perceived burdensomeness, thwarted belongingness, and fearlessness about death; Joiner, 2005) were associated with suicidal ideation among female Veterans who had experienced MST, when adjusting for known risk factors for suicide. Ninety-two female Veterans with a history of MST completed the Interpersonal Needs Questionnaire, Acquired Capability for Suicide Scale - Fearlessness about Death Scale, and Beck Scale for Suicide Ideation. Perceived burdensomeness, thwarted belongingness, and fearlessness about death were each associated with suicidal ideation in the past week, adjusting for prior suicide attempts, current depressive symptoms, and current symptoms of posttraumatic stress disorder. When including all three interpersonal-psychological constructs in the model, only perceived burdensomeness and fearlessness about death were significantly associated with suicidal ideation. These findings provide knowledge regarding interpersonal processes that may contribute to suicidal ideation among this high-risk, yet understudied, population. These results also underscore the importance of assessing for interpersonal-psychological constructs-particularly perceived burdensomeness and fearlessness about death-when working with female Veterans who have experienced MST. © 2017 Wiley Periodicals, Inc.

Effects of plot size on forest-type algorithm accuracy

Treesearch

James A. Westfall

2009-01-01

The Forest Inventory and Analysis (FIA) program utilizes an algorithm to consistently determine the forest type for forested conditions on sample plots. Forest type is determined from tree size and species information. Thus, the accuracy of results is often dependent on the number of trees present, which is highly correlated with plot area. This research examines the...

10. PARTIAL VIEW OF SOUTH FACE OF MST AND BRIDGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. PARTIAL VIEW OF SOUTH FACE OF MST AND BRIDGE CRANE MOVED TO ITS SOUTHERN LIMIT - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

11. PARTIAL VIEW OF NORTH FACE OF MST AND BRIDGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. PARTIAL VIEW OF NORTH FACE OF MST AND BRIDGE CRANE MOVED TO ITS NORTHERN LIMIT - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Fast Dating Using Least-Squares Criteria and Algorithms.

PubMed

To, Thu-Hien; Jung, Matthieu; Lycett, Samantha; Gascuel, Olivier

2016-01-01

Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g., human immunodeficiency virus (HIV)). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here, we present very fast dating algorithms, based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e., an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e., proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e., proportional to the square of the number of taxa). In all cases, very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley-Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1194 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (least-squares dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables, and figures can be found in the Supplementary Material available on Dryad at http://dx.doi.org/10.5061/dryad.968t3. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Fast Dating Using Least-Squares Criteria and Algorithms

PubMed Central

To, Thu-Hien; Jung, Matthieu; Lycett, Samantha; Gascuel, Olivier

2016-01-01

Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g., human immunodeficiency virus (HIV)). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here, we present very fast dating algorithms, based on a Gaussian model closely related to the Langley–Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e., an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e., proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e., proportional to the square of the number of taxa). In all cases, very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley–Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1194 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (least-squares dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables, and figures can be found in the Supplementary Material available on Dryad at http://dx.doi.org/10.5061/dryad.968t3. PMID:26424727

Labeled trees and the efficient computation of derivations

NASA Technical Reports Server (NTRS)

Grossman, Robert; Larson, Richard G.

1989-01-01

The effective parallel symbolic computation of operators under composition is discussed. Examples include differential operators under composition and vector fields under the Lie bracket. Data structures consisting of formal linear combinations of rooted labeled trees are discussed. A multiplication on rooted labeled trees is defined, thereby making the set of these data structures into an associative algebra. An algebra homomorphism is defined from the original algebra of operators into this algebra of trees. An algebra homomorphism from the algebra of trees into the algebra of differential operators is then described. The cancellation which occurs when noncommuting operators are expressed in terms of commuting ones occurs naturally when the operators are represented using this data structure. This leads to an algorithm which, for operators which are derivations, speeds up the computation exponentially in the degree of the operator. It is shown that the algebra of trees leads naturally to a parallel version of the algorithm.

Computational path planner for product assembly in complex environments

NASA Astrophysics Data System (ADS)

Shang, Wei; Liu, Jianhua; Ning, Ruxin; Liu, Mi

2013-03-01

Assembly path planning is a crucial problem in assembly related design and manufacturing processes. Sampling based motion planning algorithms are used for computational assembly path planning. However, the performance of such algorithms may degrade much in environments with complex product structure, narrow passages or other challenging scenarios. A computational path planner for automatic assembly path planning in complex 3D environments is presented. The global planning process is divided into three phases based on the environment and specific algorithms are proposed and utilized in each phase to solve the challenging issues. A novel ray test based stochastic collision detection method is proposed to evaluate the intersection between two polyhedral objects. This method avoids fake collisions in conventional methods and degrades the geometric constraint when a part has to be removed with surface contact with other parts. A refined history based rapidly-exploring random tree (RRT) algorithm which bias the growth of the tree based on its planning history is proposed and employed in the planning phase where the path is simple but the space is highly constrained. A novel adaptive RRT algorithm is developed for the path planning problem with challenging scenarios and uncertain environment. With extending values assigned on each tree node and extending schemes applied, the tree can adapts its growth to explore complex environments more efficiently. Experiments on the key algorithms are carried out and comparisons are made between the conventional path planning algorithms and the presented ones. The comparing results show that based on the proposed algorithms, the path planner can compute assembly path in challenging complex environments more efficiently and with higher success. This research provides the references to the study of computational assembly path planning under complex environments.

Analysis of data mining classification by comparison of C4.5 and ID algorithms

NASA Astrophysics Data System (ADS)

Sudrajat, R.; Irianingsih, I.; Krisnawan, D.

2017-01-01

The rapid development of information technology, triggered by the intensive use of information technology. For example, data mining widely used in investment. Many techniques that can be used assisting in investment, the method that used for classification is decision tree. Decision tree has a variety of algorithms, such as C4.5 and ID3. Both algorithms can generate different models for similar data sets and different accuracy. C4.5 and ID3 algorithms with discrete data provide accuracy are 87.16% and 99.83% and C4.5 algorithm with numerical data is 89.69%. C4.5 and ID3 algorithms with discrete data provides 520 and 598 customers and C4.5 algorithm with numerical data is 546 customers. From the analysis of the both algorithm it can classified quite well because error rate less than 15%.

Multi-test decision tree and its application to microarray data classification.

PubMed

Czajkowski, Marcin; Grześ, Marek; Kretowski, Marek

2014-05-01

The desirable property of tools used to investigate biological data is easy to understand models and predictive decisions. Decision trees are particularly promising in this regard due to their comprehensible nature that resembles the hierarchical process of human decision making. However, existing algorithms for learning decision trees have tendency to underfit gene expression data. The main aim of this work is to improve the performance and stability of decision trees with only a small increase in their complexity. We propose a multi-test decision tree (MTDT); our main contribution is the application of several univariate tests in each non-terminal node of the decision tree. We also search for alternative, lower-ranked features in order to obtain more stable and reliable predictions. Experimental validation was performed on several real-life gene expression datasets. Comparison results with eight classifiers show that MTDT has a statistically significantly higher accuracy than popular decision tree classifiers, and it was highly competitive with ensemble learning algorithms. The proposed solution managed to outperform its baseline algorithm on 14 datasets by an average 6%. A study performed on one of the datasets showed that the discovered genes used in the MTDT classification model are supported by biological evidence in the literature. This paper introduces a new type of decision tree which is more suitable for solving biological problems. MTDTs are relatively easy to analyze and much more powerful in modeling high dimensional microarray data than their popular counterparts. Copyright © 2014 Elsevier B.V. All rights reserved.

Music-supported therapy in the rehabilitation of subacute stroke patients: a randomized controlled trial.

PubMed

Grau-Sánchez, Jennifer; Duarte, Esther; Ramos-Escobar, Neus; Sierpowska, Joanna; Rueda, Nohora; Redón, Susana; Veciana de Las Heras, Misericordia; Pedro, Jordi; Särkämö, Teppo; Rodríguez-Fornells, Antoni

2018-04-01

The effect of music-supported therapy (MST) as a tool to restore hemiparesis of the upper extremity after a stroke has not been appropriately contrasted with conventional therapy. The aim of this trial was to test the effectiveness of adding MST to a standard rehabilitation program in subacute stroke patients. A randomized controlled trial was conducted in which patients were randomized to MST or conventional therapy in addition to the rehabilitation program. The intensity and duration of the interventions were equated in both groups. Before and after 4 weeks of treatment, motor and cognitive functions, mood, and quality of life (QoL) of participants were evaluated. A follow-up at 3 months was conducted to examine the retention of motor gains. Both groups significantly improved their motor function, and no differences between groups were found. The only difference between groups was observed in the language domain for QoL. Importantly, an association was encountered between the capacity to experience pleasure from music activities and the motor improvement in the MST group. MST as an add-on treatment showed no superiority to conventional therapies for motor recovery. Importantly, patient's intrinsic motivation to engage in musical activities was associated with better motor improvement. © 2018 New York Academy of Sciences.

The MST/Hippo Pathway and Cell Death: A Non-Canonical Affair

PubMed Central

Fallahi, Emma; O’Driscoll, Niamh A.; Matallanas, David

2016-01-01

The MST/Hippo signalling pathway was first described over a decade ago in Drosophila melanogaster and the core of the pathway is evolutionary conserved in mammals. The mammalian MST/Hippo pathway regulates organ size, cell proliferation and cell death. In addition, it has been shown to play a central role in the regulation of cellular homeostasis and it is commonly deregulated in human tumours. The delineation of the canonical pathway resembles the behaviour of the Hippo pathway in the fly where the activation of the core kinases of the pathway prevents the proliferative signal mediated by the key effector of the pathway YAP. Nevertheless, several lines of evidence support the idea that the mammalian MST/Hippo pathway has acquired new features during evolution, including different regulators and effectors, crosstalk with other essential signalling pathways involved in cellular homeostasis and the ability to actively trigger cell death. Here we describe the current knowledge of the mechanisms that mediate MST/Hippo dependent cell death, especially apoptosis. We include evidence for the existence of complex signalling networks where the core proteins of the pathway play a central role in controlling the balance between survival and cell death. Finally, we discuss the possible involvement of these signalling networks in several human diseases such as cancer, diabetes and neurodegenerative disorders. PMID:27322327

Electron Thermal Transport due to Magnetic Diffusion in the MST RFP

NASA Astrophysics Data System (ADS)

Reusch, J. A.; Anderson, J. K.; den Hartog, D. J.; Forest, C. B.; Kasten, C. P.; Schnack, D. D.; Stephens, H. D.

2011-10-01

Comparison of measurements made in the MST RFP to the results from extensive nonlinear resistive MHD simulations has provided two key observations. First, trapped particles reduce electron thermal diffusion; inclusion of this effect is required for quantitative agreement of simulation to measurement. Second, the structure and evolution of long-wavelength temperature fluctuations measured in MST shows remarkable qualitative similarity to fluctuations appearing in a finite-pressure simulation. These simulations were run at parameters matching those of 400 kA discharges in MST (S ~ 4 ×106). In a zero β simulation, the measured χe is compared to the thermal diffusion due to parallel losses along diffusing magnetic field lines, χst =v∥Dmag . Agreement is only found if the reduction in χst due to trapped particles is taken into account. In a second simulation, the pressure field was evolved self consistently assuming Ohmic heating and anisotropic thermal conduction. Fluctuations in the simulated temperature are very similar in character and time evolution to temperature fluctuations measured in MST. This includes m = 1 , n = 6 fluctuations that flatten the temperature profile as well as m = 1 , n = 5 fluctuations that generate hot island structures near the core shortly after sawtooth crashes. This work supported by the US DOE and NSF.

Music-supported therapy induces plasticity in the sensorimotor cortex in chronic stroke: a single-case study using multimodal imaging (fMRI-TMS).

PubMed

Rojo, Nuria; Amengual, Julian; Juncadella, Montserrat; Rubio, Francisco; Camara, Estela; Marco-Pallares, Josep; Schneider, Sabine; Veciana, Misericordia; Montero, Jordi; Mohammadi, Bahram; Altenmüller, Eckart; Grau, Carles; Münte, Thomas F; Rodriguez-Fornells, Antoni

2011-01-01

Music-Supported Therapy (MST) has been developed recently in order to improve the use of the affected upper extremity after stroke. This study investigated the neuroplastic mechanisms underlying effectiveness in a patient with chronic stroke. MST uses musical instruments, a midi piano and an electronic drum set emitting piano sounds, to retrain fine and gross movements of the paretic upper extremity. Data are presented from a patient with a chronic stroke (20 months post-stroke) with residual right-sided hemiparesis who took part in 20 MST sessions over the course of 4 weeks. Post-therapy, a marked improvement of movement quality, assessed by 3D movement analysis, was observed. Moreover, functional magnetic resonance imaging (fMRI) of a sequential hand movement revealed distinct therapy-related changes in the form of a reduction of excess contralateral and ipsilateral activations. This was accompanied by changes in cortical excitability evidenced by transcranial magnetic stimulation (TMS). Functional MRI in a music listening task suggests that one of the effects of MST is the task-dependent coupling of auditory and motor cortical areas. The MST appears to be a useful neurorehabilitation tool in patients with chronic stroke and leads to neural reorganization in the sensorimotor cortex.

Overview of MST Research

NASA Astrophysics Data System (ADS)

Chapman, B. E.

2017-10-01

MST progress in advancing the RFP for (1) fusion plasma confinement with ohmic heating and minimal external magnetization, (2) predictive capability in toroidal confinement physics, and (3) basic plasma physics is summarized. Validation of key plasma models is a program priority, which is enhanced by programmable power supplies (PPS) to maximize inductive capability. The existing PPS enables access to very low plasma current, down to Ip =0.02 MA. This greatly expands the Lundquist number range S =104 -108 and allows nonlinear, 3D MHD computation using NIMROD and DEBS with dimensionless parameters that overlap those of MST plasmas. A new, second PPS will allow simultaneous PPS control of the Bp and Bt circuits. The PPS also enables MST tokamak operation, thus far focused on disruptions and RMP suppression of runaway electrons. Gyrokinetic modeling with GENE predicts unstable TEM in improved-confinement RFP plasmas. Measured fluctuations have TEM properties including a density-gradient threshold larger than for tokamak plasmas. Turbulent energization of an electron tail occurs during sawtooth reconnection. Probe measurements hint that drift waves are also excited via the turbulent cascade in standard RFP plasmas. Exploration of basic plasma science frontiers in MST RFP and tokamak plasmas is proposed as part of WiPPL, a basic science user facility. Work supported by USDoE.

Suppression of high-energy electrons generated in both disrupting and sustained MST tokamak plasmas

NASA Astrophysics Data System (ADS)

Pandya, M. D.; Chapman, B. E.; Munaretto, S.; Cornille, B. S.; McCollam, K. J.; Sovinec, C. R.; Dubois, A. M.; Almagri, A. F.; Goetz, J. A.

2017-10-01

High-energy electrons appearing during MST tokamak plasma disruptions are rapidly lost from the plasma due apparently to internal MHD activity. Work has just recently begun on generating and diagnosing disruptions in MST tokamak plasmas. Initial measurements show the characteristic drop in central temperature and density preceding a quench of the plasma current. This corresponds to a burst of dominantly n=1 MHD activity, which is accompanied by a short-lived burst of high-energy electrons. The short-lived nature of these electrons is suspected to be due to stochastic transport associated with the increased MHD. Earlier work shows that runaway electrons generated in low density, sustained plasmas are suppressed by a sufficiently large m=3 RMP in plasmas with q(a) <3. RMPs of various poloidal mode number can be generated with an array of saddle coils wound around the vertical insulated gap in MST's thick conducting shell. With an m=3 RMP, the degree of runaway suppression increases with RMP amplitude, while an m=1 RMP has little effect on the runaways. Nonlinear MHD modeling with NIMROD of these MST plasmas indicates increased stochasticity with an m=3 RMP, while no such increase in stochasticity is observed with an m=1 RMP. Work supported by US DOE.

The Magellan seamount trail: implications for Cretaceous hotspot volcanism and absolute Pacific plate motion

NASA Astrophysics Data System (ADS)

Koppers, Anthony A. P.; Staudigel, Hubert; Wijbrans, Jan R.; Pringle, Malcolm S.

