Lamb wave based damage detection using Matching Pursuit and Support Vector Machine classifier

NASA Astrophysics Data System (ADS)

Agarwal, Sushant; Mitra, Mira

2014-03-01

In this paper, the suitability of using Matching Pursuit (MP) and Support Vector Machine (SVM) for damage detection using Lamb wave response of thin aluminium plate is explored. Lamb wave response of thin aluminium plate with or without damage is simulated using finite element. Simulations are carried out at different frequencies for various kinds of damage. The procedure is divided into two parts - signal processing and machine learning. Firstly, MP is used for denoising and to maintain the sparsity of the dataset. In this study, MP is extended by using a combination of time-frequency functions as the dictionary and is deployed in two stages. Selection of a particular type of atoms lead to extraction of important features while maintaining the sparsity of the waveform. The resultant waveform is then passed as input data for SVM classifier. SVM is used to detect the location of the potential damage from the reduced data. The study demonstrates that SVM is a robust classifier in presence of noise and more efficient as compared to Artificial Neural Network (ANN). Out-of-sample data is used for the validation of the trained and tested classifier. Trained classifiers are found successful in detection of the damage with more than 95% detection rate.

Research on rolling element bearing fault diagnosis based on genetic algorithm matching pursuit

NASA Astrophysics Data System (ADS)

Rong, R. W.; Ming, T. F.

2017-12-01

In order to solve the problem of slow computation speed, matching pursuit algorithm is applied to rolling bearing fault diagnosis, and the improvement are conducted from two aspects that are the construction of dictionary and the way to search for atoms. To be specific, Gabor function which can reflect time-frequency localization characteristic well is used to construct the dictionary, and the genetic algorithm to improve the searching speed. A time-frequency analysis method based on genetic algorithm matching pursuit (GAMP) algorithm is proposed. The way to set property parameters for the improvement of the decomposition results is studied. Simulation and experimental results illustrate that the weak fault feature of rolling bearing can be extracted effectively by this proposed method, at the same time, the computation speed increases obviously.

Developing a New Computer-Aided Clinical Decision Support System for Prediction of Successful Postcardioversion Patients with Persistent Atrial Fibrillation.

PubMed

Sterling, Mark; Huang, David T; Ghoraani, Behnaz

2015-01-01

We propose a new algorithm to predict the outcome of direct-current electric (DCE) cardioversion for atrial fibrillation (AF) patients. AF is the most common cardiac arrhythmia and DCE cardioversion is a noninvasive treatment to end AF and return the patient to sinus rhythm (SR). Unfortunately, there is a high risk of AF recurrence in persistent AF patients; hence clinically it is important to predict the DCE outcome in order to avoid the procedure's side effects. This study develops a feature extraction and classification framework to predict AF recurrence patients from the underlying structure of atrial activity (AA). A multiresolution signal decomposition technique, based on matching pursuit (MP), was used to project the AA over a dictionary of wavelets. Seven novel features were derived from the decompositions and were employed in a quadratic discrimination analysis classification to predict the success of post-DCE cardioversion in 40 patients with persistent AF. The proposed algorithm achieved 100% sensitivity and 95% specificity, indicating that the proposed computational approach captures detailed structural information about the underlying AA and could provide reliable information for effective management of AF.

Direct Position Determination of Unknown Signals in the Presence of Multipath Propagation

PubMed Central

Yu, Hongyi

2018-01-01

A novel geolocation architecture, termed “Multiple Transponders and Multiple Receivers for Multiple Emitters Positioning System (MTRE)” is proposed in this paper. Existing Direct Position Determination (DPD) methods take advantage of a rather simple channel assumption (line of sight channels with complex path attenuations) and a simplified MUltiple SIgnal Classification (MUSIC) algorithm cost function to avoid the high dimension searching. We point out that the simplified assumption and cost function reduce the positioning accuracy because of the singularity of the array manifold in a multi-path environment. We present a DPD model for unknown signals in the presence of Multi-path Propagation (MP-DPD) in this paper. MP-DPD adds non-negative real path attenuation constraints to avoid the mistake caused by the singularity of the array manifold. The Multi-path Propagation MUSIC (MP-MUSIC) method and the Active Set Algorithm (ASA) are designed to reduce the dimension of searching. A Multi-path Propagation Maximum Likelihood (MP-ML) method is proposed in addition to overcome the limitation of MP-MUSIC in the sense of a time-sensitive application. An iterative algorithm and an approach of initial value setting are given to make the MP-ML time consumption acceptable. Numerical results validate the performances improvement of MP-MUSIC and MP-ML. A closed form of the Cramér–Rao Lower Bound (CRLB) is derived as a benchmark to evaluate the performances of MP-MUSIC and MP-ML. PMID:29562601

Direct Position Determination of Unknown Signals in the Presence of Multipath Propagation.

PubMed

Du, Jianping; Wang, Ding; Yu, Wanting; Yu, Hongyi

2018-03-17

A novel geolocation architecture, termed "Multiple Transponders and Multiple Receivers for Multiple Emitters Positioning System (MTRE)" is proposed in this paper. Existing Direct Position Determination (DPD) methods take advantage of a rather simple channel assumption (line of sight channels with complex path attenuations) and a simplified MUltiple SIgnal Classification (MUSIC) algorithm cost function to avoid the high dimension searching. We point out that the simplified assumption and cost function reduce the positioning accuracy because of the singularity of the array manifold in a multi-path environment. We present a DPD model for unknown signals in the presence of Multi-path Propagation (MP-DPD) in this paper. MP-DPD adds non-negative real path attenuation constraints to avoid the mistake caused by the singularity of the array manifold. The Multi-path Propagation MUSIC (MP-MUSIC) method and the Active Set Algorithm (ASA) are designed to reduce the dimension of searching. A Multi-path Propagation Maximum Likelihood (MP-ML) method is proposed in addition to overcome the limitation of MP-MUSIC in the sense of a time-sensitive application. An iterative algorithm and an approach of initial value setting are given to make the MP-ML time consumption acceptable. Numerical results validate the performances improvement of MP-MUSIC and MP-ML. A closed form of the Cramér-Rao Lower Bound (CRLB) is derived as a benchmark to evaluate the performances of MP-MUSIC and MP-ML.

Improving recovery of ECG signal with deterministic guarantees using split signal for multiple supports of matching pursuit (SS-MSMP) algorithm.

PubMed

Tawfic, Israa Shaker; Kayhan, Sema Koc

2017-02-01

Compressed sensing (CS) is a new field used for signal acquisition and design of sensor that made a large drooping in the cost of acquiring sparse signals. In this paper, new algorithms are developed to improve the performance of the greedy algorithms. In this paper, a new greedy pursuit algorithm, SS-MSMP (Split Signal for Multiple Support of Matching Pursuit), is introduced and theoretical analyses are given. The SS-MSMP is suggested for sparse data acquisition, in order to reconstruct analog and efficient signals via a small set of general measurements. This paper proposes a new fast method which depends on a study of the behavior of the support indices through picking the best estimation of the corrosion between residual and measurement matrix. The term multiple supports originates from an algorithm; in each iteration, the best support indices are picked based on maximum quality created by discovering correlation for a particular length of support. We depend on this new algorithm upon our previous derivative of halting condition that we produce for Least Support Orthogonal Matching Pursuit (LS-OMP) for clear and noisy signal. For better reconstructed results, SS-MSMP algorithm provides the recovery of support set for long signals such as signals used in WBAN. Numerical experiments demonstrate that the new suggested algorithm performs well compared to existing algorithms in terms of many factors used for reconstruction performance. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Matching pursuit parallel decomposition of seismic data

NASA Astrophysics Data System (ADS)

Li, Chuanhui; Zhang, Fanchang

2017-07-01

In order to improve the computation speed of matching pursuit decomposition of seismic data, a matching pursuit parallel algorithm is designed in this paper. We pick a fixed number of envelope peaks from the current signal in every iteration according to the number of compute nodes and assign them to the compute nodes on average to search the optimal Morlet wavelets in parallel. With the help of parallel computer systems and Message Passing Interface, the parallel algorithm gives full play to the advantages of parallel computing to significantly improve the computation speed of the matching pursuit decomposition and also has good expandability. Besides, searching only one optimal Morlet wavelet by every compute node in every iteration is the most efficient implementation.

Sensitivity Simulation of Compressed Sensing Based Electronic Warfare Receiver Using Orthogonal Matching Pursuit Algorithm

DTIC Science & Technology

2016-02-01

algorithm is used to process CS data. The insufficient nature of the sparcity of the signal adversely affects the signal detection probability for...with equal probability. The scheme was proposed [2] for image processing using single pixel camera, where the field of view was masked by a grid...modulation. The orthogonal matching pursuit (OMP) algorithm is used to process CS data. The insufficient nature of the sparcity of the signal

A Direction of Arrival Estimation Algorithm Based on Orthogonal Matching Pursuit

NASA Astrophysics Data System (ADS)

Tang, Junyao; Cao, Fei; Liu, Lipeng

2018-02-01

The results show that the modified DSM is able to predict local buckling capacity of hot-rolled RHS and SHS accurately. In order to solve the problem of the weak ability of anti-radiation missile against active decoy in modern electronic warfare, a direction of arrival estimation algorithm based on orthogonal matching pursuit is proposed in this paper. The algorithm adopts the compression sensing technology. This paper uses array antennas to receive signals, gets the sparse representation of signals, and then designs the corresponding perception matrix. The signal is reconstructed by orthogonal matching pursuit algorithm to estimate the optimal solution. At the same time, the error of the whole measurement system is analyzed and simulated, and the validity of this algorithm is verified. The algorithm greatly reduces the measurement time, the quantity of equipment and the total amount of the calculation, and accurately estimates the angle and strength of the incoming signal. This technology can effectively improve the angle resolution of the missile, which is of reference significance to the research of anti-active decoy.

OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms

DOE PAGES

Meng, Zhaoyi; Koniges, Alice; He, Yun Helen; ...

2016-09-21

In this paper, we investigate the OpenMP parallelization and optimization of two novel data classification algorithms. The new algorithms are based on graph and PDE solution techniques and provide significant accuracy and performance advantages over traditional data classification algorithms in serial mode. The methods leverage the Nystrom extension to calculate eigenvalue/eigenvectors of the graph Laplacian and this is a self-contained module that can be used in conjunction with other graph-Laplacian based methods such as spectral clustering. We use performance tools to collect the hotspots and memory access of the serial codes and use OpenMP as the parallelization language to parallelizemore » the most time-consuming parts. Where possible, we also use library routines. We then optimize the OpenMP implementations and detail the performance on traditional supercomputer nodes (in our case a Cray XC30), and test the optimization steps on emerging testbed systems based on Intel’s Knights Corner and Landing processors. We show both performance improvement and strong scaling behavior. Finally, a large number of optimization techniques and analyses are necessary before the algorithm reaches almost ideal scaling.« less

Marginal semi-supervised sub-manifold projections with informative constraints for dimensionality reduction and recognition.

PubMed

Zhang, Zhao; Zhao, Mingbo; Chow, Tommy W S

2012-12-01

In this work, sub-manifold projections based semi-supervised dimensionality reduction (DR) problem learning from partial constrained data is discussed. Two semi-supervised DR algorithms termed Marginal Semi-Supervised Sub-Manifold Projections (MS³MP) and orthogonal MS³MP (OMS³MP) are proposed. MS³MP in the singular case is also discussed. We also present the weighted least squares view of MS³MP. Based on specifying the types of neighborhoods with pairwise constraints (PC) and the defined manifold scatters, our methods can preserve the local properties of all points and discriminant structures embedded in the localized PC. The sub-manifolds of different classes can also be separated. In PC guided methods, exploring and selecting the informative constraints is challenging and random constraint subsets significantly affect the performance of algorithms. This paper also introduces an effective technique to select the informative constraints for DR with consistent constraints. The analytic form of the projection axes can be obtained by eigen-decomposition. The connections between this work and other related work are also elaborated. The validity of the proposed constraint selection approach and DR algorithms are evaluated by benchmark problems. Extensive simulations show that our algorithms can deliver promising results over some widely used state-of-the-art semi-supervised DR techniques. Copyright © 2012 Elsevier Ltd. All rights reserved.

An efficient parallel algorithm for the calculation of unrestricted canonical MP2 energies.

PubMed

Baker, Jon; Wolinski, Krzysztof

2011-11-30

We present details of our efficient implementation of full accuracy unrestricted open-shell second-order canonical Møller-Plesset (MP2) energies, both serial and parallel. The algorithm is based on our previous restricted closed-shell MP2 code using the Saebo-Almlöf direct integral transformation. Depending on system details, UMP2 energies take from less than 1.5 to about 3.0 times as long as a closed-shell RMP2 energy on a similar system using the same algorithm. Several examples are given including timings for some large stable radicals with 90+ atoms and over 3600 basis functions. Copyright © 2011 Wiley Periodicals, Inc.

Generation new MP3 data set after compression

NASA Astrophysics Data System (ADS)

Atoum, Mohammed Salem; Almahameed, Mohammad

2016-02-01

The success of audio steganography techniques is to ensure imperceptibility of the embedded secret message in stego file and withstand any form of intentional or un-intentional degradation of secret message (robustness). Crucial to that using digital audio file such as MP3 file, which comes in different compression rate, however research studies have shown that performing steganography in MP3 format after compression is the most suitable one. Unfortunately until now the researchers can not test and implement their algorithm because no standard data set in MP3 file after compression is generated. So this paper focuses to generate standard data set with different compression ratio and different Genre to help researchers to implement their algorithms.

Development of Neuromorphic Sift Operator with Application to High Speed Image Matching

NASA Astrophysics Data System (ADS)

Shankayi, M.; Saadatseresht, M.; Bitetto, M. A. V.

2015-12-01

There was always a speed/accuracy challenge in photogrammetric mapping process, including feature detection and matching. Most of the researches have improved algorithm's speed with simplifications or software modifications which increase the accuracy of the image matching process. This research tries to improve speed without enhancing the accuracy of the same algorithm using Neuromorphic techniques. In this research we have developed a general design of a Neuromorphic ASIC to handle algorithms such as SIFT. We also have investigated neural assignment in each step of the SIFT algorithm. With a rough estimation based on delay of the used elements including MAC and comparator, we have estimated the resulting chip's performance for 3 scenarios, Full HD movie (Videogrammetry), 24 MP (UAV photogrammetry), and 88 MP image sequence. Our estimations led to approximate 3000 fps for Full HD movie, 250 fps for 24 MP image sequence and 68 fps for 88MP Ultracam image sequence which can be a huge improvement for current photogrammetric processing systems. We also estimated the power consumption of less than10 watts which is not comparable to current workflows.