1998-11-01

The Magellan Seamount Trail (MST) delineates a northwest trending chain of four Cretaceous guyots in the West Pacific Seamount Province (WPSP). Seamount morphology, 40Ar/ 39Ar geochronology and Sr-Nd-Pb geochemistry of the MST provides evidence for a hotspot origin between the Samoa, Rarotonga and Society hotspots of the South Pacific Isotopic and Thermal Anomaly (SOPITA). The MST yields an excellent linear age progression of 47.6±1.6 mm/yr ( r2=1.000; MSWD = 0.23; 1 σ SE) including Vlinder guyot (95.1±0.5 Ma, n=5; 2 σ SD), Pako guyot (91.3±0.3 Ma, n=3) and Ioah guyot (87.1±0.3 Ma, n=2). The MST also exhibits a small range in Sr-Nd-Pb isotopic compositions indicating enriched mantle sources with an affinity of EMI. Nevertheless, three volcanic events are found out of sequence with linear MST hotspot volcanism: (1) an independent volcanic pedestal was formed 4-7 Myr before shield-volcanism started at Vlinder guyot, (2) a post-erosional volcanic cone was formed at least 20-30 Myr after drowning of Vlinder guyot, and (3) Ita Mai Tai guyot (118.1±0.5 Ma, n=3) was formed 34-36 Myr before the MST hotspot arrived at the predicted location of this guyot. By identifying and ruling out discordant volcanic events, we can use the age progression in MST to test the fixity of its hotspot. When presuming the fixed hotspot hypothesis, the local age progressions of the MST (47.6±1.6 mm/yr) and the copolar Musicians seamount trail (55.8±6.4 mm/yr) are not compatible with their 100-80 Ma Euler pole. We investigate two options: (1) acceptance of a `forced' Euler pole obeying the hotspot hypothesis by using both the age progressions and the azimuths of the studied seamount trails, or (2) acceptance of a `best-fit' Euler pole by using the azimuths of the studied seamount trail exclusively. In the first option, the angular speed of the Pacific plate during the 100-80 Ma stage pole is calculated at 0.502±0.017°/Myr. In the second option, the `best-fit' Euler pole is found approximately 35° different from the `forced' Euler pole. We argue that the observed age progressions can only be reconciled with the `best-fit' pole when allowing for the relative movement of the MST and Musicians mantle plumes with respect to one another. The calculated maximum velocity component parallel to the line of age progression could then be as much as 23 mm/yr for the mantle plumes — when assuming one fixed hotspot in this alternate model.

SELECTIVE REMOVAL OF STRONTIUM AND CESIUM FROM SIMULATED WASTE SOLUTION WITH TITANATE ION EXCHANGERS IN A FILTER CARTRIDGE CONFIGURATION

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

Oji, L.; Martin, K.; Hobbs, D.

2011-05-26

This report describes experimental results for the selective removal of strontium and cesium from simulated waste solutions using monosodium titanate (MST) and crystalline silicotitanate (CST)-laden filter cartridges. Four types of ion exchange cartridge media (CST and MST designed by both 3M and POROX{reg_sign}) were evaluated. In these proof-of-principle tests effective uptake of both Sr-85 and Cs-137 was observed. However, the experiments were not performed long enough to determine the saturation levels or breakthrough curve for each filter cartridge. POREX{reg_sign} MST cartridges, which by design were based on co-sintering of the active titanates with polyethylene particles, seem to perform as wellmore » as the 3M-designed MST cartridges (impregnated filter membrane design) in the uptake of strontium. At low salt simulant conditions (0.29 M Na{sup +}), the instantaneous decontamination factor (D{sub F}) for Sr-85 with the 3M-design MST cartridge measured 26, representing the removal of 96% of the Sr-85. On the other hand, the Sr-85 instantaneous D{sub F} with the POREX{reg_sign} design MST cartridge measured 40 or 98% removal of the Sr-85. Strontium removal with the 3M-design MST and CST cartridges placed in series filter arrangement produced an instantaneous decontamination factor of 41 or 97.6% removal compared to an instantaneous decontamination factor of 368 or 99.7% removal of the strontium with the POREX{reg_sign} MST and CST cartridge design placed in series. At high salt simulant conditions (5.6 M Na{sup +}), strontium removal with 3M-designed MST cartridge only and with 3M-designed MST and CST cartridges operated in a series configuration were identical. The instantaneous decontamination factor and the strontium removal efficiency, under the above configuration, averaged 8.6 and 88%, respectively. There were no POREX{reg_sign} cartridge experiments using the higher ionic strength simulant solution. At low salt simulant conditions, the uptake of Cs-137 with POREX{reg_sign} CST cartridge out performed the 3M-designed CST cartridges. The POREX{reg_sign} CST cartridge, with a Cs-137 instantaneous decontamination factor of 55 and a Cs-137 removal efficiency of 98% does meet the Cs-137 decontamination goals in the low salt simulant liquor. The Cs-137 removal with 3M-designed CST cartridge produced a decontamination factor of 2 or 49% removal efficiency. The Cs-137 performance graph for the 3M-designed CST cartridge showed an early cessation in the uptake of cesium-137. This behavior was not observed with the POREX{reg_sign} CST cartridges. No Cs-137 uptake tests were performed with the POREX{reg_sign} CST cartridges at high salt simulant conditions. The 3M-designed CST cartridges, with an instantaneous Cs-137 decontamination factor of less than 3 and a Cs-137 removal efficiency of less than 50% failed to meet the Cs-137 decontamination goals in both the low and high salt simulant liquors. This poor performance in the uptake of Cs-137 by the 3M CST cartridges may be attributed to fabrication flaws for the 3M-designed CST cartridges. The reduced number of CST membrane wraps per cartridge during the cartridge design phase, from 3-whole wraps to about 1.5, may have contributed to Cs-137 laden simulant channeling/by-pass which led to the poor performance in terms of Cs-137 sorption characteristics for the 3M designed CST cartridges. The grinding of CST ion exchange materials, to reduce the particle size distribution and thus enhance their easy incorporation into the filter membranes and the co-sintering of MST with polyethylene particles, did not adversely affect the sorption kinetics of both CST and MST in the uptake of Cs-137 and Sr-85, respectively. In general, the POREX{reg_sign} based cartridges showed more resistance to simulant flow through the filter cartridges as evidenced by higher pressure differences across the cartridges. Based on these findings they conclude that incorporating MST and CST sorbents into filter membranes represent a promising method for the semi-continuous removal of radioisotopes of strontium and cesium from waste solutions.« less

Accuracy Assessment of Crown Delineation Methods for the Individual Trees Using LIDAR Data

NASA Astrophysics Data System (ADS)

Chang, K. T.; Lin, C.; Lin, Y. C.; Liu, J. K.

2016-06-01

Forest canopy density and height are used as variables in a number of environmental applications, including the estimation of biomass, forest extent and condition, and biodiversity. The airborne Light Detection and Ranging (LiDAR) is very useful to estimate forest canopy parameters according to the generated canopy height models (CHMs). The purpose of this work is to introduce an algorithm to delineate crown parameters, e.g. tree height and crown radii based on the generated rasterized CHMs. And accuracy assessment for the extraction of volumetric parameters of a single tree is also performed via manual measurement using corresponding aerial photo pairs. A LiDAR dataset of a golf course acquired by Leica ALS70-HP is used in this study. Two algorithms, i.e. a traditional one with the subtraction of a digital elevation model (DEM) from a digital surface model (DSM), and a pit-free approach are conducted to generate the CHMs firstly. Then two algorithms, a multilevel morphological active-contour (MMAC) and a variable window filter (VWF), are implemented and used in this study for individual tree delineation. Finally, experimental results of two automatic estimation methods for individual trees can be evaluated with manually measured stand-level parameters, i.e. tree height and crown diameter. The resulting CHM generated by a simple subtraction is full of empty pixels (called "pits") that will give vital impact on subsequent analysis for individual tree delineation. The experimental results indicated that if more individual trees can be extracted, tree crown shape will became more completely in the CHM data after the pit-free process.

Aneurysmal subarachnoid hemorrhage prognostic decision-making algorithm using classification and regression tree analysis.

PubMed

Lo, Benjamin W Y; Fukuda, Hitoshi; Angle, Mark; Teitelbaum, Jeanne; Macdonald, R Loch; Farrokhyar, Forough; Thabane, Lehana; Levine, Mitchell A H

2016-01-01

Classification and regression tree analysis involves the creation of a decision tree by recursive partitioning of a dataset into more homogeneous subgroups. Thus far, there is scarce literature on using this technique to create clinical prediction tools for aneurysmal subarachnoid hemorrhage (SAH). The classification and regression tree analysis technique was applied to the multicenter Tirilazad database (3551 patients) in order to create the decision-making algorithm. In order to elucidate prognostic subgroups in aneurysmal SAH, neurologic, systemic, and demographic factors were taken into account. The dependent variable used for analysis was the dichotomized Glasgow Outcome Score at 3 months. Classification and regression tree analysis revealed seven prognostic subgroups. Neurological grade, occurrence of post-admission stroke, occurrence of post-admission fever, and age represented the explanatory nodes of this decision tree. Split sample validation revealed classification accuracy of 79% for the training dataset and 77% for the testing dataset. In addition, the occurrence of fever at 1-week post-aneurysmal SAH is associated with increased odds of post-admission stroke (odds ratio: 1.83, 95% confidence interval: 1.56-2.45, P < 0.01). A clinically useful classification tree was generated, which serves as a prediction tool to guide bedside prognostication and clinical treatment decision making. This prognostic decision-making algorithm also shed light on the complex interactions between a number of risk factors in determining outcome after aneurysmal SAH.

Individual tree detection in intact forest and degraded forest areas in the north region of Mato Grosso State, Brazilian Amazon

NASA Astrophysics Data System (ADS)

Santos, E. G.; Jorge, A.; Shimabukuro, Y. E.; Gasparini, K.

2017-12-01

The State of Mato Grosso - MT has the second largest area with degraded forest among the states of the Brazilian Legal Amazon. Land use and land cover change processes that occur in this region cause the loss of forest biomass, releasing greenhouse gases that contribute to the increase of temperature on earth. These degraded forest areas lose biomass according to the intensity and magnitude of the degradation type. The estimate of forest biomass, commonly performed by forest inventory through sample plots, shows high variance in degraded forest areas. Due to this variance and complexity of tropical forests, the aim of this work was to estimate forest biomass using LiDAR point clouds in three distinct forest areas: one degraded by fire, another by selective logging and one area of intact forest. The approach applied in these areas was the Individual Tree Detection (ITD). To isolate the trees, we generated Canopy Height Models (CHM) images, which are obtained by subtracting the Digital Elevation Model (MDE) and the Digital Terrain Model (MDT), created by the cloud of LiDAR points. The trees in the CHM images are isolated by an algorithm provided by the Quantitative Ecology research group at the School of Forestry at Northern Arizona University (SILVA, 2015). With these points, metrics were calculated for some areas, which were used in the model of biomass estimation. The methodology used in this work was expected to reduce the error in biomass estimate in the study area. The cloud points of the most representative trees were analyzed, and thus field data was correlated with the individual trees found by the proposed algorithm. In a pilot study, the proposed methodology was applied generating the individual tree metrics: total height and area of the crown. When correlating 339 isolated trees, an unsatisfactory R² was obtained, as heights found by the algorithm were lower than those obtained in the field, with an average difference of 2.43 m. This shows that the algorithm used to isolate trees in temperate areas did not obtained satisfactory results in the tropical forest of Mato Grosso State. Due to this, in future works two algorithms, one developed by Dalponte et al. (2015) and another by Li et al. (2012) will be used.

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.

PubMed

Soria-Carrasco, Víctor; Talavera, Gerard; Igea, Javier; Castresana, Jose

2007-11-01

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree. http://molevol.ibmb.csic.es/Ktreedist.html

Triplet supertree heuristics for the tree of life

PubMed Central

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver

2009-01-01

Background There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogenetic tree that contains all of the taxa in the input trees. The intrinsically hard triplet supertree problem takes a collection of input species trees and seeks a species tree (supertree) that maximizes the number of triplet subtrees that it shares with the input trees. However, the utility of this supertree problem has been limited by a lack of efficient and effective heuristics. Results We introduce fast hill-climbing heuristics for the triplet supertree problem that perform a step-wise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. To realize time efficient heuristics we designed the first nontrivial algorithms for two standard search problems, which greatly improve on the time complexity to the best known (naïve) solutions by a factor of n and n2 (the number of taxa in the supertree). These algorithms enable large-scale supertree analyses based on the triplet supertree problem that were previously not possible. We implemented hill-climbing heuristics that are based on our new algorithms, and in analyses of two published supertree data sets, we demonstrate that our new heuristics outperform other standard supertree methods in maximizing the number of triplets shared with the input trees. Conclusion With our new heuristics, the triplet supertree problem is now computationally more tractable for large-scale supertree analyses, and it provides a potentially more accurate alternative to existing supertree methods. PMID:19208181

Simulating Urban Tree Effects on Air, Water, and Heat Pollution Mitigation: iTree-Hydro Model

NASA Astrophysics Data System (ADS)

Yang, Y.; Endreny, T. A.; Nowak, D.

2011-12-01

Urban and suburban development changes land surface thermal, radiative, porous, and roughness properties and pollutant loading rates, with the combined effect leading to increased air, water, and heat pollution (e.g., urban heat islands). In this research we present the USDA Forest Service urban forest ecosystem and hydrology model, iTree Eco and Hydro, used to analyze how tree cover can deliver valuable ecosystem services to mitigate air, water, and heat pollution. Air pollution mitigation is simulated by dry deposition processes based on detected pollutant levels for CO, NO2, SO2, O3 and atmospheric stability and leaf area indices. Water quality mitigation is simulated with event mean concentration loading algorithms for N, P, metals, and TSS, and by green infrastructure pollutant filtering algorithms that consider flow path dispersal areas. Urban cooling considers direct shading and indirect evapotranspiration. Spatially distributed estimates of hourly tree evapotranspiration during the growing season are used to estimate human thermal comfort. Two main factors regulating evapotranspiration are soil moisture and canopy radiation. Spatial variation of soil moisture is represented by a modified urban topographic index and radiation for each tree is modified by considering aspect, slope and shade from surrounding buildings or hills. We compare the urban cooling algorithms used in iTree-Hydro with the urban canopy and land surface physics schemes used in the Weather Research and Forecasting model. We conclude by identifying biophysical feedbacks between tree-modulated air and water quality environmental services and how these may respond to urban heating and cooling. Improvements to this iTree model are intended to assist managers identify valuable tree services for urban living.

A combined NLP-differential evolution algorithm approach for the optimization of looped water distribution systems

NASA Astrophysics Data System (ADS)

Zheng, Feifei; Simpson, Angus R.; Zecchin, Aaron C.

2011-08-01

This paper proposes a novel optimization approach for the least cost design of looped water distribution systems (WDSs). Three distinct steps are involved in the proposed optimization approach. In the first step, the shortest-distance tree within the looped network is identified using the Dijkstra graph theory algorithm, for which an extension is proposed to find the shortest-distance tree for multisource WDSs. In the second step, a nonlinear programming (NLP) solver is employed to optimize the pipe diameters for the shortest-distance tree (chords of the shortest-distance tree are allocated the minimum allowable pipe sizes). Finally, in the third step, the original looped water network is optimized using a differential evolution (DE) algorithm seeded with diameters in the proximity of the continuous pipe sizes obtained in step two. As such, the proposed optimization approach combines the traditional deterministic optimization technique of NLP with the emerging evolutionary algorithm DE via the proposed network decomposition. The proposed methodology has been tested on four looped WDSs with the number of decision variables ranging from 21 to 454. Results obtained show the proposed approach is able to find optimal solutions with significantly less computational effort than other optimization techniques.

Exploiting machine learning algorithms for tree species classification in a semiarid woodland using RapidEye image

NASA Astrophysics Data System (ADS)

Adelabu, Samuel; Mutanga, Onisimo; Adam, Elhadi; Cho, Moses Azong

2013-01-01

Classification of different tree species in semiarid areas can be challenging as a result of the change in leaf structure and orientation due to soil moisture constraints. Tree species mapping is, however, a key parameter for forest management in semiarid environments. In this study, we examined the suitability of 5-band RapidEye satellite data for the classification of five tree species in mopane woodland of Botswana using machine leaning algorithms with limited training samples.We performed classification using random forest (RF) and support vector machines (SVM) based on EnMap box. The overall accuracies for classifying the five tree species was 88.75 and 85% for both SVM and RF, respectively. We also demonstrated that the new red-edge band in the RapidEye sensor has the potential for classifying tree species in semiarid environments when integrated with other standard bands. Similarly, we observed that where there are limited training samples, SVM is preferred over RF. Finally, we demonstrated that the two accuracy measures of quantity and allocation disagreement are simpler and more helpful for the vast majority of remote sensing classification process than the kappa coefficient. Overall, high species classification can be achieved using strategically located RapidEye bands integrated with advanced processing algorithms.

Military Sexual Trauma

MedlinePlus

... associated with MST among users of VA health care are depression and other mood disorders, and substance use disorders. Fortunately, people can recover from experiences of trauma, and VA has effective services to help Veterans do ... VA health care system has a designated MST Coordinator who serves ...

21. STATION 70.5 OF MST, WEST SIDE. AIRCONDITIONING DUCT AT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

21. STATION 70.5 OF MST, WEST SIDE. AIR-CONDITIONING DUCT AT TOP; POWER BOX ON RIGHT; WINCH ON LEFT. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

4. VIEW OF NORTH FACE OF MST. NOTE: ENVIRONMENTAL DOOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. VIEW OF NORTH FACE OF MST. NOTE: ENVIRONMENTAL DOOR ON THE LOWER EAST SIDE OF THE NORTH FACE IS MISSING. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

22. DOOR CONTROL BOX AT STATION 70.5 OF MST FOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. DOOR CONTROL BOX AT STATION 70.5 OF MST FOR CONTROL OF SOUTH DOORS. NITROGEN PRESSURE REGULATOR ON LEFT. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

IDENTIFICATION OF SOURCES OF FECAL POLLUTION IN ENVIRONMENTAL WATERS

EPA Science Inventory

A number of Microbial Source Tracking (MST) methods are currently used to determine the origin of fecal pollution impacting environmental waters. MST is based on the assumption that given the appropriate method and indicator organism, the source of fecal microbial pollution can ...

Functional correlates of military sexual assault in male veterans.

PubMed

Schry, Amie R; Hibberd, Rachel; Wagner, H Ryan; Turchik, Jessica A; Kimbrel, Nathan A; Wong, Madrianne; Elbogen, Eric E; Strauss, Jennifer L; Brancu, Mira

2015-11-01

Despite research findings that similar numbers of male and female veterans are affected by military sexual trauma (MST), there has been considerably less research on the effects of MST specific to male veterans. The aim of the present study was to provide preliminary data describing functional correlates of military sexual assault (MSA) among male Iraq/Afghanistan-era veterans to identify potential health care needs for this population. We evaluated the following functional correlates: posttraumatic stress disorder (PTSD) symptoms, depression symptoms, alcohol use, drug use, suicidality, social support, violent behavior in the past 30 days, incarceration, disability eligibility status, and use of outpatient mental health treatment. We compared 3 groups: (a) male veterans who endorsed a history of MSA (n = 39), (b) a general non-MSA sample (n = 2,003), and (c) a matched non-MSA sample (n = 39) identified by matching algorithms on the basis of factors (e.g., age, education, adult premilitary sexual trauma history, childhood sexual and physical trauma history, and race) that could increase veterans' vulnerability to the functional correlates examined. MSA in men was associated with greater PTSD symptom severity, greater depression symptom severity, higher suicidality, and higher outpatient mental health treatment, above and beyond the effects of vulnerability factors. These findings suggest that, for male veterans, MSA may result in a severe and enduring overall symptom profile requiring ongoing clinical management. (c) 2015 APA, all rights reserved).

Binary tree eigen solver in finite element analysis

NASA Technical Reports Server (NTRS)

Akl, F. A.; Janetzke, D. C.; Kiraly, L. J.

1993-01-01

This paper presents a transputer-based binary tree eigensolver for the solution of the generalized eigenproblem in linear elastic finite element analysis. The algorithm is based on the method of recursive doubling, which parallel implementation of a number of associative operations on an arbitrary set having N elements is of the order of o(log2N), compared to (N-1) steps if implemented sequentially. The hardware used in the implementation of the binary tree consists of 32 transputers. The algorithm is written in OCCAM which is a high-level language developed with the transputers to address parallel programming constructs and to provide the communications between processors. The algorithm can be replicated to match the size of the binary tree transputer network. Parallel and sequential finite element analysis programs have been developed to solve for the set of the least-order eigenpairs using the modified subspace method. The speed-up obtained for a typical analysis problem indicates close agreement with the theoretical prediction given by the method of recursive doubling.

Rapid Calculation of Max-Min Fair Rates for Multi-Commodity Flows in Fat-Tree Networks

DOE PAGES

Mollah, Md Atiqul; Yuan, Xin; Pakin, Scott; ...

2017-08-29

Max-min fairness is often used in the performance modeling of interconnection networks. Existing methods to compute max-min fair rates for multi-commodity flows have high complexity and are computationally infeasible for large networks. In this paper, we show that by considering topological features, this problem can be solved efficiently for the fat-tree topology that is widely used in data centers and high performance compute clusters. Several efficient new algorithms are developed for this problem, including a parallel algorithm that can take advantage of multi-core and shared-memory architectures. Using these algorithms, we demonstrate that it is possible to find the max-min fairmore » rate allocation for multi-commodity flows in fat-tree networks that support tens of thousands of nodes. We evaluate the run-time performance of the proposed algorithms and show improvement in orders of magnitude over the previously best known method. Finally, we further demonstrate a new application of max-min fair rate allocation that is only computationally feasible using our new algorithms.« less

Rapid Calculation of Max-Min Fair Rates for Multi-Commodity Flows in Fat-Tree Networks

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

Mollah, Md Atiqul; Yuan, Xin; Pakin, Scott

Max-min fairness is often used in the performance modeling of interconnection networks. Existing methods to compute max-min fair rates for multi-commodity flows have high complexity and are computationally infeasible for large networks. In this paper, we show that by considering topological features, this problem can be solved efficiently for the fat-tree topology that is widely used in data centers and high performance compute clusters. Several efficient new algorithms are developed for this problem, including a parallel algorithm that can take advantage of multi-core and shared-memory architectures. Using these algorithms, we demonstrate that it is possible to find the max-min fairmore » rate allocation for multi-commodity flows in fat-tree networks that support tens of thousands of nodes. We evaluate the run-time performance of the proposed algorithms and show improvement in orders of magnitude over the previously best known method. Finally, we further demonstrate a new application of max-min fair rate allocation that is only computationally feasible using our new algorithms.« less

Economic Impact of the Statewide Implementation of an Evidence-Based Treatment: Multisystemic Therapy in New Mexico.

PubMed

Dopp, Alex R; Coen, Anita Saranga; Smith, Allison B; Reno, Jessica; Bernstein, David H; Kerns, Suzanne E U; Altschul, Deborah

2018-07-01

Several states have made considerable investments into large-scale implementation of evidence-based treatments (EBTs), yet little is known about key success indicators for these implementation efforts such as cost and sustainability. To that end, the present study examined the economic impact of statewide implementation of multisystemic therapy (MST; Henggeler, Schoenwald, Borduin, Rowland, & Cuningham, 2009), a family- and community-based behavioral EBT for serious juvenile offenders in New Mexico. Participants were 1,869 youth who received MST across 23 teams during the study period. We conducted a cost-benefit analysis using metrics from state data sources that compared the cost of MST to its benefits (i.e., avoided expenses from pre- to posttreatment) in two domains: (a) behavioral health services (i.e., Medicaid claims) and (b) juvenile crime (i.e., taxpayer expenses, tangible and intangible expenses to crime victims). MST costs were based on Medicaid claims, which were reimbursed at an enhanced billing rate that was intended to cover expenses for both clinical and implementation (e.g., training, quality assurance) activities. Results suggest that implementation of MST in New Mexico over the 7-year study period may have produced net benefits, through 2 years posttreatment, of more than $4,643 per youth in avoided behavioral health claims and $15,019 per youth through reductions in juvenile crime. Stated differently, every dollar that New Mexico spent on MST appeared to have returned $3.34 for a total benefit of $64.2 million over the course of the study. We discuss implications of these findings for policymakers, administrators, and researchers who are interested in increasing the sustainability of complex EBTs in community settings. Copyright © 2018. Published by Elsevier Ltd.

Autologous Cartilage Chip Transplantation Improves Repair Tissue Composition Compared With Marrow Stimulation.

PubMed

Christensen, Bjørn Borsøe; Olesen, Morten Lykke; Lind, Martin; Foldager, Casper Bindzus

2017-06-01

Repair of chondral injuries by use of cartilage chips has recently demonstrated clinical feasibility. To investigate in vivo cartilage repair outcome of autologous cartilage chips compared with marrow stimulation in full-thickness cartilage defects in a minipig model. Controlled laboratory study. Six Göttingen minipigs received two 6-mm chondral defects in the medial and lateral trochlea of each knee. The two treatment groups were (1) autologous cartilage chips embedded in fibrin glue (ACC) (n = 12) and (2) marrow stimulation (MST) (n = 12). The animals were euthanized after 6 months, and the composition of repair tissue was quantitatively determined using histomorphometry. Semiquantitative evaluation was performed by means of the International Cartilage Repair Society (ICRS) II score. Collagen type II staining was used to further evaluate the repair tissue composition. Significantly more hyaline cartilage was found in the ACC (17.1%) compared with MST (2.9%) group ( P < .01). Furthermore, the ACC group had significantly less fibrous tissue (23.8%) compared with the MST group (41.1%) ( P < .01). No significant difference in fibrocartilage content was found (54.7% for ACC vs 50.8% for MST). The ACC group had significantly higher ICRS II scores for tissue morphological characteristics, matrix staining, cell morphological characteristics, surface assessment, mid/deep assessment, and overall assessment ( P < .05). The ACC-treated defects had significantly more collagen type II staining (54.5%) compared with the MST-treated defects (28.1%) ( P < .05). ACC transplant resulted in improved quality of cartilage repair tissue compared with MST at 6 months postoperatively. Further studies are needed to investigate ACC as a possible alternative first-line treatment for focal cartilage injuries in the knee.

Does standard deviation matter? Using "standard deviation" to quantify security of multistage testing.

PubMed

Wang, Chun; Zheng, Yi; Chang, Hua-Hua

2014-01-01

With the advent of web-based technology, online testing is becoming a mainstream mode in large-scale educational assessments. Most online tests are administered continuously in a testing window, which may post test security problems because examinees who take the test earlier may share information with those who take the test later. Researchers have proposed various statistical indices to assess the test security, and one most often used index is the average test-overlap rate, which was further generalized to the item pooling index (Chang & Zhang, 2002, 2003). These indices, however, are all defined as the means (that is, the expected proportion of common items among examinees) and they were originally proposed for computerized adaptive testing (CAT). Recently, multistage testing (MST) has become a popular alternative to CAT. The unique features of MST make it important to report not only the mean, but also the standard deviation (SD) of test overlap rate, as we advocate in this paper. The standard deviation of test overlap rate adds important information to the test security profile, because for the same mean, a large SD reflects that certain groups of examinees share more common items than other groups. In this study, we analytically derived the lower bounds of the SD under MST, with the results under CAT as a benchmark. It is shown that when the mean overlap rate is the same between MST and CAT, the SD of test overlap tends to be larger in MST. A simulation study was conducted to provide empirical evidence. We also compared the security of MST under the single-pool versus the multiple-pool designs; both analytical and simulation studies show that the non-overlapping multiple-pool design will slightly increase the security risk.

Measurement of cardiorespiratory fitness in children from two commonly used field tests after accounting for body fatness and maturity.

PubMed

Hamlin, Michael J; Fraser, Meegan; Lizamore, Catherine A; Draper, Nick; Shearman, Jeremy P; Kimber, Nicholas E

2014-03-27

Body fat and maturation both influence cardiorespiratory fitness, however few studies have taken these variables into account when using field tests to predict children's fitness levels. The purpose of this study was to determine the relationship between two field tests of cardiorespiratory fitness (20 m Maximal Multistage Shuttle Run [20-MST], 550 m distance run [550-m]) and direct measurement of VO2max after adjustment for body fatness and maturity levels. Fifty-three participants (25 boys, 28 girls, age 10.6 ± 1.2 y, mean ± SD) had their body fat levels estimated using bioelectrical impedance (16.6% ± 6.0% and 20.0% ± 5.8% for boys and girls, respectively). Participants performed in random order, the 20-MST and 550-m run followed by a progressive treadmill test to exhaustion during which gas exchange measures were taken. Pearson correlation coefficient analysis revealed that the participants' performance in the 20-MST and 550-m run were highly correlated to VO2max obtained during the treadmill test to exhaustion (r = 0.70 and 0.59 for 20-MST and 550-m run, respectively). Adjusting for body fatness and maturity levels in a multivariate regression analysis increased the associations between the field tests and VO2max (r = 0.73 for 20-MST and 0.65 for 550-m). We may conclude that both the 20-MST and the 550-m distance run are valid field tests of cardiorespiratory fitness in New Zealand 8-13 year old children and incorporating body fatness and maturity levels explains an additional 5-7% of the variance.

Identifying fecal sources in a selected catchment reach using multiple source-tracking tools

USGS Publications Warehouse

Vogel, J.R.; Stoeckel, D.M.; Lamendella, R.; Zelt, R.B.; Santo, Domingo J.W.; Walker, S.R.; Oerther, D.B.

2007-01-01

Given known limitations of current microbial source-tracking (MST) tools, emphasis on small, simple study areas may enhance interpretations of fecal contamination sources in streams. In this study, three MST tools - Escherichia coli repetitive element polymerase chain reaction (rep-PCR), coliphage typing, and Bacteroidales 16S rDNA host-associated markers - were evaluated in a selected reach of Plum Creek in sooth-central Nebraska. Water-quality samples were collected from six sites. One reach was selected for MST evaluation based on observed patterns of E. coli contamination. Despite high E. coli concentrations, coliphages were detected only once among water samples, precluding their use as a MST tool in this setting. Rep-PCR classification of E. coli isolates from both water and sediment samples supported the hypothesis that cattle and wildlife were dominant sources of fecal contamination, with minor contributions by horses and humans. Conversely, neither ruminant nor human sources were detected by Bacteroidales markers in most water samples. In bed sediment, ruminant- and human-associated Bacteroidales markers were detected throughout the interval from 0 to 0.3 m, with detections independent of E. coli concentrations in the sediment. Although results by E. coli-based and Bacteroidales-based MST methods led to similar interpretations, detection of Bacteroidales markers in sediment more commonly than in water indicates that different tools to track fecal contamination (in this case, tools based on Bacteroidales DNA and E. coli isolates) may have varying relevance to the more specific goal of tracking the sources of E. coli in watersheds. This is the first report of simultaneous, toolbox approach application of a library-based and marker-based MST analyses to lowing surface water. ?? ASA, CSSA, SSSA.

Individualized Low-Amplitude Seizure Therapy: Minimizing Current for Electroconvulsive Therapy and Magnetic Seizure Therapy

PubMed Central

Peterchev, Angel V; Krystal, Andrew D; Rosa, Moacyr A; Lisanby, Sarah H

2015-01-01

Electroconvulsive therapy (ECT) at conventional current amplitudes (800–900 mA) is highly effective but carries the risk of cognitive side effects. Lowering and individualizing the current amplitude may reduce side effects by virtue of a less intense and more focal electric field exposure in the brain, but this aspect of ECT dosing is largely unexplored. Magnetic seizure therapy (MST) induces a weaker and more focal electric field than ECT; however, the pulse amplitude is not individualized and the minimum amplitude required to induce a seizure is unknown. We titrated the amplitude of long stimulus trains (500 pulses) as a means of determining the minimum current amplitude required to induce a seizure with ECT (bilateral, right unilateral, bifrontal, and frontomedial electrode placements) and MST (round coil on vertex) in nonhuman primates. Furthermore, we investigated a novel method of predicting this amplitude-titrated seizure threshold (ST) by a non-convulsive measurement of motor threshold (MT) using single pulses delivered through the ECT electrodes or MST coil. Average STs were substantially lower than conventional pulse amplitudes (112–174 mA for ECT and 37.4% of maximum device amplitude for MST). ST was more variable in ECT than in MST. MT explained 63% of the ST variance and is hence the strongest known predictor of ST. These results indicate that seizures can be induced with less intense electric fields than conventional ECT that may be safer; efficacy and side effects should be evaluated in clinical studies. MT measurement could be a faster and safer alternative to empirical ST titration for ECT and MST. PMID:25920013

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

USGS Publications Warehouse

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

2012-01-01

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

Microbial Source Tracking in Adjacent Karst Springs.