A Subspace Pursuit–based Iterative Greedy Hierarchical Solution to the Neuromagnetic Inverse Problem

PubMed Central

Babadi, Behtash; Obregon-Henao, Gabriel; Lamus, Camilo; Hämäläinen, Matti S.; Brown, Emery N.; Purdon, Patrick L.

2013-01-01

Magnetoencephalography (MEG) is an important non-invasive method for studying activity within the human brain. Source localization methods can be used to estimate spatiotemporal activity from MEG measurements with high temporal resolution, but the spatial resolution of these estimates is poor due to the ill-posed nature of the MEG inverse problem. Recent developments in source localization methodology have emphasized temporal as well as spatial constraints to improve source localization accuracy, but these methods can be computationally intense. Solutions emphasizing spatial sparsity hold tremendous promise, since the underlying neurophysiological processes generating MEG signals are often sparse in nature, whether in the form of focal sources, or distributed sources representing large-scale functional networks. Recent developments in the theory of compressed sensing (CS) provide a rigorous framework to estimate signals with sparse structure. In particular, a class of CS algorithms referred to as greedy pursuit algorithms can provide both high recovery accuracy and low computational complexity. Greedy pursuit algorithms are difficult to apply directly to the MEG inverse problem because of the high-dimensional structure of the MEG source space and the high spatial correlation in MEG measurements. In this paper, we develop a novel greedy pursuit algorithm for sparse MEG source localization that overcomes these fundamental problems. This algorithm, which we refer to as the Subspace Pursuit-based Iterative Greedy Hierarchical (SPIGH) inverse solution, exhibits very low computational complexity while achieving very high localization accuracy. We evaluate the performance of the proposed algorithm using comprehensive simulations, as well as the analysis of human MEG data during spontaneous brain activity and somatosensory stimuli. These studies reveal substantial performance gains provided by the SPIGH algorithm in terms of computational complexity, localization accuracy, and robustness. PMID:24055554

P2MP MPLS-Based Hierarchical Service Management System

NASA Astrophysics Data System (ADS)

Kumaki, Kenji; Nakagawa, Ikuo; Nagami, Kenichi; Ogishi, Tomohiko; Ano, Shigehiro

This paper proposes a point-to-multipoint (P2MP) Multi-Protocol Label Switching (MPLS) based hierarchical service management system. Traditionally, general management systems deployed in some service providers control MPLS Label Switched Paths (LSPs) (e.g., RSVP-TE and LDP) and services (e.g., L2VPN, L3VPN and IP) separately. In order for dedicated management systems for MPLS LSPs and services to cooperate with each other automatically, a hierarchical service management system has been proposed with the main focus on point-to-point (P2P) TE LSPs in MPLS path management. In the case where P2MP TE LSPs and services are deployed in MPLS networks, the dedicated management systems for P2MP TE LSPs and services must work together automatically. Therefore, this paper proposes a new algorithm that uses a correlation between P2MP TE LSPs and multicast VPN services based on a P2MP MPLS-based hierarchical service management architecture. Also, the capacity and performance of the proposed algorithm are evaluated by simulations, which are actually based on certain real MPLS production networks, and are compared to that of the algorithm for P2P TE LSPs. Results show this system is very scalable within real MPLS production networks. This system, with the automatic correlation, appears to be deployable in real MPLS production networks.

Implementing dense linear algebra algorithms using multitasking on the CRAY X-MP-4 (or approaching the gigaflop)

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

Dongarra, J.J.; Hewitt, T.

1985-08-01

This note describes some experiments on simple, dense linear algebra algorithms. These experiments show that the CRAY X-MP is capable of small-grain multitasking arising from standard implementations of LU and Cholesky decomposition. The implementation described here provides the ''fastest'' execution rate for LU decomposition, 718 MFLOPS for a matrix of order 1000.

Capacity-optimized mp2 audio watermarking

NASA Astrophysics Data System (ADS)

Steinebach, Martin; Dittmann, Jana

2003-06-01

Today a number of audio watermarking algorithms have been proposed, some of them at a quality making them suitable for commercial applications. The focus of most of these algorithms is copyright protection. Therefore, transparency and robustness are the most discussed and optimised parameters. But other applications for audio watermarking can also be identified stressing other parameters like complexity or payload. In our paper, we introduce a new mp2 audio watermarking algorithm optimised for high payload. Our algorithm uses the scale factors of an mp2 file for watermark embedding. They are grouped and masked based on a pseudo-random pattern generated from a secret key. In each group, we embed one bit. Depending on the bit to embed, we change the scale factors by adding 1 where necessary until it includes either more even or uneven scale factors. An uneven group has a 1 embedded, an even group a 0. The same rule is later applied to detect the watermark. The group size can be increased or decreased for transparency/payload trade-off. We embed 160 bits or more in an mp2 file per second without reducing perceived quality. As an application example, we introduce a prototypic Karaoke system displaying song lyrics embedded as a watermark.

An efficient parallel algorithm for the calculation of canonical MP2 energies.

PubMed

Baker, Jon; Pulay, Peter

2002-09-01

We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo-Almlöf direct-integral transformation, coupled with an efficient prescreening of the AO integrals. The parallel algorithm avoids synchronization delays by spawning a second set of slaves during the bin-sort prior to the second half-transformation. Results are presented for systems with up to 2000 basis functions. MP2 energies for molecules with 400-500 basis functions can be routinely calculated to microhartree accuracy on a small number of processors (6-8) in a matter of minutes with modern PC-based parallel computers. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1150-1156, 2002

Last-position elimination-based learning automata.

PubMed

Zhang, Junqi; Wang, Cheng; Zhou, MengChu

2014-12-01

An update scheme of the state probability vector of actions is critical for learning automata (LA). The most popular is the pursuit scheme that pursues the estimated optimal action and penalizes others. This paper proposes a reverse philosophy that leads to last-position elimination-based learning automata (LELA). The action graded last in terms of the estimated performance is penalized by decreasing its state probability and is eliminated when its state probability becomes zero. All active actions, that is, actions with nonzero state probability, equally share the penalized state probability from the last-position action at each iteration. The proposed LELA is characterized by the relaxed convergence condition for the optimal action, the accelerated step size of the state probability update scheme for the estimated optimal action, and the enriched sampling for the estimated nonoptimal actions. The proof of the ϵ-optimal property for the proposed algorithm is presented. Last-position elimination is a widespread philosophy in the real world and has proved to be also helpful for the update scheme of the learning automaton via the simulations of well-known benchmark environments. In the simulations, two versions of the LELA, using different selection strategies of the last action, are compared with the classical pursuit algorithms Discretized Pursuit Reward-Inaction (DP(RI)) and Discretized Generalized Pursuit Algorithm (DGPA). Simulation results show that the proposed schemes achieve significantly faster convergence and higher accuracy than the classical ones. Specifically, the proposed schemes reduce the interval to find the best parameter for a specific environment in the classical pursuit algorithms. Thus, they can have their parameter tuning easier to perform and can save much more time when applied to a practical case. Furthermore, the convergence curves and the corresponding variance coefficient curves of the contenders are illustrated to characterize their essential differences and verify the analysis results of the proposed algorithms.

Enhancement of dynamic myocardial perfusion PET images based on low-rank plus sparse decomposition.

PubMed

Lu, Lijun; Ma, Xiaomian; Mohy-Ud-Din, Hassan; Ma, Jianhua; Feng, Qianjin; Rahmim, Arman; Chen, Wufan

2018-02-01

The absolute quantification of dynamic myocardial perfusion (MP) PET imaging is challenged by the limited spatial resolution of individual frame images due to division of the data into shorter frames. This study aims to develop a method for restoration and enhancement of dynamic PET images. We propose that the image restoration model should be based on multiple constraints rather than a single constraint, given the fact that the image characteristic is hardly described by a single constraint alone. At the same time, it may be possible, but not optimal, to regularize the image with multiple constraints simultaneously. Fortunately, MP PET images can be decomposed into a superposition of background vs. dynamic components via low-rank plus sparse (L + S) decomposition. Thus, we propose an L + S decomposition based MP PET image restoration model and express it as a convex optimization problem. An iterative soft thresholding algorithm was developed to solve the problem. Using realistic dynamic 82 Rb MP PET scan data, we optimized and compared its performance with other restoration methods. The proposed method resulted in substantial visual as well as quantitative accuracy improvements in terms of noise versus bias performance, as demonstrated in extensive 82 Rb MP PET simulations. In particular, the myocardium defect in the MP PET images had improved visual as well as contrast versus noise tradeoff. The proposed algorithm was also applied on an 8-min clinical cardiac 82 Rb MP PET study performed on the GE Discovery PET/CT, and demonstrated improved quantitative accuracy (CNR and SNR) compared to other algorithms. The proposed method is effective for restoration and enhancement of dynamic PET images. Copyright © 2017 Elsevier B.V. All rights reserved.

Matrix-Inversion-Free Compressed Sensing With Variable Orthogonal Multi-Matching Pursuit Based on Prior Information for ECG Signals.

PubMed

Cheng, Yih-Chun; Tsai, Pei-Yun; Huang, Ming-Hao

2016-05-19

Low-complexity compressed sensing (CS) techniques for monitoring electrocardiogram (ECG) signals in wireless body sensor network (WBSN) are presented. The prior probability of ECG sparsity in the wavelet domain is first exploited. Then, variable orthogonal multi-matching pursuit (vOMMP) algorithm that consists of two phases is proposed. In the first phase, orthogonal matching pursuit (OMP) algorithm is adopted to effectively augment the support set with reliable indices and in the second phase, the orthogonal multi-matching pursuit (OMMP) is employed to rescue the missing indices. The reconstruction performance is thus enhanced with the prior information and the vOMMP algorithm. Furthermore, the computation-intensive pseudo-inverse operation is simplified by the matrix-inversion-free (MIF) technique based on QR decomposition. The vOMMP-MIF CS decoder is then implemented in 90 nm CMOS technology. The QR decomposition is accomplished by two systolic arrays working in parallel. The implementation supports three settings for obtaining 40, 44, and 48 coefficients in the sparse vector. From the measurement result, the power consumption is 11.7 mW at 0.9 V and 12 MHz. Compared to prior chip implementations, our design shows good hardware efficiency and is suitable for low-energy applications.

Using Strassen's algorithm to accelerate the solution of linear systems

NASA Technical Reports Server (NTRS)

Bailey, David H.; Lee, King; Simon, Horst D.

1990-01-01

Strassen's algorithm for fast matrix-matrix multiplication has been implemented for matrices of arbitrary shapes on the CRAY-2 and CRAY Y-MP supercomputers. Several techniques have been used to reduce the scratch space requirement for this algorithm while simultaneously preserving a high level of performance. When the resulting Strassen-based matrix multiply routine is combined with some routines from the new LAPACK library, LU decomposition can be performed with rates significantly higher than those achieved by conventional means. We succeeded in factoring a 2048 x 2048 matrix on the CRAY Y-MP at a rate equivalent to 325 MFLOPS.

Incremental principal component pursuit for video background modeling

DOEpatents

Rodriquez-Valderrama, Paul A.; Wohlberg, Brendt

2017-03-14

An incremental Principal Component Pursuit (PCP) algorithm for video background modeling that is able to process one frame at a time while adapting to changes in background, with a computational complexity that allows for real-time processing, having a low memory footprint and is robust to translational and rotational jitter.

Projection pursuit water quality evaluation model based on chicken swam algorithm

NASA Astrophysics Data System (ADS)

Hu, Zhe

2018-03-01

In view of the uncertainty and ambiguity of each index in water quality evaluation, in order to solve the incompatibility of evaluation results of individual water quality indexes, a projection pursuit model based on chicken swam algorithm is proposed. The projection index function which can reflect the water quality condition is constructed, the chicken group algorithm (CSA) is introduced, the projection index function is optimized, the best projection direction of the projection index function is sought, and the best projection value is obtained to realize the water quality evaluation. The comparison between this method and other methods shows that it is reasonable and feasible to provide decision-making basis for water pollution control in the basin.

Y-MP floating point and Cholesky factorization

NASA Technical Reports Server (NTRS)

Carter, Russell

1991-01-01

The floating point arithmetics implemented in the Cray 2 and Cray Y-MP computer systems are nearly identical, but large scale computations performed on the two systems have exhibited significant differences in accuracy. The difference in accuracy is analyzed for Cholesky factorization algorithm, and it is found that the source of the difference is the subtract magnitude operation of the Cray Y-MP. The results from numerical experiments for a range of problem sizes are presented, and an efficient method for improving the accuracy of the factorization obtained on the Y-MP is presented.

Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.

PubMed

Shrimankar, D D; Sathe, S R

2016-01-01

Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today's supercomputer often consists of clusters of SMP nodes. Programming paradigms such as OpenMP and MPI are used to write parallel codes for such architectures. However, the OpenMP programs cannot be scaled for more than a single SMP node. However, programs written in MPI can have more than single SMP nodes. But such a programming paradigm has an overhead of internode communication. In this work, we explore the tradeoffs between using OpenMP and MPI. We demonstrate that the communication overhead incurs significantly even in OpenMP loop execution and increases with the number of cores participating. We also demonstrate a communication model to approximate the overhead from communication in OpenMP loops. Our results are astonishing and interesting to a large variety of input data files. We have developed our own load balancing and cache optimization technique for message passing model. Our experimental results show that our own developed techniques give optimum performance of our parallel algorithm for various sizes of input parameter, such as sequence size and tile size, on a wide variety of multicore architectures.

Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets

PubMed Central

Shrimankar, D. D.; Sathe, S. R.

2016-01-01

Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today’s supercomputer often consists of clusters of SMP nodes. Programming paradigms such as OpenMP and MPI are used to write parallel codes for such architectures. However, the OpenMP programs cannot be scaled for more than a single SMP node. However, programs written in MPI can have more than single SMP nodes. But such a programming paradigm has an overhead of internode communication. In this work, we explore the tradeoffs between using OpenMP and MPI. We demonstrate that the communication overhead incurs significantly even in OpenMP loop execution and increases with the number of cores participating. We also demonstrate a communication model to approximate the overhead from communication in OpenMP loops. Our results are astonishing and interesting to a large variety of input data files. We have developed our own load balancing and cache optimization technique for message passing model. Our experimental results show that our own developed techniques give optimum performance of our parallel algorithm for various sizes of input parameter, such as sequence size and tile size, on a wide variety of multicore architectures. PMID:27932868

Monte Carlo MP2 on Many Graphical Processing Units.

PubMed

Doran, Alexander E; Hirata, So

2016-10-11

In the Monte Carlo second-order many-body perturbation (MC-MP2) method, the long sum-of-product matrix expression of the MP2 energy, whose literal evaluation may be poorly scalable, is recast into a single high-dimensional integral of functions of electron pair coordinates, which is evaluated by the scalable method of Monte Carlo integration. The sampling efficiency is further accelerated by the redundant-walker algorithm, which allows a maximal reuse of electron pairs. Here, a multitude of graphical processing units (GPUs) offers a uniquely ideal platform to expose multilevel parallelism: fine-grain data-parallelism for the redundant-walker algorithm in which millions of threads compute and share orbital amplitudes on each GPU; coarse-grain instruction-parallelism for near-independent Monte Carlo integrations on many GPUs with few and infrequent interprocessor communications. While the efficiency boost by the redundant-walker algorithm on central processing units (CPUs) grows linearly with the number of electron pairs and tends to saturate when the latter exceeds the number of orbitals, on a GPU it grows quadratically before it increases linearly and then eventually saturates at a much larger number of pairs. This is because the orbital constructions are nearly perfectly parallelized on a GPU and thus completed in a near-constant time regardless of the number of pairs. In consequence, an MC-MP2/cc-pVDZ calculation of a benzene dimer is 2700 times faster on 256 GPUs (using 2048 electron pairs) than on two CPUs, each with 8 cores (which can use only up to 256 pairs effectively). We also numerically determine that the cost to achieve a given relative statistical uncertainty in an MC-MP2 energy increases as O(n 3 ) or better with system size n, which may be compared with the O(n 5 ) scaling of the conventional implementation of deterministic MP2. We thus establish the scalability of MC-MP2 with both system and computer sizes.

Quartic scaling MP2 for solids: A highly parallelized algorithm in the plane wave basis

NASA Astrophysics Data System (ADS)

Schäfer, Tobias; Ramberger, Benjamin; Kresse, Georg

2017-03-01

We present a low-complexity algorithm to calculate the correlation energy of periodic systems in second-order Møller-Plesset (MP2) perturbation theory. In contrast to previous approximation-free MP2 codes, our implementation possesses a quartic scaling, O ( N 4 ) , with respect to the system size N and offers an almost ideal parallelization efficiency. The general issue that the correlation energy converges slowly with the number of basis functions is eased by an internal basis set extrapolation. The key concept to reduce the scaling is to eliminate all summations over virtual orbitals which can be elegantly achieved in the Laplace transformed MP2 formulation using plane wave basis sets and fast Fourier transforms. Analogously, this approach could allow us to calculate second order screened exchange as well as particle-hole ladder diagrams with a similar low complexity. Hence, the presented method can be considered as a step towards systematically improved correlation energies.

Communication: A reduced scaling J-engine based reformulation of SOS-MP2 using graphics processing units.

PubMed

Maurer, S A; Kussmann, J; Ochsenfeld, C

2014-08-07

We present a low-prefactor, cubically scaling scaled-opposite-spin second-order Møller-Plesset perturbation theory (SOS-MP2) method which is highly suitable for massively parallel architectures like graphics processing units (GPU). The scaling is reduced from O(N⁵) to O(N³) by a reformulation of the MP2-expression in the atomic orbital basis via Laplace transformation and the resolution-of-the-identity (RI) approximation of the integrals in combination with efficient sparse algebra for the 3-center integral transformation. In contrast to previous works that employ GPUs for post Hartree-Fock calculations, we do not simply employ GPU-based linear algebra libraries to accelerate the conventional algorithm. Instead, our reformulation allows to replace the rate-determining contraction step with a modified J-engine algorithm, that has been proven to be highly efficient on GPUs. Thus, our SOS-MP2 scheme enables us to treat large molecular systems in an accurate and efficient manner on a single GPU-server.

NavP: Structured and Multithreaded Distributed Parallel Programming

NASA Technical Reports Server (NTRS)

Pan, Lei

2007-01-01

We present Navigational Programming (NavP) -- a distributed parallel programming methodology based on the principles of migrating computations and multithreading. The four major steps of NavP are: (1) Distribute the data using the data communication pattern in a given algorithm; (2) Insert navigational commands for the computation to migrate and follow large-sized distributed data; (3) Cut the sequential migrating thread and construct a mobile pipeline; and (4) Loop back for refinement. NavP is significantly different from the current prevailing Message Passing (MP) approach. The advantages of NavP include: (1) NavP is structured distributed programming and it does not change the code structure of an original algorithm. This is in sharp contrast to MP as MP implementations in general do not resemble the original sequential code; (2) NavP implementations are always competitive with the best MPI implementations in terms of performance. Approaches such as DSM or HPF have failed to deliver satisfying performance as of today in contrast, even if they are relatively easy to use compared to MP; (3) NavP provides incremental parallelization, which is beyond the reach of MP; and (4) NavP is a unifying approach that allows us to exploit both fine- (multithreading on shared memory) and coarse- (pipelined tasks on distributed memory) grained parallelism. This is in contrast to the currently popular hybrid use of MP+OpenMP, which is known to be complex to use. We present experimental results that demonstrate the effectiveness of NavP.

Doppler distortion correction based on microphone array and matching pursuit algorithm for a wayside train bearing monitoring system

NASA Astrophysics Data System (ADS)

Liu, Xingchen; Hu, Zhiyong; He, Qingbo; Zhang, Shangbin; Zhu, Jun

2017-10-01

Doppler distortion and background noise can reduce the effectiveness of wayside acoustic train bearing monitoring and fault diagnosis. This paper proposes a method of combining a microphone array and matching pursuit algorithm to overcome these difficulties. First, a dictionary is constructed based on the characteristics and mechanism of a far-field assumption. Then, the angle of arrival of the train bearing is acquired when applying matching pursuit to analyze the acoustic array signals. Finally, after obtaining the resampling time series, the Doppler distortion can be corrected, which is convenient for further diagnostic work. Compared with traditional single-microphone Doppler correction methods, the advantages of the presented array method are its robustness to background noise and its barely requiring pre-measuring parameters. Simulation and experimental study show that the proposed method is effective in performing wayside acoustic bearing fault diagnosis.

FFTs in external or hierarchical memory

NASA Technical Reports Server (NTRS)

Bailey, David H.

1989-01-01

A description is given of advanced techniques for computing an ordered FFT on a computer with external or hierarchical memory. These algorithms (1) require as few as two passes through the external data set, (2) use strictly unit stride, long vector transfers between main memory and external storage, (3) require only a modest amount of scratch space in main memory, and (4) are well suited for vector and parallel computation. Performance figures are included for implementations of some of these algorithms on Cray supercomputers. Of interest is the fact that a main memory version outperforms the current Cray library FFT routines on the Cray-2, the Cray X-MP, and the Cray Y-MP systems. Using all eight processors on the Cray Y-MP, this main memory routine runs at nearly 2 Gflops.

Increasing feasibility of the field-programmable gate array implementation of an iterative image registration using a kernel-warping algorithm

NASA Astrophysics Data System (ADS)

Nguyen, An Hung; Guillemette, Thomas; Lambert, Andrew J.; Pickering, Mark R.; Garratt, Matthew A.

2017-09-01

Image registration is a fundamental image processing technique. It is used to spatially align two or more images that have been captured at different times, from different sensors, or from different viewpoints. There have been many algorithms proposed for this task. The most common of these being the well-known Lucas-Kanade (LK) and Horn-Schunck approaches. However, the main limitation of these approaches is the computational complexity required to implement the large number of iterations necessary for successful alignment of the images. Previously, a multi-pass image interpolation algorithm (MP-I2A) was developed to considerably reduce the number of iterations required for successful registration compared with the LK algorithm. This paper develops a kernel-warping algorithm (KWA), a modified version of the MP-I2A, which requires fewer iterations to successfully register two images and less memory space for the field-programmable gate array (FPGA) implementation than the MP-I2A. These reductions increase feasibility of the implementation of the proposed algorithm on FPGAs with very limited memory space and other hardware resources. A two-FPGA system rather than single FPGA system is successfully developed to implement the KWA in order to compensate insufficiency of hardware resources supported by one FPGA, and increase parallel processing ability and scalability of the system.

Learning Efficient Sparse and Low Rank Models.

PubMed

Sprechmann, P; Bronstein, A M; Sapiro, G

2015-09-01

Parsimony, including sparsity and low rank, has been shown to successfully model data in numerous machine learning and signal processing tasks. Traditionally, such modeling approaches rely on an iterative algorithm that minimizes an objective function with parsimony-promoting terms. The inherently sequential structure and data-dependent complexity and latency of iterative optimization constitute a major limitation in many applications requiring real-time performance or involving large-scale data. Another limitation encountered by these modeling techniques is the difficulty of their inclusion in discriminative learning scenarios. In this work, we propose to move the emphasis from the model to the pursuit algorithm, and develop a process-centric view of parsimonious modeling, in which a learned deterministic fixed-complexity pursuit process is used in lieu of iterative optimization. We show a principled way to construct learnable pursuit process architectures for structured sparse and robust low rank models, derived from the iteration of proximal descent algorithms. These architectures learn to approximate the exact parsimonious representation at a fraction of the complexity of the standard optimization methods. We also show that appropriate training regimes allow to naturally extend parsimonious models to discriminative settings. State-of-the-art results are demonstrated on several challenging problems in image and audio processing with several orders of magnitude speed-up compared to the exact optimization algorithms.

Improvement and speed optimization of numerical tsunami modelling program using OpenMP technology

NASA Astrophysics Data System (ADS)

Chernov, A.; Zaytsev, A.; Yalciner, A.; Kurkin, A.

2009-04-01

Currently, the basic problem of tsunami modeling is low speed of calculations which is unacceptable for services of the operative notification. Existing algorithms of numerical modeling of hydrodynamic processes of tsunami waves are developed without taking the opportunities of modern computer facilities. There is an opportunity to have considerable acceleration of process of calculations by using parallel algorithms. We discuss here new approach to parallelization tsunami modeling code using OpenMP Technology (for multiprocessing systems with the general memory). Nowadays, multiprocessing systems are easily accessible for everyone. The cost of the use of such systems becomes much lower comparing to the costs of clusters. This opportunity also benefits all programmers to apply multithreading algorithms on desktop computers of researchers. Other important advantage of the given approach is the mechanism of the general memory - there is no necessity to send data on slow networks (for example Ethernet). All memory is the common for all computing processes; it causes almost linear scalability of the program and processes. In the new version of NAMI DANCE using OpenMP technology and multi-threading algorithm provide 80% gain in speed in comparison with the one-thread version for dual-processor unit. The speed increased and 320% gain was attained for four core processor unit of PCs. Thus, it was possible to reduce considerably time of performance of calculations on the scientific workstations (desktops) without complete change of the program and user interfaces. The further modernization of algorithms of preparation of initial data and processing of results using OpenMP looks reasonable. The final version of NAMI DANCE with the increased computational speed can be used not only for research purposes but also in real time Tsunami Warning Systems.

Sparse Reconstruction of Regional Gravity Signal Based on Stabilized Orthogonal Matching Pursuit (SOMP)

NASA Astrophysics Data System (ADS)

Saadat, S. A.; Safari, A.; Needell, D.

2016-06-01

The main role of gravity field recovery is the study of dynamic processes in the interior of the Earth especially in exploration geophysics. In this paper, the Stabilized Orthogonal Matching Pursuit (SOMP) algorithm is introduced for sparse reconstruction of regional gravity signals of the Earth. In practical applications, ill-posed problems may be encountered regarding unknown parameters that are sensitive to the data perturbations. Therefore, an appropriate regularization method needs to be applied to find a stabilized solution. The SOMP algorithm aims to regularize the norm of the solution vector, while also minimizing the norm of the corresponding residual vector. In this procedure, a convergence point of the algorithm that specifies optimal sparsity-level of the problem is determined. The results show that the SOMP algorithm finds the stabilized solution for the ill-posed problem at the optimal sparsity-level, improving upon existing sparsity based approaches.

Coordinating with Humans by Adjustable-Autonomy for Multirobot Pursuit (CHAMP)

NASA Astrophysics Data System (ADS)

Dumond, Danielle; Ayers, Jeanine; Schurr, Nathan; Carlin, Alan; Burke, Dustin; Rousseau, Jeffrey

2012-06-01

One of the primary challenges facing the modern small-unit tactical team is the ability of the unit to safely and effectively search, explore, clear and hold urbanized terrain that includes buildings, streets, and subterranean dwellings. Buildings provide cover and concealment to an enemy and restrict the movement of forces while diminishing their ability to engage the adversary. The use of robots has significant potential to reduce the risk to tactical teams and dramatically force multiply the small unit's footprint. Despite advances in robotic mobility, sensing capabilities, and human-robot interaction, the use of robots in room clearing operations remains nascent. CHAMP is a software system in development that integrates with a team of robotic platforms to enable them to coordinate with a human operator performing a search and pursuit task. In this way, the human operator can either give control to the robots to search autonomously, or can retain control and direct the robots where needed. CHAMP's autonomy is built upon a combination of adversarial pursuit algorithms and dynamic function allocation strategies that maximize the team's resources. Multi-modal interaction with CHAMP is achieved using novel gesture-recognition based capabilities to reduce the need for heads-down tele-operation. The Champ Coordination Algorithm addresses dynamic and limited team sizes, generates a novel map of the area, and takes into account mission goals, user preferences and team roles. In this paper we show results from preliminary simulated experiments and find that the CHAMP system performs faster than traditional search and pursuit algorithms.

Accelerating MP2C dispersion corrections for dimers and molecular crystals

NASA Astrophysics Data System (ADS)

Huang, Yuanhang; Shao, Yihan; Beran, Gregory J. O.

2013-06-01

The MP2C dispersion correction of Pitonak and Hesselmann [J. Chem. Theory Comput. 6, 168 (2010)], 10.1021/ct9005882 substantially improves the performance of second-order Møller-Plesset perturbation theory for non-covalent interactions, albeit with non-trivial computational cost. Here, the MP2C correction is computed in a monomer-centered basis instead of a dimer-centered one. When applied to a single dimer MP2 calculation, this change accelerates the MP2C dispersion correction several-fold while introducing only trivial new errors. More significantly, in the context of fragment-based molecular crystal studies, combination of the new monomer basis algorithm and the periodic symmetry of the crystal reduces the cost of computing the dispersion correction by two orders of magnitude. This speed-up reduces the MP2C dispersion correction calculation from a significant computational expense to a negligible one in crystals like aspirin or oxalyl dihydrazide, without compromising accuracy.