PubMed

Ohad, Shoshanit; Vaizel-Ohayon, Dalit; Rom, Meir; Guttman, Joseph; Berger, Diego; Kravitz, Valeria; Pilo, Shlomo; Huberman, Zohar; Kashi, Yechezkel; Rorman, Efrat

2015-08-01

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Comparison of electric field strength and spatial distribution of electroconvulsive therapy and magnetic seizure therapy in a realistic human head model

PubMed Central

Lee, Won Hee; Lisanby, Sarah H.; Laine, Andrew F.; Peterchev, Angel V.

2017-01-01

Background This study examines the strength and spatial distribution of the electric field induced in the brain by electroconvulsive therapy (ECT) and magnetic seizure therapy (MST). Methods The electric field induced by standard (bilateral, right unilateral, and bifrontal) and experimental (focal electrically administered seizure therapy and frontomedial) ECT electrode configurations as well as a circular MST coil configuration was simulated in an anatomically realistic finite element model of the human head. Maps of the electric field strength relative to an estimated neural activation threshold were used to evaluate the stimulation strength and focality in specific brain regions of interest for these ECT and MST paradigms and various stimulus current amplitudes. Results The standard ECT configurations and current amplitude of 800–900 mA produced the strongest overall stimulation with median of 1.8–2.9 times neural activation threshold and more than 94% of the brain volume stimulated at suprathreshold level. All standard ECT electrode placements exposed the hippocampi to suprathreshold electric field, although there were differences across modalities with bilateral and right unilateral producing respectively the strongest and weakest hippocampal stimulation. MST stimulation is up to 9 times weaker compared to conventional ECT, resulting in direct activation of only 21% of the brain. Reducing the stimulus current amplitude can make ECT as focal as MST. Conclusions The relative differences in electric field strength may be a contributing factor for the cognitive sparing observed with right unilateral compared to bilateral ECT, and MST compared to right unilateral ECT. These simulations could help understand the mechanisms of seizure therapies and develop interventions with superior risk/benefit ratio. PMID:27318858

Mental stress test: a rapid, simple, and efficient test to unmask long QT syndrome.

PubMed

Etienne, Pauline; Huchet, François; Gaborit, Nathalie; Barc, Julien; Thollet, Aurélie; Kyndt, Florence; Guyomarch, Béatrice; Le Marec, Hervé; Charpentier, Flavien; Schott, Jean-Jacques; Redon, Richard; Probst, Vincent; Gourraud, Jean-Baptiste

2018-04-20

QT prolongation during mental stress test (MST) has been associated with familial idiopathic ventricular fibrillation. In long QT syndrome (LQTS), up to 30% of mutation carriers have normal QT duration. Our aim was to assess the QT response during MST, and its accuracy in the diagnosis of concealed LQTS. All patients who are carrier of a KCNQ1 or KCNH2 mutations without QT prolongation were enrolled. A control group was constituted of patients with negative exercise and epinephrine tests. Electrocardiogram were recorded at rest and at the maximum heart rate during MST and reviewed by two physicians. Among the 70 patients enrolled (median age 41±2.1 years, 46% male), 36 were mutation carrier for LQTS (20 KCNQ1 and 16 KCNH2), and 34 were controls. KCNQ1 and KCNH2 mutation carriers presented a longer QT interval at baseline [405(389; 416) and 421 (394; 434) ms, respectively] compared with the controls [361(338; 375)ms; P < 0.0001]. QT duration during MST varied by 9 (4; 18) ms in KCNQ1, 3 (-6; 16) ms in KCNH2, and by -22 (-29; -17) ms in controls (P < 0.0001). These QT variations were independent of heart rate (P < 0.3751). Receiver operating characteristic curve analysis identified a cut-off value of QT variation superior to -11 ms as best predictor of LQTS. It provided 97% sensitivity and 97% specificity of QT prolongation in the diagnosis of LQTS. We identified a paradoxical response of the QT interval during MST in LQTS. Easy to assess, MST may be efficient to unmask concealed LQTS in patients at risk of this pathology.

A new method of optimal capacitor switching based on minimum spanning tree theory in distribution systems

NASA Astrophysics Data System (ADS)

Li, H. W.; Pan, Z. Y.; Ren, Y. B.; Wang, J.; Gan, Y. L.; Zheng, Z. Z.; Wang, W.

2018-03-01

According to the radial operation characteristics in distribution systems, this paper proposes a new method based on minimum spanning trees method for optimal capacitor switching. Firstly, taking the minimal active power loss as objective function and not considering the capacity constraints of capacitors and source, this paper uses Prim algorithm among minimum spanning trees algorithms to get the power supply ranges of capacitors and source. Then with the capacity constraints of capacitors considered, capacitors are ranked by the method of breadth-first search. In term of the order from high to low of capacitor ranking, capacitor compensation capacity based on their power supply range is calculated. Finally, IEEE 69 bus system is adopted to test the accuracy and practicality of the proposed algorithm.

Thread Graphs, Linear Rank-Width and Their Algorithmic Applications

NASA Astrophysics Data System (ADS)

Ganian, Robert

The introduction of tree-width by Robertson and Seymour [7] was a breakthrough in the design of graph algorithms. A lot of research since then has focused on obtaining a width measure which would be more general and still allowed efficient algorithms for a wide range of NP-hard problems on graphs of bounded width. To this end, Oum and Seymour have proposed rank-width, which allows the solution of many such hard problems on a less restricted graph classes (see e.g. [3,4]). But what about problems which are NP-hard even on graphs of bounded tree-width or even on trees? The parameter used most often for these exceptionally hard problems is path-width, however it is extremely restrictive - for example the graphs of path-width 1 are exactly paths.

The Proposal of a Evolutionary Strategy Generating the Data Structures Based on a Horizontal Tree for the Tests

NASA Astrophysics Data System (ADS)

Żukowicz, Marek; Markiewicz, Michał

2016-09-01

The aim of the article is to present a mathematical definition of the object model, that is known in computer science as TreeList and to show application of this model for design evolutionary algorithm, that purpose is to generate structures based on this object. The first chapter introduces the reader to the problem of presenting data using the TreeList object. The second chapter describes the problem of testing data structures based on TreeList. The third one shows a mathematical model of the object TreeList and the parameters, used in determining the utility of structures created through this model and in evolutionary strategy, that generates these structures for testing purposes. The last chapter provides a brief summary and plans for future research related to the algorithm presented in the article.

Constraint Embedding Technique for Multibody System Dynamics

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Cheng, Michael K.

2011-01-01

Multibody dynamics play a critical role in simulation testbeds for space missions. There has been a considerable interest in the development of efficient computational algorithms for solving the dynamics of multibody systems. Mass matrix factorization and inversion techniques and the O(N) class of forward dynamics algorithms developed using a spatial operator algebra stand out as important breakthrough on this front. Techniques such as these provide the efficient algorithms and methods for the application and implementation of such multibody dynamics models. However, these methods are limited only to tree-topology multibody systems. Closed-chain topology systems require different techniques that are not as efficient or as broad as those for tree-topology systems. The closed-chain forward dynamics approach consists of treating the closed-chain topology as a tree-topology system subject to additional closure constraints. The resulting forward dynamics solution consists of: (a) ignoring the closure constraints and using the O(N) algorithm to solve for the free unconstrained accelerations for the system; (b) using the tree-topology solution to compute a correction force to enforce the closure constraints; and (c) correcting the unconstrained accelerations with correction accelerations resulting from the correction forces. This constraint-embedding technique shows how to use direct embedding to eliminate local closure-loops in the system and effectively convert the system back to a tree-topology system. At this point, standard tree-topology techniques can be brought to bear on the problem. The approach uses a spatial operator algebra approach to formulating the equations of motion. The operators are block-partitioned around the local body subgroups to convert them into aggregate bodies. Mass matrix operator factorization and inversion techniques are applied to the reformulated tree-topology system. Thus in essence, the new technique allows conversion of a system with closure-constraints into an equivalent tree-topology system, and thus allows one to take advantage of the host of techniques available to the latter class of systems. This technology is highly suitable for the class of multibody systems where the closure-constraints are local, i.e., where they are confined to small groupings of bodies within the system. Important examples of such local closure-constraints are constraints associated with four-bar linkages, geared motors, differential suspensions, etc. One can eliminate these closure-constraints and convert the system into a tree-topology system by embedding the constraints directly into the system dynamics and effectively replacing the body groupings with virtual aggregate bodies. Once eliminated, one can apply the well-known results and algorithms for tree-topology systems to solve the dynamics of such closed-chain system.

36. 1,000POUND CHAIN HOIST AT STATION 124 OF MST, WEST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

36. 1,000-POUND CHAIN HOIST AT STATION 124 OF MST, WEST SIDE. (ITS ONLY USE WAS INSTALLATION OF ELEVATOR MOTOR.) - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Application of enteric viruses for fecal pollution source tracking in environmental waters

EPA Science Inventory

Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infect...

Multisystemic Therapy Effects on Attempted Suicide by Youths Presenting Psychiatric Emergencies

ERIC Educational Resources Information Center

Huey, Stanley J.; Henggeler, Scott W.; Rowland, Melisa D.; Halliday-Boykins, Colleen A.; Cunningham, Phillippe B.; Pickrel, Susan G.; Edwards, James

2004-01-01

Objective: To evaluate the efficacy of multisystemic therapy (MST) in reducing attempted suicide among predominantly African American youths referred for emergency psychiatric hospitalization. Method: Youths presenting psychiatric emergencies were randomly assigned to MST or hospitalization. Indices of attempted suicide, suicidal ideation,…

[Screening for malnutrition among hospitalized patients in a Colombian University Hospital].

PubMed

Cruz, Viviana; Bernal, Laura; Buitrago, Giancarlo; Ruiz, Álvaro J

2017-04-01

On admission, 30 to 50% of hospitalized patients have some degree of malnutrition, which is associated with longer length of stay, higher rates of complications, mortality and greater costs. To determine the frequency of screening for risk of malnutrition in medical records and assess the usefulness of the Malnutrition Screening Tool (MST). In a cross-sectional study, we searched for malnutrition screening in medical records, and we applied the MST tool to hospitalized patients at the Internal Medicine Wards of San Ignacio University Hospital. Of 295 patients included, none had been screened for malnutrition since hospital admission. Sixty one percent were at nutritional risk, with a higher prevalence among patients with HIV (85.7%), cancer (77.5%) and pneumonia. A positive MST result was associated with a 3.2 days increase in length of hospital stay (p = 0.024). The prevalence of malnutrition risk in hospitalized patients is high, but its screening is inadequate and it is underdiagnosed. The MST tool is simple, fast, low-cost, and has a good diagnostic performance.

Reducing recidivism and symptoms in emerging adults with serious mental health conditions and justice system involvement.

PubMed

Davis, Maryann; Sheidow, Ashli J; McCart, Michael R

2015-04-01

The peak years of offending in the general population and among those with serious mental health conditions (SMHC) are during emerging adulthood. There currently are no evidence-based interventions for reducing offending behavior among 18-21 year olds, with or without SMHC. This open trial examined outcomes from an adaptation of Multisystemic Therapy (MST), an effective juvenile recidivism reduction intervention, modified for use with emerging adults with SMHC and recent justice system involvement. MST for emerging adults (MST-EA) targets MH symptoms, recidivism, problem substance use, and young adult functional capacities. All study participants (n = 41) were aged 17-20 and had a MH diagnosis and recent arrest or incarceration. Implementation outcomes indicated that MST-EA was delivered with strong fidelity, client satisfaction was high, and the majority of participants successfully completed the intervention. Research retention rates also were high. Pre-post-analyses revealed significant reductions in participants' MH symptoms, justice system involvement, and associations with antisocial peers.

The involvement of audio-motor coupling in the music-supported therapy applied to stroke patients.

PubMed

Rodriguez-Fornells, Antoni; Rojo, Nuria; Amengual, Julià L; Ripollés, Pablo; Altenmüller, Eckart; Münte, Thomas F

2012-04-01

Music-supported therapy (MST) has been developed recently to improve the use of the affected upper extremity after stroke. MST uses musical instruments, an electronic piano and an electronic drum set emitting piano sounds, to retrain fine and gross movements of the paretic upper extremity. In this paper, we first describe the rationale underlying MST, and we review the previous studies conducted on acute and chronic stroke patients using this new neurorehabilitation approach. Second, we address the neural mechanisms involved in the motor movement improvements observed in acute and chronic stroke patients. Third, we provide some recent studies on the involvement of auditory-motor coupling in the MST in chronic stroke patients using functional neuroimaging. Finally, these ideas are discussed and focused on understanding the dynamics involved in the neural circuit underlying audio-motor coupling and how functional connectivity could help to explain the neuroplastic changes observed after therapy in stroke patients. © 2012 New York Academy of Sciences.

Reducing Recidivism and Symptoms in Emerging Adults with Serious Mental Health Conditions and Justice System Involvement

PubMed Central

Davis, Maryann; Sheidow, Ashli J.; McCart, Michael R.

2014-01-01

The peak years of offending in the general population and among those with serious mental health conditions (SMHC) are during emerging adulthood. There currently are no evidence-based interventions for reducing offending behavior among 18–21 year olds, with or without SMHC. This open trial examined outcomes from an adaptation of Multisystemic Therapy (MST), an effective juvenile recidivism reduction intervention, modified for use with emerging adults with SMHC and recent justice system involvement. MST for emerging adults (MST-EA) targets MH symptoms, recidivism, problem substance use, and young adult functional capacities. All study participants (n=41) were aged 17–20 and had a MH diagnosis and recent arrest or incarceration. Implementation outcomes indicated that MST-EA was delivered with strong fidelity, client satisfaction was high, and the majority of participants successfully completed the intervention. Research retention rates also were high. Pre-post analyses revealed significant reductions in participants’ MH symptoms, justice-system involvement, and associations with antisocial peers. PMID:25023764

Multisystemic Therapy Improves the Patient-Provider Relationship in Families of Adolescents with Poorly Controlled Insulin Dependent Diabetes

PubMed Central

Carcone, April Idalski; Ellis, Deborah A.; Chen, Xinguang; Naar-King, Sylvie; Cunningham, Phillippe B.; Moltz, Kathleen

2015-01-01

Objective The purpose of this study was to determine if Multisystemic Therapy (MST), an intensive, home and community-based family treatment, significantly improved patient-provider relationships in families where youth had chronic poor glycemic control. Methods One hundred forty-six adolescents with type 1 or 2 diabetes in chronic poor glycemic control (HbA1c ≥ 8%) and their primary caregivers were randomly assigned to MST or a telephone support condition. Caregiver perceptions of their relationship with the diabetes multidisciplinary medical team were assessed at baseline and treatment termination with the Measure of Process of Care-20. Results At treatment termination, MST families reported significant improvement on the Coordinated and Comprehensive Care scale and marginally significant improvement on the Respectful and Supportive Care scale. Improvements on the Enabling and Partnership and Providing Specific Information scales were not significant. Conclusions Results suggest MST improves the ability of the families and the diabetes treatment providers to work together. PMID:25940767

Dynamic Regulation of Cell Volume and Extracellular ATP of Human Erythrocytes

PubMed Central

Leal Denis, M. Florencia; Alvarez, H. Ariel; Lauri, Natalia; Alvarez, Cora L.; Chara, Osvaldo; Schwarzbaum, Pablo J.