Communication: A reduced scaling J-engine based reformulation of SOS-MP2 using graphics processing units

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

Maurer, S. A.; Kussmann, J.; Ochsenfeld, C., E-mail: Christian.Ochsenfeld@cup.uni-muenchen.de

2014-08-07

We present a low-prefactor, cubically scaling scaled-opposite-spin second-order Møller-Plesset perturbation theory (SOS-MP2) method which is highly suitable for massively parallel architectures like graphics processing units (GPU). The scaling is reduced from O(N{sup 5}) to O(N{sup 3}) by a reformulation of the MP2-expression in the atomic orbital basis via Laplace transformation and the resolution-of-the-identity (RI) approximation of the integrals in combination with efficient sparse algebra for the 3-center integral transformation. In contrast to previous works that employ GPUs for post Hartree-Fock calculations, we do not simply employ GPU-based linear algebra libraries to accelerate the conventional algorithm. Instead, our reformulation allows tomore » replace the rate-determining contraction step with a modified J-engine algorithm, that has been proven to be highly efficient on GPUs. Thus, our SOS-MP2 scheme enables us to treat large molecular systems in an accurate and efficient manner on a single GPU-server.« less

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Landmine detection using two-tapped joint orthogonal matching pursuits

NASA Astrophysics Data System (ADS)

Goldberg, Sean; Glenn, Taylor; Wilson, Joseph N.; Gader, Paul D.

2012-06-01

Joint Orthogonal Matching Pursuits (JOMP) is used here in the context of landmine detection using data obtained from an electromagnetic induction (EMI) sensor. The response from an object containing metal can be decomposed into a discrete spectrum of relaxation frequencies (DSRF) from which we construct a dictionary. A greedy iterative algorithm is proposed for computing successive residuals of a signal by subtracting away the highest matching dictionary element at each step. The nal condence of a particular signal is a combination of the reciprocal of this residual and the mean of the complex component. A two-tap approach comparing signals on opposite sides of the geometric location of the sensor is examined and found to produce better classication. It is found that using only a single pursuit does a comparable job, reducing complexity and allowing for real-time implementation in automated target recognition systems. JOMP is particularly highlighted in comparison with a previous EMI detection algorithm known as String Match.

A new parallel algorithm of MP2 energy calculations.

PubMed

Ishimura, Kazuya; Pulay, Peter; Nagase, Shigeru

2006-03-01

A new parallel algorithm has been developed for second-order Møller-Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2-16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C(47)H(51)NO(14)) and luciferin (C(11)H(8)N(2)O(3)S(2)), the former with the 6-31G* and 6-311G** basis sets (1,032 and 1,484 basis functions, 164 correlated orbitals), and the latter with the aug-cc-pVDZ and aug-cc-pVTZ basis sets (530 and 1,198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C(130)H(10) (1,970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.

LDPC Codes--Structural Analysis and Decoding Techniques

ERIC Educational Resources Information Center

Zhang, Xiaojie

2012-01-01

Low-density parity-check (LDPC) codes have been the focus of much research over the past decade thanks to their near Shannon limit performance and to their efficient message-passing (MP) decoding algorithms. However, the error floor phenomenon observed in MP decoding, which manifests itself as an abrupt change in the slope of the error-rate curve,…

Medical Device Plug-and-Play Interoperability Standards and Technology Leadership

DTIC Science & Technology

2012-10-01

External Network Pump Adapter PulseOx Adapter • MD MP3 cart is a platform for the development of smart pump control algorithms • It includes...delivery with bounded latency Medical Device Mobile PnP Prototype Platform (MD MP3 ) • Got MDCF code to run on the BeagleBoard development boards we are

GPU Accelerated Browser for Neuroimaging Genomics.

PubMed

Zigon, Bob; Li, Huang; Yao, Xiaohui; Fang, Shiaofen; Hasan, Mohammad Al; Yan, Jingwen; Moore, Jason H; Saykin, Andrew J; Shen, Li

2018-04-25

Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates. The ANOVA algorithm is 110 times faster than the 4-core OpenMP version, while the VEGAS algorithm is 375 times faster than its 4-core OpenMP counter part. This approach lays a solid foundation for researchers to address the challenges of mining large-scale imaging genomics datasets via interactive visual exploration.

A Tensor Product Formulation of Strassen's Matrix Multiplication Algorithm with Memory Reduction

DOE PAGES

Kumar, B.; Huang, C. -H.; Sadayappan, P.; ...

1995-01-01

In this article, we present a program generation strategy of Strassen's matrix multiplication algorithm using a programming methodology based on tensor product formulas. In this methodology, block recursive programs such as the fast Fourier Transforms and Strassen's matrix multiplication algorithm are expressed as algebraic formulas involving tensor products and other matrix operations. Such formulas can be systematically translated to high-performance parallel/vector codes for various architectures. In this article, we present a nonrecursive implementation of Strassen's algorithm for shared memory vector processors such as the Cray Y-MP. A previous implementation of Strassen's algorithm synthesized from tensor product formulas required working storagemore » of size O(7 n ) for multiplying 2 n × 2 n matrices. We present a modified formulation in which the working storage requirement is reduced to O(4 n ). The modified formulation exhibits sufficient parallelism for efficient implementation on a shared memory multiprocessor. Performance results on a Cray Y-MP8/64 are presented.« less

A multi-parametric particle-pairing algorithm for particle tracking in single and multiphase flows

NASA Astrophysics Data System (ADS)

Cardwell, Nicholas D.; Vlachos, Pavlos P.; Thole, Karen A.

2011-10-01

Multiphase flows (MPFs) offer a rich area of fundamental study with many practical applications. Examples of such flows range from the ingestion of foreign particulates in gas turbines to transport of particles within the human body. Experimental investigation of MPFs, however, is challenging, and requires techniques that simultaneously resolve both the carrier and discrete phases present in the flowfield. This paper presents a new multi-parametric particle-pairing algorithm for particle tracking velocimetry (MP3-PTV) in MPFs. MP3-PTV improves upon previous particle tracking algorithms by employing a novel variable pair-matching algorithm which utilizes displacement preconditioning in combination with estimated particle size and intensity to more effectively and accurately match particle pairs between successive images. To improve the method's efficiency, a new particle identification and segmentation routine was also developed. Validation of the new method was initially performed on two artificial data sets: a traditional single-phase flow published by the Visualization Society of Japan (VSJ) and an in-house generated MPF data set having a bi-modal distribution of particles diameters. Metrics of the measurement yield, reliability and overall tracking efficiency were used for method comparison. On the VSJ data set, the newly presented segmentation routine delivered a twofold improvement in identifying particles when compared to other published methods. For the simulated MPF data set, measurement efficiency of the carrier phases improved from 9% to 41% for MP3-PTV as compared to a traditional hybrid PTV. When employed on experimental data of a gas-solid flow, the MP3-PTV effectively identified the two particle populations and reported a vector efficiency and velocity measurement error comparable to measurements for the single-phase flow images. Simultaneous measurement of the dispersed particle and the carrier flowfield velocities allowed for the calculation of instantaneous particle slip velocities, illustrating the algorithm's strength to robustly and accurately resolve polydispersed MPFs.

Factoring symmetric indefinite matrices on high-performance architectures

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1990-01-01

The Bunch-Kaufman algorithm is the method of choice for factoring symmetric indefinite matrices in many applications. However, the Bunch-Kaufman algorithm does not take advantage of high-performance architectures such as the Cray Y-MP. Three new algorithms, based on Bunch-Kaufman factorization, that take advantage of such architectures are described. Results from an implementation of the third algorithm are presented.

Identification of Patients with Statin Intolerance in a Managed Care Plan: A Comparison of 2 Claims-Based Algorithms.

PubMed

Bellows, Brandon K; Sainski-Nguyen, Amy M; Olsen, Cody J; Boklage, Susan H; Charland, Scott; Mitchell, Matthew P; Brixner, Diana I

2017-09-01

While statins are safe and efficacious, some patients may experience statin intolerance or treatment-limiting adverse events. Identifying patients with statin intolerance may allow optimal management of cardiovascular event risk through other strategies. Recently, an administrative claims data (ACD) algorithm was developed to identify patients with statin intolerance and validated against electronic medical records. However, how this algorithm compared with perceptions of statin intolerance by integrated delivery networks remains largely unknown. To determine the concurrent validity of an algorithm developed by a regional integrated delivery network multidisciplinary panel (MP) and a published ACD algorithm in identifying patients with statin intolerance. The MP consisted of 3 physicians and 2 pharmacists with expertise in cardiology, internal medicine, and formulary management. The MP algorithm used pharmacy and medical claims to identify patients with statin intolerance, classifying them as having statin intolerance if they met any of the following criteria: (a) medical claim for rhabdomyolysis, (b) medical claim for muscle weakness, (c) an outpatient medical claim for creatinine kinase assay, (d) fills for ≥ 2 different statins excluding dose increases, (e) decrease in statin dose, or (f) discontinuation of a statin with a subsequent fill for a nonstatin lipid-lowering therapy. The validated ACD algorithm identified statin intolerance as absolute intolerance with rhabdomyolysis; absolute intolerance without rhabdomyolysis (i.e., other adverse events); or as dose titration intolerance. Adult patients (aged ≥ 18 years) from the integrated delivery network with at least 1 prescription fill for a statin between January 1, 2011, and December 31, 2012 (first fill defined the index date) were identified. Patients with ≥ 1 year pre- and ≥ 2 years post-index continuous enrollment and no statin prescription fills in the pre-index period were included. The MP and ACD algorithms were applied to the population, and concordance was examined using individual (i.e., sensitivity, specificity, positive predictive value [PPV], and negative predictive value [NPV]) and overall performance measures (i.e., accuracy, Cohen's kappa coefficient, balanced accuracy, F-1 score, and phi coefficient). After applying the inclusion criteria, 7,490 patients were evaluated for statin intolerance. The mean (SD) age of the population was 51.1 (8.5) years, and 55.7% were male. The MP and ACD algorithms classified 11.3% and 5.4% of patients as having statin intolerance, respectively. The concordance of the MP algorithm was mixed, with negative classification of statin intolerance measures having high concordance (specificity 0.91, NPV 0.97) and positive classification of statin intolerance measures having poor concordance (sensitivity 0.45, PPV 0.21). Overall performance measures showed mixed agreement between the algorithms. Both algorithms used a mix of pharmacy and medical claims and may be useful for organizations interested in identifying patients with statin intolerance. By identifying patients with statin intolerance, organizations may consider a variety of options, including using nonstatin lipid-lowering therapies, to manage cardiovascular event risk in these patients. This study was funded by Regeneron Pharmaceuticals and Sanofi US. Boklage is employed by, and owns stock in, Regeneron, and Charland is employed by Sanofi. Bellows has received fees from Avenir for advisory board membership and grants from Myriad Genetics, Biogen, Janssen, and National Institutes of Health. Brixner reports advisory board and consultancy fees and grants from Sanofi. Mitchell reports consultancy fees from Sanofi. Study concept and design were contributed by Bellows, Boklage, Charland, and Brixner. Bellows, Sainski-Nguyen, and Olsen took the lead in data collection, along with Mitchell. Data interpretation was performed by Mitchell, along with the other authors. The manuscript was written by Bellows, Sainski-Nguyen, and Olsen and revised by all the authors.

Duration analysis using matching pursuit algorithm reveals longer bouts of gamma rhythm.

PubMed

Chandran Ks, Subhash; Seelamantula, Chandra Sekhar; Ray, Supratim

2018-03-01

The gamma rhythm (30-80 Hz), often associated with high-level cortical functions, is believed to provide a temporal reference frame for spiking activity, for which it should have a stable center frequency and linear phase for an extended duration. However, recent studies that have estimated the power and phase of gamma as a function of time suggest that gamma occurs in short bursts and lacks the temporal structure required to act as a reference frame. Here, we show that the bursty appearance of gamma arises from the variability in the spectral estimator used in these studies. To overcome this problem, we use another duration estimator based on a matching pursuit algorithm that robustly estimates the duration of gamma in simulated data. Applying this algorithm to gamma oscillations recorded from implanted microelectrodes in the primary visual cortex of awake monkeys, we show that the median gamma duration is greater than 300 ms, which is three times longer than previously reported values. NEW & NOTEWORTHY Gamma oscillations (30-80 Hz) have been hypothesized to provide a temporal reference frame for coordination of spiking activity, but recent studies have shown that gamma occurs in very short bursts. We show that existing techniques have severely underestimated the rhythm duration, use a technique based on the Matching Pursuit algorithm, which provides a robust estimate of the duration, and show that the median duration of gamma is greater than 300 ms, much longer than previous estimates.

Duration analysis using matching pursuit algorithm reveals longer bouts of gamma rhythm

PubMed Central

Chandran KS, Subhash; Seelamantula, Chandra Sekhar

2018-01-01

The gamma rhythm (30–80 Hz), often associated with high-level cortical functions, is believed to provide a temporal reference frame for spiking activity, for which it should have a stable center frequency and linear phase for an extended duration. However, recent studies that have estimated the power and phase of gamma as a function of time suggest that gamma occurs in short bursts and lacks the temporal structure required to act as a reference frame. Here, we show that the bursty appearance of gamma arises from the variability in the spectral estimator used in these studies. To overcome this problem, we use another duration estimator based on a matching pursuit algorithm that robustly estimates the duration of gamma in simulated data. Applying this algorithm to gamma oscillations recorded from implanted microelectrodes in the primary visual cortex of awake monkeys, we show that the median gamma duration is greater than 300 ms, which is three times longer than previously reported values. NEW & NOTEWORTHY Gamma oscillations (30–80 Hz) have been hypothesized to provide a temporal reference frame for coordination of spiking activity, but recent studies have shown that gamma occurs in very short bursts. We show that existing techniques have severely underestimated the rhythm duration, use a technique based on the Matching Pursuit algorithm, which provides a robust estimate of the duration, and show that the median duration of gamma is greater than 300 ms, much longer than previous estimates. PMID:29118193

Scaling Up Coordinate Descent Algorithms for Large ℓ1 Regularization Problems

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

Scherrer, Chad; Halappanavar, Mahantesh; Tewari, Ambuj

2012-07-03

We present a generic framework for parallel coordinate descent (CD) algorithms that has as special cases the original sequential algorithms of Cyclic CD and Stochastic CD, as well as the recent parallel Shotgun algorithm of Bradley et al. We introduce two novel parallel algorithms that are also special cases---Thread-Greedy CD and Coloring-Based CD---and give performance measurements for an OpenMP implementation of these.

The VLSI design of the sub-band filterbank in MP3 decoding

NASA Astrophysics Data System (ADS)

Liu, Jia-Xin; Luo, Li

2018-03-01

The sub-band filterbank is one of the most important modules which has the largest amount of calculation in MP3 decoding. In order to save CPU resources and integrate the sub-band filterbank part into MP3 IP core, the hardware circuit of the sub-band filterbank module is designed in this paper. A fast algorithm suit for hardware implementation is proposed and achieved on FPGA development board. The results show that the sub-band filterbank function is correct in the case of using very few registers and the amount of calculation and ROM resources are reduced greatly.

Clutter and target discrimination in forward-looking ground penetrating radar using sparse structured basis pursuits

NASA Astrophysics Data System (ADS)

Camilo, Joseph A.; Malof, Jordan M.; Torrione, Peter A.; Collins, Leslie M.; Morton, Kenneth D.

2015-05-01

Forward-looking ground penetrating radar (FLGPR) is a remote sensing modality that has recently been investigated for buried threat detection. FLGPR offers greater standoff than other downward-looking modalities such as electromagnetic induction and downward-looking GPR, but it suffers from high false alarm rates due to surface and ground clutter. A stepped frequency FLGPR system consists of multiple radars with varying polarizations and bands, each of which interacts differently with subsurface materials and therefore might potentially be able to discriminate clutter from true buried targets. However, it is unclear which combinations of bands and polarizations would be most useful for discrimination or how to fuse them. This work applies sparse structured basis pursuit, a supervised statistical model which searches for sets of bands that are collectively effective for discriminating clutter from targets. The algorithm works by trying to minimize the number of selected items in a dictionary of signals; in this case the separate bands and polarizations make up the dictionary elements. A structured basis pursuit algorithm is employed to gather groups of modes together in collections to eliminate whole polarizations or sensors. The approach is applied to a large collection of FLGPR data for data around emplaced target and non-target clutter. The results show that a sparse structure basis pursuits outperforms a conventional CFAR anomaly detector while also pruning out unnecessary bands of the FLGPR sensor.

Research on evaluating water resource resilience based on projection pursuit classification model

NASA Astrophysics Data System (ADS)

Liu, Dong; Zhao, Dan; Liang, Xu; Wu, Qiuchen

2016-03-01

Water is a fundamental natural resource while agriculture water guarantees the grain output, which shows that the utilization and management of water resource have a significant practical meaning. Regional agricultural water resource system features with unpredictable, self-organization, and non-linear which lays a certain difficulty on the evaluation of regional agriculture water resource resilience. The current research on water resource resilience remains to focus on qualitative analysis and the quantitative analysis is still in the primary stage, thus, according to the above issues, projection pursuit classification model is brought forward. With the help of artificial fish-swarm algorithm (AFSA), it optimizes the projection index function, seeks for the optimal projection direction, and improves AFSA with the application of self-adaptive artificial fish step and crowding factor. Taking Hongxinglong Administration of Heilongjiang as the research base and on the basis of improving AFSA, it established the evaluation of projection pursuit classification model to agriculture water resource system resilience besides the proceeding analysis of projection pursuit classification model on accelerating genetic algorithm. The research shows that the water resource resilience of Hongxinglong is the best than Raohe Farm, and the last 597 Farm. And the further analysis shows that the key driving factors influencing agricultural water resource resilience are precipitation and agriculture water consumption. The research result reveals the restoring situation of the local water resource system, providing foundation for agriculture water resource management.

Using OpenMP vs. Threading Building Blocks for Medical Imaging on Multi-cores

NASA Astrophysics Data System (ADS)

Kegel, Philipp; Schellmann, Maraike; Gorlatch, Sergei

We compare two parallel programming approaches for multi-core systems: the well-known OpenMP and the recently introduced Threading Building Blocks (TBB) library by Intel®. The comparison is made using the parallelization of a real-world numerical algorithm for medical imaging. We develop several parallel implementations, and compare them w.r.t. programming effort, programming style and abstraction, and runtime performance. We show that TBB requires a considerable program re-design, whereas with OpenMP simple compiler directives are sufficient. While TBB appears to be less appropriate for parallelizing existing implementations, it fosters a good programming style and higher abstraction level for newly developed parallel programs. Our experimental measurements on a dual quad-core system demonstrate that OpenMP slightly outperforms TBB in our implementation.

Voxel-wise prostate cell density prediction using multiparametric magnetic resonance imaging and machine learning.

PubMed

Sun, Yu; Reynolds, Hayley M; Wraith, Darren; Williams, Scott; Finnegan, Mary E; Mitchell, Catherine; Murphy, Declan; Haworth, Annette

2018-04-26

There are currently no methods to estimate cell density in the prostate. This study aimed to develop predictive models to estimate prostate cell density from multiparametric magnetic resonance imaging (mpMRI) data at a voxel level using machine learning techniques. In vivo mpMRI data were collected from 30 patients before radical prostatectomy. Sequences included T2-weighted imaging, diffusion-weighted imaging and dynamic contrast-enhanced imaging. Ground truth cell density maps were computed from histology and co-registered with mpMRI. Feature extraction and selection were performed on mpMRI data. Final models were fitted using three regression algorithms including multivariate adaptive regression spline (MARS), polynomial regression (PR) and generalised additive model (GAM). Model parameters were optimised using leave-one-out cross-validation on the training data and model performance was evaluated on test data using root mean square error (RMSE) measurements. Predictive models to estimate voxel-wise prostate cell density were successfully trained and tested using the three algorithms. The best model (GAM) achieved a RMSE of 1.06 (± 0.06) × 10 3 cells/mm 2 and a relative deviation of 13.3 ± 0.8%. Prostate cell density can be quantitatively estimated non-invasively from mpMRI data using high-quality co-registered data at a voxel level. These cell density predictions could be used for tissue classification, treatment response evaluation and personalised radiotherapy.

Temporal dynamics of retinal and extraretinal signals in the FEFsem during smooth pursuit eye movements

PubMed Central

Bakst, Leah; Fleuriet, Jérome

2017-01-01

Neurons in the smooth eye movement subregion of the frontal eye field (FEFsem) are known to play an important role in voluntary smooth pursuit eye movements. Underlying this function are projections to parietal and prefrontal visual association areas and subcortical structures, all known to play vital but differing roles in the execution of smooth pursuit. Additionally, the FEFsem has been shown to carry a diverse array of signals (e.g., eye velocity, acceleration, gain control). We hypothesized that distinct subpopulations of FEFsem neurons subserve these diverse functions and projections, and that the relative weights of retinal and extraretinal signals could form the basis for categorization of units. To investigate this, we used a step-ramp tracking task with a target blink to determine the relative contributions of retinal and extraretinal signals in individual FEFsem neurons throughout pursuit. We found that the contributions of retinal and extraretinal signals to neuronal activity and behavior change throughout the time course of pursuit. A clustering algorithm revealed three distinct neuronal subpopulations: cluster 1 was defined by a higher sensitivity to eye velocity, acceleration, and retinal image motion; cluster 2 had greater activity during blinks; and cluster 3 had significantly greater eye position sensitivity. We also performed a comparison with a sample of medial superior temporal neurons to assess similarities and differences between the two areas. Our results indicate the utility of simple tests such as the target blink for parsing the complex and multifaceted roles of cortical areas in behavior. NEW & NOTEWORTHY The frontal eye field (FEF) is known to play a critical role in volitional smooth pursuit, carrying a variety of signals that are distributed throughout the brain. This study used a novel application of a target blink task during step ramp tracking to determine, in combination with a clustering algorithm, the relative contributions of retinal and extraretinal signals to FEF activity and the extent to which these contributions could form the basis for a categorization of neurons. PMID:28202571

Multiagent pursuit-evasion games: Algorithms and experiments

NASA Astrophysics Data System (ADS)

Kim, Hyounjin

Deployment of intelligent agents has been made possible through advances in control software, microprocessors, sensor/actuator technology, communication technology, and artificial intelligence. Intelligent agents now play important roles in many applications where human operation is too dangerous or inefficient. There is little doubt that the world of the future will be filled with intelligent robotic agents employed to autonomously perform tasks, or embedded in systems all around us, extending our capabilities to perceive, reason and act, and replacing human efforts. There are numerous real-world applications in which a single autonomous agent is not suitable and multiple agents are required. However, after years of active research in multi-agent systems, current technology is still far from achieving many of these real-world applications. Here, we consider the problem of deploying a team of unmanned ground vehicles (UGV) and unmanned aerial vehicles (UAV) to pursue a second team of UGV evaders while concurrently building a map in an unknown environment. This pursuit-evasion game encompasses many of the challenging issues that arise in operations using intelligent multi-agent systems. We cast the problem in a probabilistic game theoretic framework and consider two computationally feasible pursuit policies: greedy and global-max. We also formulate this probabilistic pursuit-evasion game as a partially observable Markov decision process and employ a policy search algorithm to obtain a good pursuit policy from a restricted class of policies. The estimated value of this policy is guaranteed to be uniformly close to the optimal value in the given policy class under mild conditions. To implement this scenario on real UAVs and UGVs, we propose a distributed hierarchical hybrid system architecture which emphasizes the autonomy of each agent yet allows for coordinated team efforts. We then describe our implementation on a fleet of UGVs and UAVs, detailing components such as high level pursuit policy computation, inter-agent communication, navigation, sensing, and regulation. We present both simulation and experimental results on real pursuit-evasion games between our fleet of UAVs and UGVs and evaluate the pursuit policies, relating expected capture times to the speed and intelligence of the evaders and the sensing capabilities of the pursuers. The architecture and algorithmsis described in this dissertation are general enough to be applied to many real-world applications.

Massively parallel algorithm and implementation of RI-MP2 energy calculation for peta-scale many-core supercomputers.

PubMed

Katouda, Michio; Naruse, Akira; Hirano, Yukihiko; Nakajima, Takahito

2016-11-15

A new parallel algorithm and its implementation for the RI-MP2 energy calculation utilizing peta-flop-class many-core supercomputers are presented. Some improvements from the previous algorithm (J. Chem. Theory Comput. 2013, 9, 5373) have been performed: (1) a dual-level hierarchical parallelization scheme that enables the use of more than 10,000 Message Passing Interface (MPI) processes and (2) a new data communication scheme that reduces network communication overhead. A multi-node and multi-GPU implementation of the present algorithm is presented for calculations on a central processing unit (CPU)/graphics processing unit (GPU) hybrid supercomputer. Benchmark results of the new algorithm and its implementation using the K computer (CPU clustering system) and TSUBAME 2.5 (CPU/GPU hybrid system) demonstrate high efficiency. The peak performance of 3.1 PFLOPS is attained using 80,199 nodes of the K computer. The peak performance of the multi-node and multi-GPU implementation is 514 TFLOPS using 1349 nodes and 4047 GPUs of TSUBAME 2.5. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Quantized Overcomplete Expansions: Analysis, Synthesis and Algorithms

DTIC Science & Technology

1995-07-01

would be in the spirit of the Lempel - Ziv algorithm . The decoder would have to be aware of changes in the dictionary, but depending on the nature of the...37 3.4 A General Vector Compression Algorithm Based on Frames : : : : : : : : : : 40 ii 3.4.1 Design Considerations...x3.3. Along with exploring general properties of matching pursuit, we are interested in its application to compressing data vectors in RN. A general

Automated Handling of Garments for Pressing

DTIC Science & Technology

1991-09-30

Parallel Algorithms for 2D Kalman Filtering ................................. 47 DJ. Potter and M.P. Cline Hash Table and Sorted Array: A Case Study of... Kalman Filtering on the Connection Machine ............................ 55 MA. Palis and D.K. Krecker Parallel Sorting of Large Arrays on the MasPar...ALGORITHM’VS FOR SEAM SENSING. .. .. .. ... ... .... ..... 24 6.1 KarelTW Algorithms .. .. ... ... ... ... .... ... ...... 24 6.1.1 Image Filtering

Learning algorithms for human-machine interfaces.

PubMed

Danziger, Zachary; Fishbach, Alon; Mussa-Ivaldi, Ferdinando A

2009-05-01

The goal of this study is to create and examine machine learning algorithms that adapt in a controlled and cadenced way to foster a harmonious learning environment between the user and the controlled device. To evaluate these algorithms, we have developed a simple experimental framework. Subjects wear an instrumented data glove that records finger motions. The high-dimensional glove signals remotely control the joint angles of a simulated planar two-link arm on a computer screen, which is used to acquire targets. A machine learning algorithm was applied to adaptively change the transformation between finger motion and the simulated robot arm. This algorithm was either LMS gradient descent or the Moore-Penrose (MP) pseudoinverse transformation. Both algorithms modified the glove-to-joint angle map so as to reduce the endpoint errors measured in past performance. The MP group performed worse than the control group (subjects not exposed to any machine learning), while the LMS group outperformed the control subjects. However, the LMS subjects failed to achieve better generalization than the control subjects, and after extensive training converged to the same level of performance as the control subjects. These results highlight the limitations of coadaptive learning using only endpoint error reduction.

Learning Algorithms for Human–Machine Interfaces

PubMed Central

Fishbach, Alon; Mussa-Ivaldi, Ferdinando A.

2012-01-01

The goal of this study is to create and examine machine learning algorithms that adapt in a controlled and cadenced way to foster a harmonious learning environment between the user and the controlled device. To evaluate these algorithms, we have developed a simple experimental framework. Subjects wear an instrumented data glove that records finger motions. The high-dimensional glove signals remotely control the joint angles of a simulated planar two-link arm on a computer screen, which is used to acquire targets. A machine learning algorithm was applied to adaptively change the transformation between finger motion and the simulated robot arm. This algorithm was either LMS gradient descent or the Moore–Penrose (MP) pseudoinverse transformation. Both algorithms modified the glove-to-joint angle map so as to reduce the endpoint errors measured in past performance. The MP group performed worse than the control group (subjects not exposed to any machine learning), while the LMS group outperformed the control subjects. However, the LMS subjects failed to achieve better generalization than the control subjects, and after extensive training converged to the same level of performance as the control subjects. These results highlight the limitations of coadaptive learning using only endpoint error reduction. PMID:19203886

Automated volumetric evaluation of stereoscopic disc photography

PubMed Central

Xu, Juan; Ishikawa, Hiroshi; Wollstein, Gadi; Bilonick, Richard A; Kagemann, Larry; Craig, Jamie E; Mackey, David A; Hewitt, Alex W; Schuman, Joel S

2010-01-01

PURPOSE: To develop a fully automated algorithm (AP) to perform a volumetric measure of the optic disc using conventional stereoscopic optic nerve head (ONH) photographs, and to compare algorithm-produced parameters with manual photogrammetry (MP), scanning laser ophthalmoscope (SLO) and optical coherence tomography (OCT) measurements. METHODS: One hundred twenty-two stereoscopic optic disc photographs (61 subjects) were analyzed. Disc area, rim area, cup area, cup/disc area ratio, vertical cup/disc ratio, rim volume and cup volume were automatically computed by the algorithm. Latent variable measurement error models were used to assess measurement reproducibility for the four techniques. RESULTS: AP had better reproducibility for disc area and cup volume and worse reproducibility for cup/disc area ratio and vertical cup/disc ratio, when the measurements were compared to the MP, SLO and OCT methods. CONCLUSION: AP provides a useful technique for an objective quantitative assessment of 3D ONH structures. PMID:20588996

A parallel algorithm for generation and assembly of finite element stiffness and mass matrices

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Carmona, E. A.; Nguyen, D. T.; Baddourah, M. A.