2016-01-01

Introduction The peptide mastoparan 7 (MST7) triggered in human erythrocytes (rbcs) the release of ATP and swelling. Since swelling is a well-known inducer of ATP release, and extracellular (ATPe), interacting with P (purinergic) receptors, can affect cell volume (Vr), we explored the dynamic regulation between Vr and ATPe. Methods and Treatments We made a quantitative assessment of MST7-dependent kinetics of Vr and of [ATPe], both in the absence and presence of blockers of ATP efflux, swelling and P receptors. Results In rbcs 10 μM MST7 promoted acute, strongly correlated changes in [ATPe] and Vr. Whereas MST7 induced increases of 10% in Vr and 190 nM in [ATPe], blocking swelling in a hyperosmotic medium + MST7 reduced [ATPe] by 40%. Pre-incubation of rbcs with 10 μM of either carbenoxolone or probenecid, two inhibitors of the ATP conduit pannexin 1, reduced [ATPe] by 40–50% and swelling by 40–60%, while in the presence of 80 U/mL apyrase, an ATPe scavenger, cell swelling was prevented. While exposure to 10 μM NF110, a blocker of ATP-P2X receptors mediating sodium influx, reduced [ATPe] by 48%, and swelling by 80%, incubation of cells in sodium free medium reduced swelling by 92%. Analysis and Discussion Results were analyzed by means of a mathematical model where ATPe kinetics and Vr kinetics were mutually regulated. Model dependent fit to experimental data showed that, upon MST7 exposure, ATP efflux required a fast 1960-fold increase of ATP permeability, mediated by two kinetically different conduits, both of which were activated by swelling and inactivated by time. Both experimental and theoretical results suggest that, following MST7 exposure, ATP is released via two conduits, one of which is mediated by pannexin 1. The accumulated ATPe activates P2X receptors, followed by sodium influx, resulting in cell swelling, which in turn further activates ATP release. Thus swelling and P2X receptors constitute essential components of a positive feedback loop underlying ATP-induced ATP release of rbcs. PMID:27355484

Global interrupt and barrier networks

DOEpatents

Blumrich, Matthias A.; Chen, Dong; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E; Heidelberger, Philip; Kopcsay, Gerard V.; Steinmacher-Burow, Burkhard D.; Takken, Todd E.

2008-10-28

A system and method for generating global asynchronous signals in a computing structure. Particularly, a global interrupt and barrier network is implemented that implements logic for generating global interrupt and barrier signals for controlling global asynchronous operations performed by processing elements at selected processing nodes of a computing structure in accordance with a processing algorithm; and includes the physical interconnecting of the processing nodes for communicating the global interrupt and barrier signals to the elements via low-latency paths. The global asynchronous signals respectively initiate interrupt and barrier operations at the processing nodes at times selected for optimizing performance of the processing algorithms. In one embodiment, the global interrupt and barrier network is implemented in a scalable, massively parallel supercomputing device structure comprising a plurality of processing nodes interconnected by multiple independent networks, with each node including one or more processing elements for performing computation or communication activity as required when performing parallel algorithm operations. One multiple independent network includes a global tree network for enabling high-speed global tree communications among global tree network nodes or sub-trees thereof. The global interrupt and barrier network may operate in parallel with the global tree network for providing global asynchronous sideband signals.

Cost-effectiveness Analysis with Influence Diagrams.

PubMed

Arias, M; Díez, F J

2015-01-01

Cost-effectiveness analysis (CEA) is used increasingly in medicine to determine whether the health benefit of an intervention is worth the economic cost. Decision trees, the standard decision modeling technique for non-temporal domains, can only perform CEA for very small problems. To develop a method for CEA in problems involving several dozen variables. We explain how to build influence diagrams (IDs) that explicitly represent cost and effectiveness. We propose an algorithm for evaluating cost-effectiveness IDs directly, i.e., without expanding an equivalent decision tree. The evaluation of an ID returns a set of intervals for the willingness to pay - separated by cost-effectiveness thresholds - and, for each interval, the cost, the effectiveness, and the optimal intervention. The algorithm that evaluates the ID directly is in general much more efficient than the brute-force method, which is in turn more efficient than the expansion of an equivalent decision tree. Using OpenMarkov, an open-source software tool that implements this algorithm, we have been able to perform CEAs on several IDs whose equivalent decision trees contain millions of branches. IDs can perform CEA on large problems that cannot be analyzed with decision trees.

Tanglegrams for rooted phylogenetic trees and networks

PubMed Central

Scornavacca, Celine; Zickmann, Franziska; Huson, Daniel H.

2011-01-01

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de PMID:21685078

Consensus properties and their large-scale applications for the gene duplication problem.

PubMed

Moon, Jucheol; Lin, Harris T; Eulenstein, Oliver

2016-06-01

Solving the gene duplication problem is a classical approach for species tree inference from gene trees that are confounded by gene duplications. This problem takes a collection of gene trees and seeks a species tree that implies the minimum number of gene duplications. Wilkinson et al. posed the conjecture that the gene duplication problem satisfies the desirable Pareto property for clusters. That is, for every instance of the problem, all clusters that are commonly present in the input gene trees of this instance, called strict consensus, will also be found in every solution to this instance. We prove that this conjecture does not generally hold. Despite this negative result we show that the gene duplication problem satisfies a weaker version of the Pareto property where the strict consensus is found in at least one solution (rather than all solutions). This weaker property contributes to our design of an efficient scalable algorithm for the gene duplication problem. We demonstrate the performance of our algorithm in analyzing large-scale empirical datasets. Finally, we utilize the algorithm to evaluate the accuracy of standard heuristics for the gene duplication problem using simulated datasets.

Node Deployment Algorithm Based on Connected Tree for Underwater Sensor Networks

PubMed Central

Jiang, Peng; Wang, Xingmin; Jiang, Lurong

2015-01-01

Designing an efficient deployment method to guarantee optimal monitoring quality is one of the key topics in underwater sensor networks. At present, a realistic approach of deployment involves adjusting the depths of nodes in water. One of the typical algorithms used in such process is the self-deployment depth adjustment algorithm (SDDA). This algorithm mainly focuses on maximizing network coverage by constantly adjusting node depths to reduce coverage overlaps between two neighboring nodes, and thus, achieves good performance. However, the connectivity performance of SDDA is irresolute. In this paper, we propose a depth adjustment algorithm based on connected tree (CTDA). In CTDA, the sink node is used as the first root node to start building a connected tree. Finally, the network can be organized as a forest to maintain network connectivity. Coverage overlaps between the parent node and the child node are then reduced within each sub-tree to optimize coverage. The hierarchical strategy is used to adjust the distance between the parent node and the child node to reduce node movement. Furthermore, the silent mode is adopted to reduce communication cost. Simulations show that compared with SDDA, CTDA can achieve high connectivity with various communication ranges and different numbers of nodes. Moreover, it can realize coverage as high as that of SDDA with various sensing ranges and numbers of nodes but with less energy consumption. Simulations under sparse environments show that the connectivity and energy consumption performances of CTDA are considerably better than those of SDDA. Meanwhile, the connectivity and coverage performances of CTDA are close to those depth adjustment algorithms base on connected dominating set (CDA), which is an algorithm similar to CTDA. However, the energy consumption of CTDA is less than that of CDA, particularly in sparse underwater environments. PMID:26184209

Detection of stratosphere troposphere exchange in cut-off low systems

NASA Technical Reports Server (NTRS)

Price, Jeremy D.; Vaughan, Geraint

1994-01-01

The Aberystwyth MST radar has been used as part of the TOASTE program to study the structure of the tropopause in cut-off-low system with an aim to identifying regions where stratosphere-troposphere exchange are taking place. Theory predicts that the vertical gradient in reflected power is proportional to the static stability of the reflecting region, and should therefore resolve tropopause structure. Comparisons of MST power profiles with radiosonde data are presented and show good agreement, revealing regions of indefinite tropopauses, where stratosphere-troposphere exchange is thought to take place. The continuous nature of MST data allows an estimation of the size of these regions.

Amazon Forest Structure from IKONOS Satellite Data and the Automated Characterization of Forest Canopy Properties

Treesearch

Michael Palace; Michael Keller; Gregory P. Asner; Stephen Hagen; Bobby Braswell

2008-01-01

We developed an automated tree crown analysis algorithm using 1-m panchromatic IKONOS satellite images to examine forest canopy structure in the Brazilian Amazon. The algorithm was calibrated on the landscape level with tree geometry and forest stand data at the Fazenda Cauaxi (3.75◦ S, 48.37◦ W) in the eastern Amazon, and then compared with forest...

Vlsi implementation of flexible architecture for decision tree classification in data mining

NASA Astrophysics Data System (ADS)

Sharma, K. Venkatesh; Shewandagn, Behailu; Bhukya, Shankar Nayak

2017-07-01

The Data mining algorithms have become vital to researchers in science, engineering, medicine, business, search and security domains. In recent years, there has been a terrific raise in the size of the data being collected and analyzed. Classification is the main difficulty faced in data mining. In a number of the solutions developed for this problem, most accepted one is Decision Tree Classification (DTC) that gives high precision while handling very large amount of data. This paper presents VLSI implementation of flexible architecture for Decision Tree classification in data mining using c4.5 algorithm.

Logistic regression trees for initial selection of interesting loci in case-control studies

PubMed Central

Nickolov, Radoslav Z; Milanov, Valentin B

2007-01-01

Modern genetic epidemiology faces the challenge of dealing with hundreds of thousands of genetic markers. The selection of a small initial subset of interesting markers for further investigation can greatly facilitate genetic studies. In this contribution we suggest the use of a logistic regression tree algorithm known as logistic tree with unbiased selection. Using the simulated data provided for Genetic Analysis Workshop 15, we show how this algorithm, with incorporation of multifactor dimensionality reduction method, can reduce an initial large pool of markers to a small set that includes the interesting markers with high probability. PMID:18466557

An IPv6 routing lookup algorithm using weight-balanced tree based on prefix value for virtual router

NASA Astrophysics Data System (ADS)

Chen, Lingjiang; Zhou, Shuguang; Zhang, Qiaoduo; Li, Fenghua

2016-10-01

Virtual router enables the coexistence of different networks on the same physical facility and has lately attracted a great deal of attention from researchers. As the number of IPv6 addresses is rapidly increasing in virtual routers, designing an efficient IPv6 routing lookup algorithm is of great importance. In this paper, we present an IPv6 lookup algorithm called weight-balanced tree (WBT). WBT merges Forwarding Information Bases (FIBs) of virtual routers into one spanning tree, and compresses the space cost. WBT's average time complexity and the worst case time complexity of lookup and update process are both O(logN) and space complexity is O(cN) where N is the size of routing table and c is a constant. Experiments show that WBT helps reduce more than 80% Static Random Access Memory (SRAM) cost in comparison to those separation schemes. WBT also achieves the least average search depth comparing with other homogeneous algorithms.

Combinatorics of least-squares trees.

PubMed

Mihaescu, Radu; Pachter, Lior

2008-09-09

A recurring theme in the least-squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least-squares estimates of edge lengths. These formulas have proved useful for the development of efficient algorithms, and have also been important for understanding connections among popular phylogeny algorithms. For example, the selection criterion of the neighbor-joining algorithm is now understood in terms of the combinatorial formulas of Pauplin for estimating tree length. We highlight a phylogenetically desirable property that weighted least-squares methods should satisfy, and provide a complete characterization of methods that satisfy the property. The necessary and sufficient condition is a multiplicative four-point condition that the variance matrix needs to satisfy. The proof is based on the observation that the Lagrange multipliers in the proof of the Gauss-Markov theorem are tree-additive. Our results generalize and complete previous work on ordinary least squares, balanced minimum evolution, and the taxon-weighted variance model. They also provide a time-optimal algorithm for computation.

41. VIEW OF UMBILICAL MAST AND LAUNCH PAD FROM LAUNCHER; ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

41. VIEW OF UMBILICAL MAST AND LAUNCH PAD FROM LAUNCHER; SOUTH FACE OF MST IN BACKGROUND. RAIL SYSTEM FROM BASE OF MST PARALLEL TO MAST. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

COMPARISON OF DIRECT AND INDIRECT IMPACTS OF FECAL CONTAMINATION IN TWO DIFFERENT WATERSHEDS

EPA Science Inventory

There are many environmental parameters that could affect the accuracy of microbial source tracking (MST) methods. Spatial and temporal determinants are among the most common factors missing in MST studies. To understand how spatial and temporal variability affect the level of fe...

Gaseous signalling molecule SO2 via Hippo-MST pathway to improve myocardial fibrosis of diabetic rats

PubMed Central

Liu, Maojun; Liu, Shengquan; Tan, Wenting; Tang, Fen; Long, Junrong; Li, Zining; Liang, Biao; Chu, Chun; Yang, Jun

2017-01-01

Recent studies have indicated the existence of an endogenous sulfur dioxide (SO2)-generating system in the cardiovascular system. The present study aimed to discuss the function and regulatory mechanism of gaseous signal molecule SO2 in inhibiting apoptosis and endoplasmic reticulum stress (ERS) via the Hippo-MST signaling pathway to improve myocardial fibrosis of diabetic rats. A total of 40 male Sprague-Dawley rats were randomly divided into four groups (10 rats per group): Normal control group (control group), diabetic rats group [streptozotocin (STZ) group], SO2 intervention group (STZ+SO2 group) and diabetes mellitus rats treated with L-Aspartic acid β-hydroxamate (HDX) group (HDX group). Diabetic rats models were established by intra-peritoneal injection of STZ (40 mg/kg) Following model establishment, intra-peritoneal injection of Na2SO3/NaHSO3 solution (0.54 mmol/kg) was administered in the STZ+SO2 group, and HDX solution (25 mg/kg/week) was administered in the HDX group. A total of 4 weeks later, echocardiography was performed to evaluate rats' cardiac function; Masson staining, terminal deoxynucleotidyl transferase dUTP nick end labeling staining and transmission electron microscopy examinations were performed to observe myocardial morphological changes. ELISA was employed to determine the SO2 content. Western blot analysis was performed to detect the expression of proteins associated with apoptosis, ERS and the Hippo-MST signalling pathway. Compared with the control group, the STZ group and HDX group had a disordered arrangement of myocardial cells with apparent myocardial fibrosis, and echocardiography indicated that the cardiac function was lowered, there was an obvious increase of apoptosis in myocardial tissue, the expression levels of apoptosis-associated protein B-cell lymphoma associated protein X, caspase-3 and caspase-9 were upregulated, and Bcl-2 expression was downregulated. The expression of ERS and Hippo-MST pathway-associated proteins, including CHOP, GRP94, MST1 and MST2, were significantly upregulated. By contrast, these above-mentioned changes were reversed by SO2 treatment. Compared with STZ group, the HDX group had a further increase of myocardial fibrosis and apoptosis, while there were no statistically significant differences in the expression of Bax/Bcl-2, caspase-3, caspase-9 and ERS and Hippo-MST pathway-associated proteins. The results of the present study demonstrated that the gaseous signal molecule SO2 can effectively improve the myocardial fibrosis of diabetic rats, and its mechanism may be associated with reduced apoptosis and ERS by downregulated Hippo-MST pathway. PMID:28990064

Gaseous signalling molecule SO2 via Hippo‑MST pathway to improve myocardial fibrosis of diabetic rats.

PubMed

Liu, Maojun; Liu, Shengquan; Tan, Wenting; Tang, Fen; Long, Junrong; Li, Zining; Liang, Biao; Chu, Chun; Yang, Jun

2017-12-01

Recent studies have indicated the existence of an endogenous sulfur dioxide (SO2)‑generating system in the cardiovascular system. The present study aimed to discuss the function and regulatory mechanism of gaseous signal molecule SO2 in inhibiting apoptosis and endoplasmic reticulum stress (ERS) via the Hippo‑MST signaling pathway to improve myocardial fibrosis of diabetic rats. A total of 40 male Sprague‑Dawley rats were randomly divided into four groups (10 rats per group): Normal control group (control group), diabetic rats group [streptozotocin (STZ) group], SO2 intervention group (STZ+SO2 group) and diabetes mellitus rats treated with L‑Aspartic acid β‑hydroxamate (HDX) group (HDX group). Diabetic rats models were established by intra‑peritoneal injection of STZ (40 mg/kg) Following model establishment, intra‑peritoneal injection of Na2SO3/NaHSO3 solution (0.54 mmol/kg) was administered in the STZ+SO2 group, and HDX solution (25 mg/kg/week) was administered in the HDX group. A total of 4 weeks later, echocardiography was performed to evaluate rats' cardiac function; Masson staining, terminal deoxynucleotidyl transferase dUTP nick end labeling staining and transmission electron microscopy examinations were performed to observe myocardial morphological changes. ELISA was employed to determine the SO2 content. Western blot analysis was performed to detect the expression of proteins associated with apoptosis, ERS and the Hippo‑MST signalling pathway. Compared with the control group, the STZ group and HDX group had a disordered arrangement of myocardial cells with apparent myocardial fibrosis, and echocardiography indicated that the cardiac function was lowered, there was an obvious increase of apoptosis in myocardial tissue, the expression levels of apoptosis‑associated protein B‑cell lymphoma associated protein X, caspase‑3 and caspase‑9 were upregulated, and Bcl‑2 expression was downregulated. The expression of ERS and Hippo‑MST pathway‑associated proteins, including CHOP, GRP94, MST1 and MST2, were significantly upregulated. By contrast, these above‑mentioned changes were reversed by SO2 treatment. Compared with STZ group, the HDX group had a further increase of myocardial fibrosis and apoptosis, while there were no statistically significant differences in the expression of Bax/Bcl‑2, caspase‑3, caspase‑9 and ERS and Hippo‑MST pathway‑associated proteins. The results of the present study demonstrated that the gaseous signal molecule SO2 can effectively improve the myocardial fibrosis of diabetic rats, and its mechanism may be associated with reduced apoptosis and ERS by downregulated Hippo‑MST pathway.