1991-01-01

A new algorithm is proposed for parallel generation and assembly of the finite element stiffness and mass matrices. The proposed assembly algorithm is based on a node-by-node approach rather than the more conventional element-by-element approach. The new algorithm's generality and computation speed-up when using multiple processors are demonstrated for several practical applications on multi-processor Cray Y-MP and Cray 2 supercomputers.

Cooperative Surveillance and Pursuit Using Unmanned Aerial Vehicles and Unattended Ground Sensors

PubMed Central

Las Fargeas, Jonathan; Kabamba, Pierre; Girard, Anouck

2015-01-01

This paper considers the problem of path planning for a team of unmanned aerial vehicles performing surveillance near a friendly base. The unmanned aerial vehicles do not possess sensors with automated target recognition capability and, thus, rely on communicating with unattended ground sensors placed on roads to detect and image potential intruders. The problem is motivated by persistent intelligence, surveillance, reconnaissance and base defense missions. The problem is formulated and shown to be intractable. A heuristic algorithm to coordinate the unmanned aerial vehicles during surveillance and pursuit is presented. Revisit deadlines are used to schedule the vehicles' paths nominally. The algorithm uses detections from the sensors to predict intruders' locations and selects the vehicles' paths by minimizing a linear combination of missed deadlines and the probability of not intercepting intruders. An analysis of the algorithm's completeness and complexity is then provided. The effectiveness of the heuristic is illustrated through simulations in a variety of scenarios. PMID:25591168

Multilevel Parallelization of AutoDock 4.2.

PubMed

Norgan, Andrew P; Coffman, Paul K; Kocher, Jean-Pierre A; Katzmann, David J; Sosa, Carlos P

2011-04-28

Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4). Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

PubMed

Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

Shared Memory Parallelization of an Implicit ADI-type CFD Code

NASA Technical Reports Server (NTRS)

Hauser, Th.; Huang, P. G.

1999-01-01

A parallelization study designed for ADI-type algorithms is presented using the OpenMP specification for shared-memory multiprocessor programming. Details of optimizations specifically addressed to cache-based computer architectures are described and performance measurements for the single and multiprocessor implementation are summarized. The paper demonstrates that optimization of memory access on a cache-based computer architecture controls the performance of the computational algorithm. A hybrid MPI/OpenMP approach is proposed for clusters of shared memory machines to further enhance the parallel performance. The method is applied to develop a new LES/DNS code, named LESTool. A preliminary DNS calculation of a fully developed channel flow at a Reynolds number of 180, Re(sub tau) = 180, has shown good agreement with existing data.

Multi-stage approach for structural damage detection problem using basis pursuit and particle swarm optimization

NASA Astrophysics Data System (ADS)

Gerist, Saleheh; Maheri, Mahmoud R.

2016-12-01

In order to solve structural damage detection problem, a multi-stage method using particle swarm optimization is presented. First, a new spars recovery method, named Basis Pursuit (BP), is utilized to preliminarily identify structural damage locations. The BP method solves a system of equations which relates the damage parameters to the structural modal responses using the sensitivity matrix. Then, the results of this stage are subsequently enhanced to the exact damage locations and extents using the PSO search engine. Finally, the search space is reduced by elimination of some low damage variables using micro search (MS) operator embedded in the PSO algorithm. To overcome the noise present in structural responses, a method known as Basis Pursuit De-Noising (BPDN) is also used. The efficiency of the proposed method is investigated by three numerical examples: a cantilever beam, a plane truss and a portal plane frame. The frequency response is used to detect damage in the examples. The simulation results demonstrate the accuracy and efficiency of the proposed method in detecting multiple damage cases and exhibit its robustness regarding noise and its advantages compared to other reported solution algorithms.

PARALLELISATION OF THE MODEL-BASED ITERATIVE RECONSTRUCTION ALGORITHM DIRA.

PubMed

Örtenberg, A; Magnusson, M; Sandborg, M; Alm Carlsson, G; Malusek, A

2016-06-01

New paradigms for parallel programming have been devised to simplify software development on multi-core processors and many-core graphical processing units (GPU). Despite their obvious benefits, the parallelisation of existing computer programs is not an easy task. In this work, the use of the Open Multiprocessing (OpenMP) and Open Computing Language (OpenCL) frameworks is considered for the parallelisation of the model-based iterative reconstruction algorithm DIRA with the aim to significantly shorten the code's execution time. Selected routines were parallelised using OpenMP and OpenCL libraries; some routines were converted from MATLAB to C and optimised. Parallelisation of the code with the OpenMP was easy and resulted in an overall speedup of 15 on a 16-core computer. Parallelisation with OpenCL was more difficult owing to differences between the central processing unit and GPU architectures. The resulting speedup was substantially lower than the theoretical peak performance of the GPU; the cause was explained. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Multitasking domain decomposition fast Poisson solvers on the Cray Y-MP

NASA Technical Reports Server (NTRS)

Chan, Tony F.; Fatoohi, Rod A.

1990-01-01

The results of multitasking implementation of a domain decomposition fast Poisson solver on eight processors of the Cray Y-MP are presented. The object of this research is to study the performance of domain decomposition methods on a Cray supercomputer and to analyze the performance of different multitasking techniques using highly parallel algorithms. Two implementations of multitasking are considered: macrotasking (parallelism at the subroutine level) and microtasking (parallelism at the do-loop level). A conventional FFT-based fast Poisson solver is also multitasked. The results of different implementations are compared and analyzed. A speedup of over 7.4 on the Cray Y-MP running in a dedicated environment is achieved for all cases.

Comparing the OpenMP, MPI, and Hybrid Programming Paradigm on an SMP Cluster

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Hao-Qiang; anMey, Dieter; Hatay, Ferhat F.

2003-01-01

Clusters of SMP (Symmetric Multi-Processors) nodes provide support for a wide range of parallel programming paradigms. The shared address space within each node is suitable for OpenMP parallelization. Message passing can be employed within and across the nodes of a cluster. Multiple levels of parallelism can be achieved by combining message passing and OpenMP parallelization. Which programming paradigm is the best will depend on the nature of the given problem, the hardware components of the cluster, the network, and the available software. In this study we compare the performance of different implementations of the same CFD benchmark application, using the same numerical algorithm but employing different programming paradigms.

Crohn's disease mistaken for long-standing idiopathic mesenteric panniculitis: A case report and management algorithm.

PubMed

Nuzzo, Alexandre; Zappa, Magaly; Cazals-Hatem, Dominique; Bouhnik, Yoram

2016-09-01

Mesenteric panniculitis (MP) is mostly an associated sign of an intra-abdominal or systemic inflammatory primary disease. Nevertheless, etiological and differential diagnosis of idiopathic MP can be challenging when an associate primary cause is not in the foreground. We report here the case of an isolated small bowel Crohn's disease, long time considered as idiopathic MP. This patient presented to our department with a 10-year history of acute abdominal symptoms evolving with flare-up and remission. A diagnosis of idiopathic MP was made based on compatible CT-scan features along with normal laboratory tests and upper and lower bowel endoscopies. As symptoms recurred, a steroid course was proposed which dramatically improved his condition for years. Finally, an explorative laparoscopy was performed because of concern of malignancy when he returned to our unit with a steroid refractory flare-up and weight loss, along with MP nodes growing up to 10 mm. Crohn's disease was eventually diagnosed, based on histopathological middle-gut bowel resection and numerous granulomas in mesenteric nodes without necrosis. This case emphasizes the importance of excluding inflammatory intestinal lesions before making the diagnosis of idiopathic MP (fecal calprotectin, magnetic resonance enterography, wireless capsule endoscopy).

A projection pursuit algorithm to classify individuals using fMRI data: Application to schizophrenia.

PubMed

Demirci, Oguz; Clark, Vincent P; Calhoun, Vince D

2008-02-15

Schizophrenia is diagnosed based largely upon behavioral symptoms. Currently, no quantitative, biologically based diagnostic technique has yet been developed to identify patients with schizophrenia. Classification of individuals into patient with schizophrenia and healthy control groups based on quantitative biologically based data is of great interest to support and refine psychiatric diagnoses. We applied a novel projection pursuit technique on various components obtained with independent component analysis (ICA) of 70 subjects' fMRI activation maps obtained during an auditory oddball task. The validity of the technique was tested with a leave-one-out method and the detection performance varied between 80% and 90%. The findings suggest that the proposed data reduction algorithm is effective in classifying individuals into schizophrenia and healthy control groups and may eventually prove useful as a diagnostic tool.

Algorithms for Scheduling and Network Problems

DTIC Science & Technology

1991-09-01

time. We already know, by Lemma 2.2.1, that WOPT = O(log( mpU )), so if we could solve this integer program optimally we would be done. However, the...Folydirat, 15:177-191, 1982. [6] I.S. Belov and Ya. N. Stolin. An algorithm in a single path operations scheduling problem. In Mathematical Economics and

RMP: Reduced-set matching pursuit approach for efficient compressed sensing signal reconstruction.

PubMed

Abdel-Sayed, Michael M; Khattab, Ahmed; Abu-Elyazeed, Mohamed F

2016-11-01

Compressed sensing enables the acquisition of sparse signals at a rate that is much lower than the Nyquist rate. Compressed sensing initially adopted [Formula: see text] minimization for signal reconstruction which is computationally expensive. Several greedy recovery algorithms have been recently proposed for signal reconstruction at a lower computational complexity compared to the optimal [Formula: see text] minimization, while maintaining a good reconstruction accuracy. In this paper, the Reduced-set Matching Pursuit (RMP) greedy recovery algorithm is proposed for compressed sensing. Unlike existing approaches which either select too many or too few values per iteration, RMP aims at selecting the most sufficient number of correlation values per iteration, which improves both the reconstruction time and error. Furthermore, RMP prunes the estimated signal, and hence, excludes the incorrectly selected values. The RMP algorithm achieves a higher reconstruction accuracy at a significantly low computational complexity compared to existing greedy recovery algorithms. It is even superior to [Formula: see text] minimization in terms of the normalized time-error product, a new metric introduced to measure the trade-off between the reconstruction time and error. RMP superior performance is illustrated with both noiseless and noisy samples.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

NASA Astrophysics Data System (ADS)

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-01

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution time/parallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

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

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f , (e.g. Verlet algorithm) is available to propagate the system from time ti (trajectory positions and velocities xi = (ri; vi)) to time ti+1 (xi+1) by xi+1 = fi(xi), the dynamics problem spanning an interval from t0 : : : tM can be transformed into a root finding problem, F(X) = [xi - f (x(i-1)]i=1;M = 0, for the trajectory variables. The root finding problem is solved using amore » variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton optimization schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed and the effectiveness of various approaches to solving the root finding problem are tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl+4H2O AIMD simulation at the MP2 level. The maximum speedup obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow TCP/IP networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl+4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. By using these algorithms we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 seconds per time step to 6.9 seconds per time step.« less

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

PubMed

Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Temporal dynamics of retinal and extraretinal signals in the FEFsem during smooth pursuit eye movements.

PubMed

Bakst, Leah; Fleuriet, Jérome; Mustari, Michael J

2017-05-01

Neurons in the smooth eye movement subregion of the frontal eye field (FEFsem) are known to play an important role in voluntary smooth pursuit eye movements. Underlying this function are projections to parietal and prefrontal visual association areas and subcortical structures, all known to play vital but differing roles in the execution of smooth pursuit. Additionally, the FEFsem has been shown to carry a diverse array of signals (e.g., eye velocity, acceleration, gain control). We hypothesized that distinct subpopulations of FEFsem neurons subserve these diverse functions and projections, and that the relative weights of retinal and extraretinal signals could form the basis for categorization of units. To investigate this, we used a step-ramp tracking task with a target blink to determine the relative contributions of retinal and extraretinal signals in individual FEFsem neurons throughout pursuit. We found that the contributions of retinal and extraretinal signals to neuronal activity and behavior change throughout the time course of pursuit. A clustering algorithm revealed three distinct neuronal subpopulations: cluster 1 was defined by a higher sensitivity to eye velocity, acceleration, and retinal image motion; cluster 2 had greater activity during blinks; and cluster 3 had significantly greater eye position sensitivity. We also performed a comparison with a sample of medial superior temporal neurons to assess similarities and differences between the two areas. Our results indicate the utility of simple tests such as the target blink for parsing the complex and multifaceted roles of cortical areas in behavior. NEW & NOTEWORTHY The frontal eye field (FEF) is known to play a critical role in volitional smooth pursuit, carrying a variety of signals that are distributed throughout the brain. This study used a novel application of a target blink task during step ramp tracking to determine, in combination with a clustering algorithm, the relative contributions of retinal and extraretinal signals to FEF activity and the extent to which these contributions could form the basis for a categorization of neurons. Copyright © 2017 the American Physiological Society.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2017-01-01

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N2.5) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction.

PubMed

Song, Chenchen; Martínez, Todd J

2017-01-21

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N 2.5 ) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

Direct methanol fuel cells: A database-driven design procedure

NASA Astrophysics Data System (ADS)

Flipsen, S. F. J.; Spitas, C.

2011-10-01

To test the feasibility of DMFC systems in preliminary stages of the design process the design engineer can make use of heuristic models identifying the opportunity of DMFC systems in a specific application. In general these models are to generic and have a low accuracy. To improve the accuracy a second-order model is proposed in this paper. The second-order model consists of an evolutionary algorithm written in Mathematica, which selects a component-set satisfying the fuel-cell systems' performance requirements, places the components in 3D space and optimizes for volume. The results are presented as a 3D draft proposal together with a feasibility metric. To test the algorithm the design of DMFC system applied in the MP3 player is evaluated. The results show that volume and costs are an issue for the feasibility of the fuel-cell power-system applied in the MP3 player. The generated designs and the algorithm are evaluated and recommendations are given.

Compressed sensing of ECG signal for wireless system with new fast iterative method.

PubMed

Tawfic, Israa; Kayhan, Sema

2015-12-01

Recent experiments in wireless body area network (WBAN) show that compressive sensing (CS) is a promising tool to compress the Electrocardiogram signal ECG signal. The performance of CS is based on algorithms use to reconstruct exactly or approximately the original signal. In this paper, we present two methods work with absence and presence of noise, these methods are Least Support Orthogonal Matching Pursuit (LS-OMP) and Least Support Denoising-Orthogonal Matching Pursuit (LSD-OMP). The algorithms achieve correct support recovery without requiring sparsity knowledge. We derive an improved restricted isometry property (RIP) based conditions over the best known results. The basic procedures are done by observational and analytical of a different Electrocardiogram signal downloaded them from PhysioBankATM. Experimental results show that significant performance in term of reconstruction quality and compression rate can be obtained by these two new proposed algorithms, and help the specialist gathering the necessary information from the patient in less time if we use Magnetic Resonance Imaging (MRI) application, or reconstructed the patient data after sending it through the network. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Cognitive Radios Exploiting Gray Spaces via Compressed Sensing

NASA Astrophysics Data System (ADS)

Wieruch, Dennis; Jung, Peter; Wirth, Thomas; Dekorsy, Armin; Haustein, Thomas

2016-07-01

We suggest an interweave cognitive radio system with a gray space detector, which is properly identifying a small fraction of unused resources within an active band of a primary user system like 3GPP LTE. Therefore, the gray space detector can cope with frequency fading holes and distinguish them from inactive resources. Different approaches of the gray space detector are investigated, the conventional reduced-rank least squares method as well as the compressed sensing-based orthogonal matching pursuit and basis pursuit denoising algorithm. In addition, the gray space detector is compared with the classical energy detector. Simulation results present the receiver operating characteristic at several SNRs and the detection performance over further aspects like base station system load for practical false alarm rates. The results show, that especially for practical false alarm rates the compressed sensing algorithm are more suitable than the classical energy detector and reduced-rank least squares approach.

Parallel computing of physical maps--a comparative study in SIMD and MIMD parallelism.

PubMed

Bhandarkar, S M; Chirravuri, S; Arnold, J

1996-01-01

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are proposed and applied to the problem of chromosome reconstruction via clone ordering. Perturbation methods and problem-specific annealing heuristics are proposed and described. The SIMD algorithms are implemented on a 2048 processor MasPar MP-2 system which is an SIMD 2-D toroidal mesh architecture whereas the MIMD algorithms are implemented on an 8 processor Intel iPSC/860 which is an MIMD hypercube architecture. A comparative analysis of the various SIMD and MIMD algorithms is presented in which the convergence, speedup, and scalability characteristics of the various algorithms are analyzed and discussed. On a fine-grained, massively parallel SIMD architecture with a low synchronization overhead such as the MasPar MP-2, a parallel simulated annealing algorithm based on multiple periodically interacting searches performs the best. For a coarse-grained MIMD architecture with high synchronization overhead such as the Intel iPSC/860, a parallel simulated annealing algorithm based on multiple independent searches yields the best results. In either case, distribution of clonal data across multiple processors is shown to exacerbate the tendency of the parallel simulated annealing algorithm to get trapped in a local optimum.

Comparison of the MPP with other supercomputers for LANDSAT data processing

NASA Technical Reports Server (NTRS)

Ozga, Martin

1987-01-01

The massively parallel processor is compared to the CRAY X-MP and the CYBER-205 for LANDSAT data processing. The maximum likelihood classification algorithm is the basis for comparison since this algorithm is simple to implement and vectorizes very well. The algorithm was implemented on all three machines and tested by classifying the same full scene of LANDSAT multispectral scan data. Timings are compared as well as features of the machines and available software.

GPU acceleration of a petascale application for turbulent mixing at high Schmidt number using OpenMP 4.5

NASA Astrophysics Data System (ADS)

Clay, M. P.; Buaria, D.; Yeung, P. K.; Gotoh, T.

2018-07-01

This paper reports on the successful implementation of a massively parallel GPU-accelerated algorithm for the direct numerical simulation of turbulent mixing at high Schmidt number. The work stems from a recent development (Comput. Phys. Commun., vol. 219, 2017, 313-328), in which a low-communication algorithm was shown to attain high degrees of scalability on the Cray XE6 architecture when overlapping communication and computation via dedicated communication threads. An even higher level of performance has now been achieved using OpenMP 4.5 on the Cray XK7 architecture, where on each node the 16 integer cores of an AMD Interlagos processor share a single Nvidia K20X GPU accelerator. In the new algorithm, data movements are minimized by performing virtually all of the intensive scalar field computations in the form of combined compact finite difference (CCD) operations on the GPUs. A memory layout in departure from usual practices is found to provide much better performance for a specific kernel required to apply the CCD scheme. Asynchronous execution enabled by adding the OpenMP 4.5 NOWAIT clause to TARGET constructs improves scalability when used to overlap computation on the GPUs with computation and communication on the CPUs. On the 27-petaflops supercomputer Titan at Oak Ridge National Laboratory, USA, a GPU-to-CPU speedup factor of approximately 5 is consistently observed at the largest problem size of 81923 grid points for the scalar field computed with 8192 XK7 nodes.

AMR on the CM-2

NASA Technical Reports Server (NTRS)

Berger, Marsha J.; Saltzman, Jeff S.

1992-01-01

We describe the development of a structured adaptive mesh algorithm (AMR) for the Connection Machine-2 (CM-2). We develop a data layout scheme that preserves locality even for communication between fine and coarse grids. On 8K of a 32K machine we achieve performance slightly less than 1 CPU of the Cray Y-MP. We apply our algorithm to an inviscid compressible flow problem.

BPF-type region-of-interest reconstruction for parallel translational computed tomography.

PubMed

Wu, Weiwen; Yu, Hengyong; Wang, Shaoyu; Liu, Fenglin

2017-01-01

The objective of this study is to present and test a new ultra-low-cost linear scan based tomography architecture. Similar to linear tomosynthesis, the source and detector are translated in opposite directions and the data acquisition system targets on a region-of-interest (ROI) to acquire data for image reconstruction. This kind of tomographic architecture was named parallel translational computed tomography (PTCT). In previous studies, filtered backprojection (FBP)-type algorithms were developed to reconstruct images from PTCT. However, the reconstructed ROI images from truncated projections have severe truncation artefact. In order to overcome this limitation, we in this study proposed two backprojection filtering (BPF)-type algorithms named MP-BPF and MZ-BPF to reconstruct ROI images from truncated PTCT data. A weight function is constructed to deal with data redundancy for multi-linear translations modes. Extensive numerical simulations are performed to evaluate the proposed MP-BPF and MZ-BPF algorithms for PTCT in fan-beam geometry. Qualitative and quantitative results demonstrate that the proposed BPF-type algorithms cannot only more accurately reconstruct ROI images from truncated projections but also generate high-quality images for the entire image support in some circumstances.

An improved optimization algorithm and Bayes factor termination criterion for sequential projection pursuit

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

Webb-Robertson, Bobbie-Jo M.; Jarman, Kristin H.; Harvey, Scott D.

2005-05-28

A fundamental problem in analysis of highly multivariate spectral or chromatographic data is reduction of dimensionality. Principal components analysis (PCA), concerned with explaining the variance-covariance structure of the data, is a commonly used approach to dimension reduction. Recently an attractive alternative to PCA, sequential projection pursuit (SPP), has been introduced. Designed to elicit clustering tendencies in the data, SPP may be more appropriate when performing clustering or classification analysis. However, the existing genetic algorithm (GA) implementation of SPP has two shortcomings, computation time and inability to determine the number of factors necessary to explain the majority of the structure inmore » the data. We address both these shortcomings. First, we introduce a new SPP algorithm, a random scan sampling algorithm (RSSA), that significantly reduces computation time. We compare the computational burden of the RSS and GA implementation for SPP on a dataset containing Raman spectra of twelve organic compounds. Second, we propose a Bayes factor criterion, BFC, as an effective measure for selecting the number of factors needed to explain the majority of the structure in the data. We compare SPP to PCA on two datasets varying in type, size, and difficulty; in both cases SPP achieves a higher accuracy with a lower number of latent variables.« less

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

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

Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov; Weare, Jonathan Q., E-mail: weare@uchicago.edu; Weare, John H., E-mail: jweare@ucsd.edu

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for themore » trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.« less

[Magnetic resonance semiotics of prostate cancer according to the PI-RADS classification. The clinical diagnostic algorithm of a study].

PubMed

Korobkin, A S; Shariya, M A; Chaban, A S; Voskanvan, G A; Vinarov, A Z

2015-01-01

to elaborate the magnetic resonance imaging (MRI) signs of prostate cancer (PC) in accordance with the PI-RADS classification during multiparametric MRI (mpMRI). A total of 89 men aged 20 to 82 years were examined. A control group consisted of 8 (9%) healthy volunteers younger than 30 years of age with no urological history to obtain control images and MRI plots and 20 (22.5%) men aged 26-76 years, whose morphological changes were inflammatory and hyperplastic. The second age-matched group included 61 (68.5%) patients diagnosed with prostate cancer at morphological examination. A set of studies included digital rectal examination, serum prostate-specific antigen, and transrectal ultrasound-guided prostate biopsy. All the patients underwent prostate mpMRI applying a 3.0 T Achieva MRI scanner (Philips, the Netherlands). The patients have been found to have mpMRI signs that were typical of PC; its MRI semiotics according to the PI-RADS classification is presented. Each mpMRI procedure has been determined to be of importance and informative value in detecting PC. The comprehensive mpMRI approach to diagnosing PC improves the quality and diagnostic value of prostate MRI.

Epileptic seizure onset detection based on EEG and ECG data fusion.

PubMed

Qaraqe, Marwa; Ismail, Muhammad; Serpedin, Erchin; Zulfi, Haneef

2016-05-01

This paper presents a novel method for seizure onset detection using fused information extracted from multichannel electroencephalogram (EEG) and single-channel electrocardiogram (ECG). In existing seizure detectors, the analysis of the nonlinear and nonstationary ECG signal is limited to the time-domain or frequency-domain. In this work, heart rate variability (HRV) extracted from ECG is analyzed using a Matching-Pursuit (MP) and Wigner-Ville Distribution (WVD) algorithm in order to effectively extract meaningful HRV features representative of seizure and nonseizure states. The EEG analysis relies on a common spatial pattern (CSP) based feature enhancement stage that enables better discrimination between seizure and nonseizure features. The EEG-based detector uses logical operators to pool SVM seizure onset detections made independently across different EEG spectral bands. Two fusion systems are adopted. In the first system, EEG-based and ECG-based decisions are directly fused to obtain a final decision. The second fusion system adopts an override option that allows for the EEG-based decision to override the fusion-based decision in the event that the detector observes a string of EEG-based seizure decisions. The proposed detectors exhibit an improved performance, with respect to sensitivity and detection latency, compared with the state-of-the-art detectors. Experimental results demonstrate that the second detector achieves a sensitivity of 100%, detection latency of 2.6s, and a specificity of 99.91% for the MAJ fusion case. Copyright © 2016 Elsevier Inc. All rights reserved.

Systems Engineering Approach to Develop Guidance, Navigation and Control Algorithms for Unmanned Ground Vehicle

DTIC Science & Technology

2016-09-01

identification and tracking algorithm. 14. SUBJECT TERMS unmanned ground vehicles , pure pursuit, vector field histogram, feature recognition 15. NUMBER OF...located within the various theaters of war. The pace for the development and deployment of unmanned ground vehicles (UGV) was, however, not keeping...DEVELOPMENT OF UNMANNED GROUND VEHICLES The development and fielding of UGVs in an operational role are not a new concept in the battlefield. In

Design consideration of a multipinhole collimator with septa for ultra high-resolution silicon drift detector modules

NASA Astrophysics Data System (ADS)

Min, Byung Jun; Choi, Yong; Lee, Nam-Yong; Lee, Kisung; Ahn, Young Bok; Joung, Jinhun

2009-07-01

The aim of this study was to design a multipinhole (MP) collimator with lead vertical septa coupled to a high-resolution detector module containing silicon drift detectors (SDDs) with an intrinsic resolution approaching the sub-millimeter level. Monte Carlo simulations were performed to determine pinhole parameters such as pinhole diameter, focal length, and number of pinholes. Effects of parallax error and collimator penetration were investigated for the new MP collimator design. The MP detector module was evaluated using reconstructed images of resolution and mathematical cardiac torso (MCAT) phantoms. In addition, the reduced angular sampling effect was investigated over 180°. The images were reconstructed using dedicated maximum likelihood expectation maximization (MLEM) algorithm. An MP collimator with 81-pinhole was designed with a 2-mm-diameter pinhole and a focal length of 40 mm . Planar sensitivity and resolution obtained using the devised MP collimator were 3.9 cps/μCi and 6 mm full-width at half-maximum (FWHM) at a 10 cm distance. The parallax error and penetration ratio were significantly improved using the proposed MP collimation design. The simulation results demonstrated that the proposed MP detector provided enlarged imaging field of view (FOV) and improved the angular sampling effect in resolution and MCAT phantom studies. Moreover, the novel design enables tomography images by simultaneously obtaining eight projections with eight-detector modules located along the 180° orbit surrounding a patient, which allows designing of a stationary cardiac SPECT. In conclusion, the MP collimator with lead vertical septa was designed to have comparable system resolution and sensitivity to those of the low-energy high-resolution (LEHR) collimator per detector. The system sensitivity with an eight-detector configuration would be four times higher than that with a standard dual-detector cardiac SPECT.

Radiofrequency pulse design using nonlinear gradient magnetic fields.