Downstream of human NDR kinases: impacting on c-myc and p21 protein stability to control cell cycle progression.

PubMed

Cornils, Hauke; Kohler, Reto S; Hergovich, Alexander; Hemmings, Brian A

2011-06-15

The mammalian genome encodes four members of the NDR/LATS kinase family: NDR1 (STK38), NDR2 (STK38L), LATS1 and LATS2, which are highly conserved from yeast to man. Members of the NDR/LATS kinase family have been implicated in a variety of biological processes ranging from cell division and morphology to apoptosis and tumor suppression. In mammals, LATS1/2 function as central parts of the HIPPO tumor suppressor pathway by restricting the activity of the YAP/TAZ proto-oncogenes. Recent evidence suggested that NDR1/2 are also part of an extended HIPPO tumor suppressor pathway. Apart from functions in apoptosis signaling and tumor suppression, NDR1/2 have been implicated in controlling centrosome duplication and mitotic chromosome alignment downstream of the HIPPO kinase homologs MST1 and MST2. Significantly, we also reported recently that NDR1/2 are controlling G 1/S transition downstream of a third MST family member MST3. Intriguingly, this newly described MST3-NDR1/2 axis promotes G 1 progression by stabilizing c-myc and preventing p21 accumulation, indicating a potential pro-tumorigenic role for NDR kinases. Here, we discuss these novel cell cycle functions of NDR kinases in a broader context and elaborate on possible explanations for the opposing functions of NDR kinases in normal and tumor biology.

Reporting Military Sexual Trauma: A Mixed-Methods Study of Women Veterans' Experiences Who Served From World War II to the War in Afghanistan.

PubMed

Wolff, Kristina B; Mills, Peter D

2016-08-01

Since 2004, there has been increased effort to reduce military sexual trauma (MST) in the U.S. military. Although MST covers a range of inappropriate behaviors, the majority of research, treatment, and outreach are focused on sexual assault and the experiences of individuals serving in Afghanistan and Iraq. During a study on veterans' involvement in a national peace organization, participants were asked about their military experiences. Veterans served from World War II to current conflicts in Iraq and Afghanistan. Emerging out of the responses were descriptions of women's experiences with MST, barriers to reporting incidents of sexual misconduct and sexual assault, and the challenges they faced when seeking care. Data were gathered using anonymous questionnaires and semi-structured interviews. Out of 52 female veterans, the majority (90%) was subjected to at least one form of MST, and 15% (8) attempted to report the incident(s). Over half of the assailants were of a higher rank than the survivors. The majority of veterans remained silent due to lack of options to report, the status of perpetrators, and fear of retaliation. These data provide a glimpse into the challenges many women veterans faced when seeking assistance reporting incidents or obtaining health care for their MST. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

[Intraoperative intraperitoneal chemoperfusion treatment with cisplatin and dioxadet on a model of peritoneal carcinomatosis in ovarian cancer: safety and efficacy evaluation].

PubMed

Bespalov, V G; Kireeva, G S; Belyaeva, O A; Senchik, K Yu; Stukov, A N; Gafton, G I; Soloviev, L A; Vasilchenko, M V; Guseinov, K D; Alexeev, V V; Belyaev, A M

2015-01-01

A comparative study of safety and efficacy of normothermic and hyperthermic intraperitoneal chemoperfusion (IPEC and HIPEC) with cisplatin and dioxadet was carried out in 143 female Wistar rats. Ovarian cancer was inoculated intraperitoneally (i.p.). In 48 hours after ovarian cancer inoculation the drugs were administered i.p. or IPEC and HIPEC with the drugs were performed using maximum tolerated doses (MTD). Content of cisplatin was determined in the perfusate and blood plasma during HIPEC with the drug. The leukocyte count was measured using veterinary hematologic analyzer in peripheral blood of rats at different time points after HIPEC with dioxadet. Efficacy of the treatment was estimated in increase in median survival time (MST). During HIPEC cisplatin was accumulated in the abdominal cavity in a considerable amount with minimal systemic absorption. HIPEC with dioxadet didn't significantly affect the leukocyte count in peripheral blood while i.p. administration of dioxadet suppressed leukopoiesis. MST of rats after IPEC with cisplatin was 37.5 days which was significantly higher compared to MST after i.p. administration of cisplatin (19.5 days, p = 0.037). HIPEC with dioxadet was the most effective regimen of treatment with MST of rats reaching 49 days which was significantly higher compared to MST after HIPEC with cisplatin (25.5 days, p = 0.002).

The effects of music-supported therapy on motor, cognitive, and psychosocial functions in chronic stroke.

PubMed

Fujioka, Takako; Dawson, Deirdre R; Wright, Rebecca; Honjo, Kie; Chen, Joyce L; Chen, J Jean; Black, Sandra E; Stuss, Donald T; Ross, Bernhard

2018-05-24

Neuroplasticity accompanying learning is a key mediator of stroke rehabilitation. Training in playing music in healthy populations and patients with movement disorders requires resources within motor, sensory, cognitive, and affective systems, and coordination among these systems. We investigated effects of music-supported therapy (MST) in chronic stroke on motor, cognitive, and psychosocial functions compared to conventional physical training (GRASP). Twenty-eight adults with unilateral arm and hand impairment were randomly assigned to MST (n = 14) and GRASP (n = 14) and received 30 h of training over a 10-week period. The assessment was conducted at four time points: before intervention, after 5 weeks, after 10 weeks, and 3 months after training completion. As for two of our three primary outcome measures concerning motor function, all patients slightly improved in Chedoke-McMaster Stroke Assessment hand score, while the time to complete Action Research Arm Test became shorter in the MST group. The third primary outcome measure for well-being, Stroke Impact Scale, was improved for emotion and social communication earlier in MST and coincided with the improved executive function for task switching and music rhythm perception. The results confirmed previous findings and expanded the potential usage of MST for enhancing quality of life in community-dwelling chronic-stage survivors. © 2018 New York Academy of Sciences.

Tearing mode dynamics and locking in the presence of external magnetic perturbations

NASA Astrophysics Data System (ADS)

Fridström, R.; Munaretto, S.; Frassinetti, L.; Chapman, B. E.; Brunsell, P. R.; Sarff, J. S.

2016-06-01

In normal operation, Madison Symmetric Torus (MST) [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)] reversed-field pinch plasmas exhibit several rotating tearing modes (TMs). Application of a resonant magnetic perturbation (RMP) results in braking of mode rotation and, if the perturbation amplitude is sufficiently high, in a wall-locked state. The coils that produce the magnetic perturbation in MST give rise to RMPs with several toroidal harmonics. As a result, simultaneous deceleration of all modes is observed. The measured TM dynamics is shown to be in qualitative agreement with a magnetohydrodynamical model of the RMP interaction with the TM [R. Fitzpatrick, Nucl. Fusion 33, 1049 (1993)] adapted to MST. To correctly model the TM dynamics, the electromagnetic torque acting on several TMs is included. Quantitative agreement of the TM slowing-down time was obtained for a kinematic viscosity in the order of νki n≈10 -20 m2/s. Analysis of discharges with different plasma densities shows an increase of the locking threshold with increasing density. Modeling results show good agreement with the experimental trend, assuming a density-independent kinematic viscosity. Comparison of the viscosity estimates in this paper to those made previously with other techniques in MST plasmas suggests the possibility that the RMP technique may allow for estimates of the viscosity over a broad range of plasmas in MST and other devices.

Overview of results from the MST reversed field pinch experiment

NASA Astrophysics Data System (ADS)

Sarff, J. S.; Almagri, A. F.; Anderson, J. K.; Borchardt, M.; Carmody, D.; Caspary, K.; Chapman, B. E.; Den Hartog, D. J.; Duff, J.; Eilerman, S.; Falkowski, A.; Forest, C. B.; Goetz, J. A.; Holly, D. J.; Kim, J.-H.; King, J.; Ko, J.; Koliner, J.; Kumar, S.; Lee, J. D.; Liu, D.; Magee, R.; McCollam, K. J.; McGarry, M.; Mirnov, V. V.; Nornberg, M. D.; Nonn, P. D.; Oliva, S. P.; Parke, E.; Reusch, J. A.; Sauppe, J. P.; Seltzman, A.; Sovinec, C. R.; Stephens, H.; Stone, D.; Theucks, D.; Thomas, M.; Triana, J.; Terry, P. W.; Waksman, J.; Bergerson, W. F.; Brower, D. L.; Ding, W. X.; Lin, L.; Demers, D. R.; Fimognari, P.; Titus, J.; Auriemma, F.; Cappello, S.; Franz, P.; Innocente, P.; Lorenzini, R.; Martines, E.; Momo, B.; Piovesan, P.; Puiatti, M.; Spolaore, M.; Terranova, D.; Zanca, P.; Belykh, V.; Davydenko, V. I.; Deichuli, P.; Ivanov, A. A.; Polosatkin, S.; Stupishin, N. V.; Spong, D.; Craig, D.; Harvey, R. W.; Cianciosa, M.; Hanson, J. D.

2013-10-01

An overview of recent results from the MST programme on physics important for the advancement of the reversed field pinch (RFP) as well as for improved understanding of toroidal magnetic confinement more generally is reported. Evidence for the classical confinement of ions in the RFP is provided by analysis of impurity ions and energetic ions created by 1 MW neutral beam injection (NBI). The first appearance of energetic-particle-driven modes by NBI in a RFP plasma is described. MST plasmas robustly access the quasi-single-helicity state that has commonalities to the stellarator and ‘snake’ formation in tokamaks. In MST the dominant mode grows to 8% of the axisymmetric field strength, while the remaining modes are reduced. Predictive capability for tearing mode behaviour has been improved through nonlinear, 3D, resistive magnetohydrodynamic computation using the measured resistivity profile and Lundquist number, which reproduces the sawtooth cycle dynamics. Experimental evidence and computational analysis indicates two-fluid effects, e.g., Hall physics and gyro-viscosity, are needed to understand the coupling of parallel momentum transport and current profile relaxation. Large Reynolds and Maxwell stresses, plus separately measured kinetic stress, indicate an intricate momentum balance and a possible origin for MST's intrinsic plasma rotation. Gyrokinetic analysis indicates that micro-tearing modes can be unstable at high beta, with a critical gradient for the electron temperature that is larger than for tokamak plasmas by roughly the aspect ratio.

Application of decision tree model for the ground subsidence hazard mapping near abandoned underground coal mines.

PubMed

Lee, Saro; Park, Inhye

2013-09-30

Subsidence of ground caused by underground mines poses hazards to human life and property. This study analyzed the hazard to ground subsidence using factors that can affect ground subsidence and a decision tree approach in a geographic information system (GIS). The study area was Taebaek, Gangwon-do, Korea, where many abandoned underground coal mines exist. Spatial data, topography, geology, and various ground-engineering data for the subsidence area were collected and compiled in a database for mapping ground-subsidence hazard (GSH). The subsidence area was randomly split 50/50 for training and validation of the models. A data-mining classification technique was applied to the GSH mapping, and decision trees were constructed using the chi-squared automatic interaction detector (CHAID) and the quick, unbiased, and efficient statistical tree (QUEST) algorithms. The frequency ratio model was also applied to the GSH mapping for comparing with probabilistic model. The resulting GSH maps were validated using area-under-the-curve (AUC) analysis with the subsidence area data that had not been used for training the model. The highest accuracy was achieved by the decision tree model using CHAID algorithm (94.01%) comparing with QUEST algorithms (90.37%) and frequency ratio model (86.70%). These accuracies are higher than previously reported results for decision tree. Decision tree methods can therefore be used efficiently for GSH analysis and might be widely used for prediction of various spatial events. Copyright © 2013. Published by Elsevier Ltd.

An Isometric Mapping Based Co-Location Decision Tree Algorithm

NASA Astrophysics Data System (ADS)

Zhou, G.; Wei, J.; Zhou, X.; Zhang, R.; Huang, W.; Sha, H.; Chen, J.

2018-05-01

Decision tree (DT) induction has been widely used in different pattern classification. However, most traditional DTs have the disadvantage that they consider only non-spatial attributes (ie, spectral information) as a result of classifying pixels, which can result in objects being misclassified. Therefore, some researchers have proposed a co-location decision tree (Cl-DT) method, which combines co-location and decision tree to solve the above the above-mentioned traditional decision tree problems. Cl-DT overcomes the shortcomings of the existing DT algorithms, which create a node for each value of a given attribute, which has a higher accuracy than the existing decision tree approach. However, for non-linearly distributed data instances, the euclidean distance between instances does not reflect the true positional relationship between them. In order to overcome these shortcomings, this paper proposes an isometric mapping method based on Cl-DT (called, (Isomap-based Cl-DT), which is a method that combines heterogeneous and Cl-DT together. Because isometric mapping methods use geodetic distances instead of Euclidean distances between non-linearly distributed instances, the true distance between instances can be reflected. The experimental results and several comparative analyzes show that: (1) The extraction method of exposed carbonate rocks is of high accuracy. (2) The proposed method has many advantages, because the total number of nodes, the number of leaf nodes and the number of nodes are greatly reduced compared to Cl-DT. Therefore, the Isomap -based Cl-DT algorithm can construct a more accurate and faster decision tree.

Automated Reconstruction of Neural Trees Using Front Re-initialization

PubMed Central

Mukherjee, Amit; Stepanyants, Armen

2013-01-01

This paper proposes a greedy algorithm for automated reconstruction of neural arbors from light microscopy stacks of images. The algorithm is based on the minimum cost path method. While the minimum cost path, obtained using the Fast Marching Method, results in a trace with the least cumulative cost between the start and the end points, it is not sufficient for the reconstruction of neural trees. This is because sections of the minimum cost path can erroneously travel through the image background with undetectable detriment to the cumulative cost. To circumvent this problem we propose an algorithm that grows a neural tree from a specified root by iteratively re-initializing the Fast Marching fronts. The speed image used in the Fast Marching Method is generated by computing the average outward flux of the gradient vector flow field. Each iteration of the algorithm produces a candidate extension by allowing the front to travel a specified distance and then tracking from the farthest point of the front back to the tree. Robust likelihood ratio test is used to evaluate the quality of the candidate extension by comparing voxel intensities along the extension to those in the foreground and the background. The qualified extensions are appended to the current tree, the front is re-initialized, and Fast Marching is continued until the stopping criterion is met. To evaluate the performance of the algorithm we reconstructed 6 stacks of two-photon microscopy images and compared the results to the ground truth reconstructions by using the DIADEM metric. The average comparison score was 0.82 out of 1.0, which is on par with the performance achieved by expert manual tracers. PMID:24386539

Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms

NASA Astrophysics Data System (ADS)

Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho

The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.

An Education in Gender and Agroecology in Brazil's Landless Rural Workers' Movement

ERIC Educational Resources Information Center

Schwendler, Sônia Fátima; Thompson, Lucia Amaranta

2017-01-01

This article explores the implications of a blended agroecology and gender education within "Brazil's Landless Rural Workers' Movement" (MST). The discussion is first situated within MST's struggle for land and for peasant families' livelihoods, generally, and under neoliberalism, specifically. Central to the struggle against…

LIBRARY-DEPENDENT MICROBIAL SOURCE TRACKING OF ENTEROCOCCUS SP. USING AFLP AND BOX-PCR

EPA Science Inventory

Library-dependent microbial source tracking (LD MST) methods are one of the approaches used to identify nonpoint sources of fecal contamination in support of total maximum daily load implementation. However, LD MST methods have been questioned due to the high temporal and spatial...

3. VIEW OF NORTHEAST CORNER OF MST. NOTE: ENVIRONMENTAL DOOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

3. VIEW OF NORTHEAST CORNER OF MST. NOTE: ENVIRONMENTAL DOOR ON THE LOWER EAST SIDE OF THE NORTH FACE IS MISSING. NORTH CAMERA TOWER IN FOREGROUND. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

TEMPORAL AND SPATIAL VARIABILITY OF FECAL INDICATOR BACTERIA: IMPLICATIONS FOR THE APPLICATION OF MST METHODOLOGIES TO DIFFERENTIATE SOURCES OF FECAL CONTAMINATION

EPA Science Inventory

Temporal variability in the gastrointestinal flora of animals impacting water resources with fecal material can be one of the factors producing low source identification rates when applying microbial source tracking (MST) methods. Understanding how bacterial species and genotype...

Test Information Targeting Strategies for Adaptive Multistage Testing Designs.

ERIC Educational Resources Information Center

Luecht, Richard M.; Burgin, William

Adaptive multistage testlet (MST) designs appear to be gaining popularity for many large-scale computer-based testing programs. These adaptive MST designs use a modularized configuration of preconstructed testlets and embedded score-routing schemes to prepackage different forms of an adaptive test. The conditional information targeting (CIT)…

42. VIEW OF UMBILICAL MAST AND LAUNCH PAD FROM MST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

42. VIEW OF UMBILICAL MAST AND LAUNCH PAD FROM MST BASE. LAUNCHER IS BEHIND UMBILICAL MAST AND RAIL SYSTEM IS PARALLEL TO MAST ON RIGHT AND LEFT. - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 East, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

EVALUATION OF HOST SPECIFIC PCR-BASED METHODS FOR THE IDENTIFICATION OF FECAL POLLUTION

EPA Science Inventory

Microbial Source Tracking (MST) is an approach to determine the origin of fecal pollution impacting a body of water. MST is based on the assumption that, given the appropriate method and indicator, the source of microbial pollution can be identified. One of the key elements of...

Decay of Fecal Indicator Bacteria and Microbial Source Tracking Markers in Cattle Feces

EPA Science Inventory

The survival of fecal indicator bacteria (FIB) and microbial source tracking (MST) markers in water microcosms and manure amended soils has been well documented; however, little is known about the survival of MST markers in bovine feces deposited on pastures. We conducted a study...

Paternal Involvement in Multisystemic Therapy: Effects on Adolescent Outcomes and Maternal Depression

ERIC Educational Resources Information Center

Gervan, Shannon; Granic, Isabela; Solomon, Tracy; Blokland, Kirsten; Ferguson, Bruce

2012-01-01

The association between paternal involvement in therapy, adolescent outcomes and maternal depression was examined within the context of Multisystemic Therapy (MST), an empirically supported, family- and community-based treatment for antisocial adolescents. Ninety-nine families were recruited from five mental health agencies providing MST. We…

Comparison of rule induction, decision trees and formal concept analysis approaches for classification

NASA Astrophysics Data System (ADS)

Kotelnikov, E. V.; Milov, V. R.

2018-05-01

Rule-based learning algorithms have higher transparency and easiness to interpret in comparison with neural networks and deep learning algorithms. These properties make it possible to effectively use such algorithms to solve descriptive tasks of data mining. The choice of an algorithm depends also on its ability to solve predictive tasks. The article compares the quality of the solution of the problems with binary and multiclass classification based on the experiments with six datasets from the UCI Machine Learning Repository. The authors investigate three algorithms: Ripper (rule induction), C4.5 (decision trees), In-Close (formal concept analysis). The results of the experiments show that In-Close demonstrates the best quality of classification in comparison with Ripper and C4.5, however the latter two generate more compact rule sets.

A junction-tree based learning algorithm to optimize network wide traffic control: A coordinated multi-agent framework

DOE PAGES

Zhu, Feng; Aziz, H. M. Abdul; Qian, Xinwu; ...

2015-01-31

Our study develops a novel reinforcement learning algorithm for the challenging coordinated signal control problem. Traffic signals are modeled as intelligent agents interacting with the stochastic traffic environment. The model is built on the framework of coordinated reinforcement learning. The Junction Tree Algorithm (JTA) based reinforcement learning is proposed to obtain an exact inference of the best joint actions for all the coordinated intersections. Moreover, the algorithm is implemented and tested with a network containing 18 signalized intersections in VISSIM. Finally, our results show that the JTA based algorithm outperforms independent learning (Q-learning), real-time adaptive learning, and fixed timing plansmore » in terms of average delay, number of stops, and vehicular emissions at the network level.« less

Applied Swarm-based medicine: collecting decision trees for patterns of algorithms analysis.

PubMed

Panje, Cédric M; Glatzer, Markus; von Rappard, Joscha; Rothermundt, Christian; Hundsberger, Thomas; Zumstein, Valentin; Plasswilm, Ludwig; Putora, Paul Martin

2017-08-16

The objective consensus methodology has recently been applied in consensus finding in several studies on medical decision-making among clinical experts or guidelines. The main advantages of this method are an automated analysis and comparison of treatment algorithms of the participating centers which can be performed anonymously. Based on the experience from completed consensus analyses, the main steps for the successful implementation of the objective consensus methodology were identified and discussed among the main investigators. The following steps for the successful collection and conversion of decision trees were identified and defined in detail: problem definition, population selection, draft input collection, tree conversion, criteria adaptation, problem re-evaluation, results distribution and refinement, tree finalisation, and analysis. This manuscript provides information on the main steps for successful collection of decision trees and summarizes important aspects at each point of the analysis.

Prediction of Baseflow Index of Catchments using Machine Learning Algorithms

NASA Astrophysics Data System (ADS)

Yadav, B.; Hatfield, K.

2017-12-01

We present the results of eight machine learning techniques for predicting the baseflow index (BFI) of ungauged basins using a surrogate of catchment scale climate and physiographic data. The tested algorithms include ordinary least squares, ridge regression, least absolute shrinkage and selection operator (lasso), elasticnet, support vector machine, gradient boosted regression trees, random forests, and extremely randomized trees. Our work seeks to identify the dominant controls of BFI that can be readily obtained from ancillary geospatial databases and remote sensing measurements, such that the developed techniques can be extended to ungauged catchments. More than 800 gauged catchments spanning the continental United States were selected to develop the general methodology. The BFI calculation was based on the baseflow separated from daily streamflow hydrograph using HYSEP filter. The surrogate catchment attributes were compiled from multiple sources including digital elevation model, soil, landuse, climate data, other publicly available ancillary and geospatial data. 80% catchments were used to train the ML algorithms, and the remaining 20% of the catchments were used as an independent test set to measure the generalization performance of fitted models. A k-fold cross-validation using exhaustive grid search was used to fit the hyperparameters of each model. Initial model development was based on 19 independent variables, but after variable selection and feature ranking, we generated revised sparse models of BFI prediction that are based on only six catchment attributes. These key predictive variables selected after the careful evaluation of bias-variance tradeoff include average catchment elevation, slope, fraction of sand, permeability, temperature, and precipitation. The most promising algorithms exceeding an accuracy score (r-square) of 0.7 on test data include support vector machine, gradient boosted regression trees, random forests, and extremely randomized trees. Considering both the accuracy and the computational complexity of these algorithms, we identify the extremely randomized trees as the best performing algorithm for BFI prediction in ungauged basins.

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

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

Soner Yorgun, M.; Rood, Richard B.

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

DOE PAGES

Soner Yorgun, M.; Rood, Richard B.

2016-11-11

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

Towards a hybrid energy efficient multi-tree-based optimized routing protocol for wireless networks.

PubMed

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-12-13

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm.

Towards a Hybrid Energy Efficient Multi-Tree-Based Optimized Routing Protocol for Wireless Networks

PubMed Central

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-01-01

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm. PMID:23443398

Resolution of the 1D regularized Burgers equation using a spatial wavelet approximation

NASA Technical Reports Server (NTRS)

Liandrat, J.; Tchamitchian, PH.

1990-01-01

The Burgers equation with a small viscosity term, initial and periodic boundary conditions is resolved using a spatial approximation constructed from an orthonormal basis of wavelets. The algorithm is directly derived from the notions of multiresolution analysis and tree algorithms. Before the numerical algorithm is described these notions are first recalled. The method uses extensively the localization properties of the wavelets in the physical and Fourier spaces. Moreover, the authors take advantage of the fact that the involved linear operators have constant coefficients. Finally, the algorithm can be considered as a time marching version of the tree algorithm. The most important point is that an adaptive version of the algorithm exists: it allows one to reduce in a significant way the number of degrees of freedom required for a good computation of the solution. Numerical results and description of the different elements of the algorithm are provided in combination with different mathematical comments on the method and some comparison with more classical numerical algorithms.

A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery Using a Probabilistic Learning Framework

NASA Technical Reports Server (NTRS)

Basu, Saikat; Ganguly, Sangram; Michaelis, Andrew; Votava, Petr; Roy, Anshuman; Mukhopadhyay, Supratik; Nemani, Ramakrishna

2015-01-01

Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets, which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery using a Probabilistic Learning Framework

NASA Astrophysics Data System (ADS)

Basu, S.; Ganguly, S.; Michaelis, A.; Votava, P.; Roy, A.; Mukhopadhyay, S.; Nemani, R. R.

2015-12-01

Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

hs-CRP is strongly associated with coronary heart disease (CHD): A data mining approach using decision tree algorithm.

PubMed

Tayefi, Maryam; Tajfard, Mohammad; Saffar, Sara; Hanachi, Parichehr; Amirabadizadeh, Ali Reza; Esmaeily, Habibollah; Taghipour, Ali; Ferns, Gordon A; Moohebati, Mohsen; Ghayour-Mobarhan, Majid

2017-04-01

Coronary heart disease (CHD) is an important public health problem globally. Algorithms incorporating the assessment of clinical biomarkers together with several established traditional risk factors can help clinicians to predict CHD and support clinical decision making with respect to interventions. Decision tree (DT) is a data mining model for extracting hidden knowledge from large databases. We aimed to establish a predictive model for coronary heart disease using a decision tree algorithm. Here we used a dataset of 2346 individuals including 1159 healthy participants and 1187 participant who had undergone coronary angiography (405 participants with negative angiography and 782 participants with positive angiography). We entered 10 variables of a total 12 variables into the DT algorithm (including age, sex, FBG, TG, hs-CRP, TC, HDL, LDL, SBP and DBP). Our model could identify the associated risk factors of CHD with sensitivity, specificity, accuracy of 96%, 87%, 94% and respectively. Serum hs-CRP levels was at top of the tree in our model, following by FBG, gender and age. Our model appears to be an accurate, specific and sensitive model for identifying the presence of CHD, but will require validation in prospective studies. Copyright © 2017 Elsevier B.V. All rights reserved.

A Depth-Adjustment Deployment Algorithm Based on Two-Dimensional Convex Hull and Spanning Tree for Underwater Wireless Sensor Networks.

PubMed

Jiang, Peng; Liu, Shuai; Liu, Jun; Wu, Feng; Zhang, Le

2016-07-14

Most of the existing node depth-adjustment deployment algorithms for underwater wireless sensor networks (UWSNs) just consider how to optimize network coverage and connectivity rate. However, these literatures don't discuss full network connectivity, while optimization of network energy efficiency and network reliability are vital topics for UWSN deployment. Therefore, in this study, a depth-adjustment deployment algorithm based on two-dimensional (2D) convex hull and spanning tree (NDACS) for UWSNs is proposed. First, the proposed algorithm uses the geometric characteristics of a 2D convex hull and empty circle to find the optimal location of a sleep node and activate it, minimizes the network coverage overlaps of the 2D plane, and then increases the coverage rate until the first layer coverage threshold is reached. Second, the sink node acts as a root node of all active nodes on the 2D convex hull and then forms a small spanning tree gradually. Finally, the depth-adjustment strategy based on time marker is used to achieve the three-dimensional overall network deployment. Compared with existing depth-adjustment deployment algorithms, the simulation results show that the NDACS algorithm can maintain full network connectivity with high network coverage rate, as well as improved network average node degree, thus increasing network reliability.

A Depth-Adjustment Deployment Algorithm Based on Two-Dimensional Convex Hull and Spanning Tree for Underwater Wireless Sensor Networks

PubMed Central

Jiang, Peng; Liu, Shuai; Liu, Jun; Wu, Feng; Zhang, Le

2016-01-01

Most of the existing node depth-adjustment deployment algorithms for underwater wireless sensor networks (UWSNs) just consider how to optimize network coverage and connectivity rate. However, these literatures don’t discuss full network connectivity, while optimization of network energy efficiency and network reliability are vital topics for UWSN deployment. Therefore, in this study, a depth-adjustment deployment algorithm based on two-dimensional (2D) convex hull and spanning tree (NDACS) for UWSNs is proposed. First, the proposed algorithm uses the geometric characteristics of a 2D convex hull and empty circle to find the optimal location of a sleep node and activate it, minimizes the network coverage overlaps of the 2D plane, and then increases the coverage rate until the first layer coverage threshold is reached. Second, the sink node acts as a root node of all active nodes on the 2D convex hull and then forms a small spanning tree gradually. Finally, the depth-adjustment strategy based on time marker is used to achieve the three-dimensional overall network deployment. Compared with existing depth-adjustment deployment algorithms, the simulation results show that the NDACS algorithm can maintain full network connectivity with high network coverage rate, as well as improved network average node degree, thus increasing network reliability. PMID:27428970

AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

PubMed

Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

2003-01-01

In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.

How Hierarchical Topics Evolve in Large Text Corpora.

PubMed

Cui, Weiwei; Liu, Shixia; Wu, Zhuofeng; Wei, Hao

2014-12-01

Using a sequence of topic trees to organize documents is a popular way to represent hierarchical and evolving topics in text corpora. However, following evolving topics in the context of topic trees remains difficult for users. To address this issue, we present an interactive visual text analysis approach to allow users to progressively explore and analyze the complex evolutionary patterns of hierarchical topics. The key idea behind our approach is to exploit a tree cut to approximate each tree and allow users to interactively modify the tree cuts based on their interests. In particular, we propose an incremental evolutionary tree cut algorithm with the goal of balancing 1) the fitness of each tree cut and the smoothness between adjacent tree cuts; 2) the historical and new information related to user interests. A time-based visualization is designed to illustrate the evolving topics over time. To preserve the mental map, we develop a stable layout algorithm. As a result, our approach can quickly guide users to progressively gain profound insights into evolving hierarchical topics. We evaluate the effectiveness of the proposed method on Amazon's Mechanical Turk and real-world news data. The results show that users are able to successfully analyze evolving topics in text data.

Detection of dead standing Eucalyptus camaldulensis without tree delineation for managing biodiversity in native Australian forest

NASA Astrophysics Data System (ADS)

Miltiadou, Milto; Campbell, Neil D. F.; Gonzalez Aracil, Susana; Brown, Tony; Grant, Michael G.

2018-05-01

In Australia, many birds and arboreal animals use hollows for shelters, but studies predict shortage of hollows in near future. Aged dead trees are more likely to contain hollows and therefore automated detection of them plays a substantial role in preserving biodiversity and consequently maintaining a resilient ecosystem. For this purpose full-waveform LiDAR data were acquired from a native Eucalypt forest in Southern Australia. The structure of the forest significantly varies in terms of tree density, age and height. Additionally, Eucalyptus camaldulensis have multiple trunk splits making tree delineation very challenging. For that reason, this paper investigates automated detection of dead standing Eucalyptus camaldulensis without tree delineation. It also presents the new feature of the open source software DASOS, which extracts features for 3D object detection in voxelised FW LiDAR. A random forest classifier, a weighted-distance KNN algorithm and a seed growth algorithm are used to create a 2D probabilistic field and to then predict potential positions of dead trees. It is shown that tree health assessment is possible without tree delineation but since it is a new research directions there are many improvements to be made.

An efficient group multicast routing for multimedia communication

NASA Astrophysics Data System (ADS)

Wang, Yanlin; Sun, Yugen; Yan, Xinfang

2004-04-01

Group multicasting is a kind of communication mechanism whereby each member of a group sends messages to all the other members of the same group. Group multicast routing algorithms capable of satisfying quality of service (QoS) requirements of multimedia applications are essential for high-speed networks. We present a heuristic algorithm for group multicast routing with end to end delay constraint. Source-specific routing trees for each member are generated in our algorithm, which satisfy member"s bandwidth and end to end delay requirements. Simulations over random network were carried out to compare proposed algorithm performance with Low and Song"s. The experimental results show that our proposed algorithm performs better in terms of network cost and ability in constructing feasible multicast trees for group members. Moreover, our algorithm achieves good performance in balancing traffic, which can avoid link blocking and enhance the network behavior efficiently.

Enhancement of Fast Face Detection Algorithm Based on a Cascade of Decision Trees

NASA Astrophysics Data System (ADS)

Khryashchev, V. V.; Lebedev, A. A.; Priorov, A. L.

2017-05-01

Face detection algorithm based on a cascade of ensembles of decision trees (CEDT) is presented. The new approach allows detecting faces other than the front position through the use of multiple classifiers. Each classifier is trained for a specific range of angles of the rotation head. The results showed a high rate of productivity for CEDT on images with standard size. The algorithm increases the area under the ROC-curve of 13% compared to a standard Viola-Jones face detection algorithm. Final realization of given algorithm consist of 5 different cascades for frontal/non-frontal faces. One more thing which we take from the simulation results is a low computational complexity of CEDT algorithm in comparison with standard Viola-Jones approach. This could prove important in the embedded system and mobile device industries because it can reduce the cost of hardware and make battery life longer.

Using traveling salesman problem algorithms for evolutionary tree construction.

PubMed

Korostensky, C; Gonnet, G H

2000-07-01

The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity. We present a new tree construction method that constructs a tree with minimum score for a given set of sequences, where the score is the amount of evolution measured in PAM distances. To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). The input for the TSP algorithm are the pairwise distances of the sequences and the output is a circular tour through the optimal, unknown tree plus the minimum score of the tree. The circular order and the score can be used to construct the topology of the optimal tree. Our method can be used for any scoring function that correlates to the amount of changes along the branches of an evolutionary tree, for instance it could also be used for parsimony scores, but it cannot be used for least squares fit of distances. A TSP solution reduces the space of all possible trees to 2n. Using this order, we can guarantee that we reconstruct a correct evolutionary tree if the absolute value of the error for each distance measurement is smaller than f2.gif" BORDER="0">, where f3.gif" BORDER="0">is the length of the shortest edge in the tree. For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. Finally simulations and experiments with real data are shown.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Middle Atmosphere Program. Handbook for MAP, volume 9

NASA Technical Reports Server (NTRS)

Bowhill, S. A. (Editor); Edwards, B. (Editor)

1983-01-01

The term Mesosphere-Stratosphere-Troposphere radar (MST) was invented to describe the use of a high power radar transmitter together with a large vertically, or near vertically, pointing antenna to study the dynamics and structure of the atmosphere from about 10 to 100 km, using the very weak coherently scattered radiation returned from small scale irregularities in refractive index. Nine topics were addressed including: meteorological and dynamic requirements for MST radar networks; interpretation of radar returns for clear air; techniques for the measurement of horizontal and vertical velocities; techniques for studying gravity waves and turbulence; capabilities and limitations of existing MST radar; design considerations for high power VHF radar transceivers; optimum radar antenna configurations; and data analysis techniques.

Economic Impact of Multisystemic Therapy for Child Abuse and Neglect.

PubMed

Dopp, Alex R; Schaeffer, Cindy M; Swenson, Cynthia Cupit; Powell, Jennifer S

2018-04-04

This study evaluated the economics of Multisystemic Therapy for Child Abuse and Neglect (MST-CAN) by applying the Washington State Institute for Public Policy (WSIPP) cost-benefit model to data from a randomized effectiveness trial with 86 families (Swenson et al. in JFP 24:497-507, 2010b). The net benefit of MST-CAN, versus enhanced outpatient treatment, was $26,655 per family at 16 months post-baseline. Stated differently, every dollar spent on MST-CAN recovered $3.31 in savings to participants, taxpayers, and society at large. Policymakers and public service agencies should consider these findings when making investments into interventions for high-need families involved with child protective services.

KSC-99pp1216

NASA Image and Video Library

1999-10-14

KENNEDY SPACE CENTER, FLA. -- The 300-foot, five-million-pound Mobile Service Tower (MST) on Launch Complex 41, Cape Canaveral Air Force Station, lies on its side after being demolished. The MST and a 200-foot-high umbilical tower nearby were demolished to make room for Lockheed Martin's 14-acre Vehicle Integration Facility (VIF), under construction. Only lightning protection towers, such as the one seen behind the MST, remain standing at the site. About 200 pounds of linear-shaped charges were used to bring down the towers so that the materials can be recycled. The implosion and removal of the tower debris is expected to be completed in two months. The VIF will be used for Lockheed Martin's Atlas V Launch System.

Comparison of Naive Bayes and Decision Tree on Feature Selection Using Genetic Algorithm for Classification Problem

NASA Astrophysics Data System (ADS)

Rahmadani, S.; Dongoran, A.; Zarlis, M.; Zakarias

2018-03-01

This paper discusses the problem of feature selection using genetic algorithms on a dataset for classification problems. The classification model used is the decicion tree (DT), and Naive Bayes. In this paper we will discuss how the Naive Bayes and Decision Tree models to overcome the classification problem in the dataset, where the dataset feature is selectively selected using GA. Then both models compared their performance, whether there is an increase in accuracy or not. From the results obtained shows an increase in accuracy if the feature selection using GA. The proposed model is referred to as GADT (GA-Decision Tree) and GANB (GA-Naive Bayes). The data sets tested in this paper are taken from the UCI Machine Learning repository.

A stepwise regression tree for nonlinear approximation: applications to estimating subpixel land cover

USGS Publications Warehouse

Huang, C.; Townshend, J.R.G.

2003-01-01

A stepwise regression tree (SRT) algorithm was developed for approximating complex nonlinear relationships. Based on the regression tree of Breiman et al . (BRT) and a stepwise linear regression (SLR) method, this algorithm represents an improvement over SLR in that it can approximate nonlinear relationships and over BRT in that it gives more realistic predictions. The applicability of this method to estimating subpixel forest was demonstrated using three test data sets, on all of which it gave more accurate predictions than SLR and BRT. SRT also generated more compact trees and performed better than or at least as well as BRT at all 10 equal forest proportion interval ranging from 0 to 100%. This method is appealing to estimating subpixel land cover over large areas.

Improving generalized inverted index lock wait times

NASA Astrophysics Data System (ADS)

Borodin, A.; Mirvoda, S.; Porshnev, S.; Ponomareva, O.

2018-01-01

Concurrent operations on tree like data structures is a cornerstone of any database system. Concurrent operations intended for improving read\\write performance and usually implemented via some way of locking. Deadlock-free methods of concurrency control are known as tree locking protocols. These protocols provide basic operations(verbs) and algorithm (ways of operation invocations) for applying it to any tree-like data structure. These algorithms operate on data, managed by storage engine which are very different among RDBMS implementations. In this paper, we discuss tree locking protocol implementation for General inverted index (Gin) applied to multiversion concurrency control (MVCC) storage engine inside PostgreSQL RDBMS. After that we introduce improvements to locking protocol and provide usage statistics about evaluation of our improvement in very high load environment in one of the world’s largest IT company.

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

Isosurface Extraction in Time-Varying Fields Using a Temporal Hierarchical Index Tree

NASA Technical Reports Server (NTRS)

Shen, Han-Wei; Gerald-Yamasaki, Michael (Technical Monitor)

1998-01-01

Many high-performance isosurface extraction algorithms have been proposed in the past several years as a result of intensive research efforts. When applying these algorithms to large-scale time-varying fields, the storage overhead incurred from storing the search index often becomes overwhelming. this paper proposes an algorithm for locating isosurface cells in time-varying fields. We devise a new data structure, called Temporal Hierarchical Index Tree, which utilizes the temporal coherence that exists in a time-varying field and adoptively coalesces the cells' extreme values over time; the resulting extreme values are then used to create the isosurface cell search index. For a typical time-varying scalar data set, not only does this temporal hierarchical index tree require much less storage space, but also the amount of I/O required to access the indices from the disk at different time steps is substantially reduced. We illustrate the utility and speed of our algorithm with data from several large-scale time-varying CID simulations. Our algorithm can achieve more than 80% of disk-space savings when compared with the existing techniques, while the isosurface extraction time is nearly optimal.

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees.

PubMed

van Iersel, Leo; Kelk, Steven; Lekić, Nela; Scornavacca, Celine

2014-05-05

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

2011-01-01

Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. PMID:22165819

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

The Way of Openness: Moral Sphere Theory, Education, Ethics, and Classroom Management

ERIC Educational Resources Information Center

Bullough, Robert V., Jr.

2014-01-01

Noting the challenges of radical pluralism and uncertainty to ethics and education, the author describes, then explores Moral Sphere Theory (MST) developed by the philosopher Robert Kane and in relationship to insights drawn from American pragmatism. The argument is that MST offers fresh ways for thinking about education and the profound…

EVALUATE THE UTILITY OF ENTEROCOCCI AS INDICATORS OF THE SOURCES OF FECAL CONTAMINATION IN IMPAIRED SUBWATERSHEDS THROUGH DNA-BASED MOLECULAR TECHNIQUES

EPA Science Inventory

Microbial source tracking (MST) is based on the assumption that specific strains of bacteria are associated with specific host species. MST methods are attractive because their application on environmental samples could help define the nature of water quality problems in impaire...

Common and Specific Factors Approaches to Home-Based Treatment: I-FAST and MST

ERIC Educational Resources Information Center

Lee, Mo Yee; Greene, Gilbert J.; Fraser, J. Scott; Edwards, Shivani G.; Grove, David; Solovey, Andrew D.; Scott, Pamela

2013-01-01

Objectives: This study examined the treatment outcomes of integrated families and systems treatment (I-FAST), a moderated common factors approach, in reference to multisystemic therapy (MST), an established specific factor approach, for treating at risk children and adolescents and their families in an intensive community-based setting. Method:…

Multisystemic Therapy for Child Non-Externalizing Psychological and Health Problems: A Preliminary Review

ERIC Educational Resources Information Center

Pane, Heather T.; White, Rachel S.; Nadorff, Michael R.; Grills-Taquechel, Amie; Stanley, Melinda A.

2013-01-01

Multisystemic therapy (MST) is effective for decreasing or preventing delinquency and other externalizing behaviors and increasing prosocial or adaptive behaviors. The purpose of this project was to review the literature examining the efficacy of MST for other child psychological and health problems reflecting non-externalizing behaviors,…

Information Flow Analysis of Level 4 Payload Processing Operations

NASA Technical Reports Server (NTRS)

Danz, Mary E.

1991-01-01

The Level 4 Mission Sequence Test (MST) was studied to develop strategies and recommendations to facilitate information flow. Recommendations developed as a result of this study include revised format of the Test and Assembly Procedure (TAP) document and a conceptualized software based system to assist in the management of information flow during the MST.

Predicting early positive change in multisystemic therapy with youth exhibiting antisocial behaviors.

PubMed

Tiernan, Kristine; Foster, Sharon L; Cunningham, Phillippe B; Brennan, Patricia; Whitmore, Elizabeth

2015-03-01

This study examined individual and family characteristics that predicted early positive change in the context of Multisystemic Therapy (MST). Families (n = 185; 65% male; average youth age 15 years) receiving MST in community settings completed assessments at the outset of treatment and 6-12 weeks into treatment. Early positive changes in youth antisocial behavior were assessed using the caregiver report on the Child Behavior Checklist Externalizing Behaviors subscale and youth report on the Self-Report Delinquency Scale. Overall, families showed significant positive changes by 6-12 weeks into treatment; these early changes were maintained into midtreatment 6-12 weeks later. Families who exhibited clinically significant gains early in treatment were more likely to terminate treatment successfully compared with those who did not show these gains. Low youth internalizing behaviors and absence of youth drug use predicted early positive changes in MST. High levels of parental monitoring and low levels of affiliation with deviant peers (mechanisms known to be associated with MST success) were also associated with early positive change. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Inherited MST1 deficiency underlies susceptibility to EV-HPV infections.

PubMed

Crequer, Amandine; Picard, Capucine; Patin, Etienne; D'Amico, Aurelia; Abhyankar, Avinash; Munzer, Martine; Debré, Marianne; Zhang, Shen-Ying; de Saint-Basile, Geneviève; Fischer, Alain; Abel, Laurent; Orth, Gérard; Casanova, Jean-Laurent; Jouanguy, Emmanuelle

2012-01-01

Epidermodysplasia verruciformis (EV) is characterized by persistent cutaneous lesions caused by a specific group of related human papillomavirus genotypes (EV-HPVs) in otherwise healthy individuals. Autosomal recessive (AR) EVER1 and EVER2 deficiencies account for two thirds of known cases of EV. AR RHOH deficiency has recently been described in two siblings with EV-HPV infections as well as other infectious and tumoral manifestations. We report here the whole-exome based discovery of AR MST1 deficiency in a 19-year-old patient with a T-cell deficiency associated with EV-HPV, bacterial and fungal infections. MST1 deficiency has recently been described in seven patients from three unrelated kindreds with profound T-cell deficiency and various viral and bacterial infections. The patient was also homozygous for a rare ERCC3 variation. Our findings broaden the clinical range of infections seen in MST1 deficiency and provide a new genetic etiology of susceptibility to EV-HPV infections. Together with the recent discovery of RHOH deficiency, they suggest that T cells are involved in the control of EV-HPVs, at least in some individuals.

Microbial source tracking: a tool for identifying sources of microbial contamination in the food chain.

PubMed

Fu, Ling-Lin; Li, Jian-Rong

2014-01-01

The ability to trace fecal indicators and food-borne pathogens to the point of origin has major ramifications for food industry, food regulatory agencies, and public health. Such information would enable food producers and processors to better understand sources of contamination and thereby take corrective actions to prevent transmission. Microbial source tracking (MST), which currently is largely focused on determining sources of fecal contamination in waterways, is also providing the scientific community tools for tracking both fecal bacteria and food-borne pathogens contamination in the food chain. Approaches to MST are commonly classified as library-dependent methods (LDMs) or library-independent methods (LIMs). These tools will have widespread applications, including the use for regulatory compliance, pollution remediation, and risk assessment. These tools will reduce the incidence of illness associated with food and water. Our aim in this review is to highlight the use of molecular MST methods in application to understanding the source and transmission of food-borne pathogens. Moreover, the future directions of MST research are also discussed.

Military sexual trauma, combat exposure, and negative urgency as independent predictors of PTSD and subsequent alcohol problems among OEF/OIF veterans.

PubMed

Hahn, Austin M; Tirabassi, Christine K; Simons, Raluca M; Simons, Jeffrey S

2015-11-01

This study tested a path model of relationships between military sexual trauma (MST), combat exposure, negative urgency, posttraumatic stress disorder (PTSD) symptoms, and alcohol use and related problems. The sample consisted of 86 Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) veterans who reported drinking at least one alcoholic beverage per week. PTSD mediated the relationships between MST and alcohol-related problems, negative urgency and alcohol-related problems, and combat exposure and alcohol-related problems. In addition, negative urgency had a direct effect on alcohol problems. These results indicate that MST, combat exposure, and negative urgency independently predict PTSD symptoms and PTSD symptoms mediate their relationship with alcohol-related problems. Findings support previous literature on the effect of combat exposure and negative urgency on PTSD and subsequent alcohol-related problems. The current study also contributes to the limited research regarding the relationship between MST, PSTD, and alcohol use and related problems. Clinical interventions aimed at reducing emotional dysregulation and posttraumatic stress symptomology may subsequently improve alcohol-related outcomes. (c) 2015 APA, all rights reserved).

A novel method for the study of molecular interaction by using microscale thermophoresis.

PubMed

Mao, Yexuan; Yu, Lanlan; Yang, Ran; Qu, Ling-bo; Harrington, Perter de B

2015-01-01

The fundamental studies for the binding events of protein and its partner are crucial in drug development. In this study, a novel technology named microscale thermophoresis (MST) was applied in the investigation of molecular interaction between an organic dye fluorescein isothiocyanate (FITC) and bovine serum albumin (BSA), and the results were compared with those obtained from conventional fluorescence spectroscopy. The MST data demonstrated that with a short interaction time, FITC showed a high binding affinity for BSA by weak interaction instead of labeling the protein. By using competitive strategies in which warfarin and ibuprofen acted as the site markers of BSA, FITC was proven to mainly bind to the hydrophobic pocket of site II of BSA compared to site I of BSA. Except for the binding affinity, MST also provided additional information with respect to the aggregation of BSA and the binding of FITC to BSA aggregates, which is unobtainable by fluorescence spectroscopy. This work proves that MST as a new approach is powerful and reliable for investigation of protein-small molecule interaction. Copyright © 2014 Elsevier B.V. All rights reserved.