PubMed

Kopanoglu, Emre; Constable, R Todd

2015-09-01

An iterative k-space trajectory and radiofrequency (RF) pulse design method is proposed for excitation using nonlinear gradient magnetic fields. The spatial encoding functions (SEFs) generated by nonlinear gradient fields are linearly dependent in Cartesian coordinates. Left uncorrected, this may lead to flip angle variations in excitation profiles. In the proposed method, SEFs (k-space samples) are selected using a matching pursuit algorithm, and the RF pulse is designed using a conjugate gradient algorithm. Three variants of the proposed approach are given: the full algorithm, a computationally cheaper version, and a third version for designing spoke-based trajectories. The method is demonstrated for various target excitation profiles using simulations and phantom experiments. The method is compared with other iterative (matching pursuit and conjugate gradient) and noniterative (coordinate-transformation and Jacobian-based) pulse design methods as well as uniform density spiral and EPI trajectories. The results show that the proposed method can increase excitation fidelity. An iterative method for designing k-space trajectories and RF pulses using nonlinear gradient fields is proposed. The method can either be used for selecting the SEFs individually to guide trajectory design, or can be adapted to design and optimize specific trajectories of interest. © 2014 Wiley Periodicals, Inc.

A Locality-Based Threading Algorithm for the Configuration-Interaction Method

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

Shan, Hongzhang; Williams, Samuel; Johnson, Calvin

The Configuration Interaction (CI) method has been widely used to solve the non-relativistic many-body Schrodinger equation. One great challenge to implementing it efficiently on manycore architectures is its immense memory and data movement requirements. To address this issue, within each node, we exploit a hybrid MPI+OpenMP programming model in lieu of the traditional flat MPI programming model. Here in this paper, we develop optimizations that partition the workloads among OpenMP threads based on data locality,-which is essential in ensuring applications with complex data access patterns scale well on manycore architectures. The new algorithm scales to 256 threadson the 64-core Intelmore » Knights Landing (KNL) manycore processor and 24 threads on dual-socket Ivy Bridge (Xeon) nodes. Compared with the original implementation, the performance has been improved by up to 7× on theKnights Landing processor and 3× on the dual-socket Ivy Bridge node.« less

A Locality-Based Threading Algorithm for the Configuration-Interaction Method

DOE PAGES

Shan, Hongzhang; Williams, Samuel; Johnson, Calvin; ...

2017-07-03

The Configuration Interaction (CI) method has been widely used to solve the non-relativistic many-body Schrodinger equation. One great challenge to implementing it efficiently on manycore architectures is its immense memory and data movement requirements. To address this issue, within each node, we exploit a hybrid MPI+OpenMP programming model in lieu of the traditional flat MPI programming model. Here in this paper, we develop optimizations that partition the workloads among OpenMP threads based on data locality,-which is essential in ensuring applications with complex data access patterns scale well on manycore architectures. The new algorithm scales to 256 threadson the 64-core Intelmore » Knights Landing (KNL) manycore processor and 24 threads on dual-socket Ivy Bridge (Xeon) nodes. Compared with the original implementation, the performance has been improved by up to 7× on theKnights Landing processor and 3× on the dual-socket Ivy Bridge node.« less

OpenMP performance for benchmark 2D shallow water equations using LBM

NASA Astrophysics Data System (ADS)

Sabri, Khairul; Rabbani, Hasbi; Gunawan, Putu Harry

2018-03-01

Shallow water equations or commonly referred as Saint-Venant equations are used to model fluid phenomena. These equations can be solved numerically using several methods, like Lattice Boltzmann method (LBM), SIMPLE-like Method, Finite Difference Method, Godunov-type Method, and Finite Volume Method. In this paper, the shallow water equation will be approximated using LBM or known as LABSWE and will be simulated in performance of parallel programming using OpenMP. To evaluate the performance between 2 and 4 threads parallel algorithm, ten various number of grids Lx and Ly are elaborated. The results show that using OpenMP platform, the computational time for solving LABSWE can be decreased. For instance using grid sizes 1000 × 500, the speedup of 2 and 4 threads is observed 93.54 s and 333.243 s respectively.

CaSPIAN: A Causal Compressive Sensing Algorithm for Discovering Directed Interactions in Gene Networks

PubMed Central

Emad, Amin; Milenkovic, Olgica

2014-01-01

We introduce a novel algorithm for inference of causal gene interactions, termed CaSPIAN (Causal Subspace Pursuit for Inference and Analysis of Networks), which is based on coupling compressive sensing and Granger causality techniques. The core of the approach is to discover sparse linear dependencies between shifted time series of gene expressions using a sequential list-version of the subspace pursuit reconstruction algorithm and to estimate the direction of gene interactions via Granger-type elimination. The method is conceptually simple and computationally efficient, and it allows for dealing with noisy measurements. Its performance as a stand-alone platform without biological side-information was tested on simulated networks, on the synthetic IRMA network in Saccharomyces cerevisiae, and on data pertaining to the human HeLa cell network and the SOS network in E. coli. The results produced by CaSPIAN are compared to the results of several related algorithms, demonstrating significant improvements in inference accuracy of documented interactions. These findings highlight the importance of Granger causality techniques for reducing the number of false-positives, as well as the influence of noise and sampling period on the accuracy of the estimates. In addition, the performance of the method was tested in conjunction with biological side information of the form of sparse “scaffold networks”, to which new edges were added using available RNA-seq or microarray data. These biological priors aid in increasing the sensitivity and precision of the algorithm in the small sample regime. PMID:24622336

Parallel protein secondary structure prediction based on neural networks.

PubMed

Zhong, Wei; Altun, Gulsah; Tian, Xinmin; Harrison, Robert; Tai, Phang C; Pan, Yi

2004-01-01

Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.

Highly Scalable Matching Pursuit Signal Decomposition Algorithm

NASA Technical Reports Server (NTRS)

Christensen, Daniel; Das, Santanu; Srivastava, Ashok N.

2009-01-01

Matching Pursuit Decomposition (MPD) is a powerful iterative algorithm for signal decomposition and feature extraction. MPD decomposes any signal into linear combinations of its dictionary elements or atoms . A best fit atom from an arbitrarily defined dictionary is determined through cross-correlation. The selected atom is subtracted from the signal and this procedure is repeated on the residual in the subsequent iterations until a stopping criterion is met. The reconstructed signal reveals the waveform structure of the original signal. However, a sufficiently large dictionary is required for an accurate reconstruction; this in return increases the computational burden of the algorithm, thus limiting its applicability and level of adoption. The purpose of this research is to improve the scalability and performance of the classical MPD algorithm. Correlation thresholds were defined to prune insignificant atoms from the dictionary. The Coarse-Fine Grids and Multiple Atom Extraction techniques were proposed to decrease the computational burden of the algorithm. The Coarse-Fine Grids method enabled the approximation and refinement of the parameters for the best fit atom. The ability to extract multiple atoms within a single iteration enhanced the effectiveness and efficiency of each iteration. These improvements were implemented to produce an improved Matching Pursuit Decomposition algorithm entitled MPD++. Disparate signal decomposition applications may require a particular emphasis of accuracy or computational efficiency. The prominence of the key signal features required for the proper signal classification dictates the level of accuracy necessary in the decomposition. The MPD++ algorithm may be easily adapted to accommodate the imposed requirements. Certain feature extraction applications may require rapid signal decomposition. The full potential of MPD++ may be utilized to produce incredible performance gains while extracting only slightly less energy than the standard algorithm. When the utmost accuracy must be achieved, the modified algorithm extracts atoms more conservatively but still exhibits computational gains over classical MPD. The MPD++ algorithm was demonstrated using an over-complete dictionary on real life data. Computational times were reduced by factors of 1.9 and 44 for the emphases of accuracy and performance, respectively. The modified algorithm extracted similar amounts of energy compared to classical MPD. The degree of the improvement in computational time depends on the complexity of the data, the initialization parameters, and the breadth of the dictionary. The results of the research confirm that the three modifications successfully improved the scalability and computational efficiency of the MPD algorithm. Correlation Thresholding decreased the time complexity by reducing the dictionary size. Multiple Atom Extraction also reduced the time complexity by decreasing the number of iterations required for a stopping criterion to be reached. The Course-Fine Grids technique enabled complicated atoms with numerous variable parameters to be effectively represented in the dictionary. Due to the nature of the three proposed modifications, they are capable of being stacked and have cumulative effects on the reduction of the time complexity.

A fast and direct spectrophotometric method for the simultaneous determination of methyl paraben and hydroquinone in cosmetic products using successive projections algorithm.

PubMed

Esteki, M; Nouroozi, S; Shahsavari, Z

2016-02-01

To develop a simple and efficient spectrophotometric technique combined with chemometrics for the simultaneous determination of methyl paraben (MP) and hydroquinone (HQ) in cosmetic products, and specifically, to: (i) evaluate the potential use of successive projections algorithm (SPA) to derivative spectrophotometric data in order to provide sufficient accuracy and model robustness and (ii) determine MP and HQ concentration in cosmetics without tedious pre-treatments such as derivatization or extraction techniques which are time-consuming and require hazardous solvents. The absorption spectra were measured in the wavelength range of 200-350 nm. Prior to performing chemometric models, the original and first-derivative absorption spectra of binary mixtures were used as calibration matrices. Variable selected by successive projections algorithm was used to obtain multiple linear regression (MLR) models based on a small subset of wavelengths. The number of wavelengths and the starting vector were optimized, and the comparison of the root mean square error of calibration (RMSEC) and cross-validation (RMSECV) was applied to select effective wavelengths with the least collinearity and redundancy. Principal component regression (PCR) and partial least squares (PLS) were also developed for comparison. The concentrations of the calibration matrix ranged from 0.1 to 20 μg mL(-1) for MP, and from 0.1 to 25 μg mL(-1) for HQ. The constructed models were tested on an external validation data set and finally cosmetic samples. The results indicated that successive projections algorithm-multiple linear regression (SPA-MLR), applied on the first-derivative spectra, achieved the optimal performance for two compounds when compared with the full-spectrum PCR and PLS. The root mean square error of prediction (RMSEP) was 0.083, 0.314 for MP and HQ, respectively. To verify the accuracy of the proposed method, a recovery study on real cosmetic samples was carried out with satisfactory results (84-112%). The proposed method, which is an environmentally friendly approach, using minimum amount of solvent, is a simple, fast and low-cost analysis method that can provide high accuracy and robust models. The suggested method does not need any complex extraction procedure which is time-consuming and requires hazardous solvents. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

P ≠NP Millenium-Problem(MP) TRIVIAL Physics Proof Via NATURAL TRUMPS Artificial-``Intelligence'' Via: Euclid Geometry, Plato Forms, Aristotle Square-of-Opposition, Menger Dimension-Theory Connections!!! NO Computational-Complexity(CC)/ANYthing!!!: Geometry!!!

NASA Astrophysics Data System (ADS)

Clay, London; Menger, Karl; Rota, Gian-Carlo; Euclid, Alexandria; Siegel, Edward

P ≠NP MP proof is by computer-''science''/SEANCE(!!!)(CS) computational-''intelligence'' lingo jargonial-obfuscation(JO) NATURAL-Intelligence(NI) DISambiguation! CS P =(?) =NP MEANS (Deterministic)(PC) = (?) =(Non-D)(PC) i.e. D(P) =(?) = N(P). For inclusion(equality) vs. exclusion (inequality) irrelevant (P) simply cancels!!! (Equally any/all other CCs IF both sides identical). Crucial question left: (D) =(?) =(ND), i.e. D =(?) = N. Algorithmics[Sipser[Intro. Thy.Comp.(`97)-p.49Fig.1.15!!!

Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method

NASA Astrophysics Data System (ADS)

Izsák, Róbert; Neese, Frank

2013-07-01

The 'chain of spheres' approximation, developed earlier for the efficient evaluation of the self-consistent field exchange term, is introduced here into the evaluation of the external exchange term of higher order correlation methods. Its performance is studied in the specific case of the spin-component-scaled third-order Møller--Plesset perturbation (SCS-MP3) theory. The results indicate that the approximation performs excellently in terms of both computer time and achievable accuracy. Significant speedups over a conventional method are obtained for larger systems and basis sets. Owing to this development, SCS-MP3 calculations on molecules of the size of penicillin (42 atoms) with a polarised triple-zeta basis set can be performed in ∼3 hours using 16 cores of an Intel Xeon E7-8837 processor with a 2.67 GHz clock speed, which represents a speedup by a factor of 8-9 compared to the previously most efficient algorithm. Thus, the increased accuracy offered by SCS-MP3 can now be explored for at least medium-sized molecules.

An Efficient Distributed Compressed Sensing Algorithm for Decentralized Sensor Network.

PubMed

Liu, Jing; Huang, Kaiyu; Zhang, Guoxian

2017-04-20

We consider the joint sparsity Model 1 (JSM-1) in a decentralized scenario, where a number of sensors are connected through a network and there is no fusion center. A novel algorithm, named distributed compact sensing matrix pursuit (DCSMP), is proposed to exploit the computational and communication capabilities of the sensor nodes. In contrast to the conventional distributed compressed sensing algorithms adopting a random sensing matrix, the proposed algorithm focuses on the deterministic sensing matrices built directly on the real acquisition systems. The proposed DCSMP algorithm can be divided into two independent parts, the common and innovation support set estimation processes. The goal of the common support set estimation process is to obtain an estimated common support set by fusing the candidate support set information from an individual node and its neighboring nodes. In the following innovation support set estimation process, the measurement vector is projected into a subspace that is perpendicular to the subspace spanned by the columns indexed by the estimated common support set, to remove the impact of the estimated common support set. We can then search the innovation support set using an orthogonal matching pursuit (OMP) algorithm based on the projected measurement vector and projected sensing matrix. In the proposed DCSMP algorithm, the process of estimating the common component/support set is decoupled with that of estimating the innovation component/support set. Thus, the inaccurately estimated common support set will have no impact on estimating the innovation support set. It is proven that under the condition the estimated common support set contains the true common support set, the proposed algorithm can find the true innovation set correctly. Moreover, since the innovation support set estimation process is independent of the common support set estimation process, there is no requirement for the cardinality of both sets; thus, the proposed DCSMP algorithm is capable of tackling the unknown sparsity problem successfully.

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

PubMed Central

Giaro, Krzysztof

2017-01-01

Abstract Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson–Foulds distance. In this article, we define a new metric for rooted trees—the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events. PMID:28177699

Communication: A novel implementation to compute MP2 correlation energies without basis set superposition errors and complete basis set extrapolation.

PubMed

Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario

2017-06-07

By using a formulation based on the dynamical polarizability, we propose a novel implementation of second-order Møller-Plesset perturbation (MP2) theory within a plane wave (PW) basis set. Because of the intrinsic properties of PWs, this method is not affected by basis set superposition errors. Additionally, results are converged without relying on complete basis set extrapolation techniques; this is achieved by using the eigenvectors of the static polarizability as an auxiliary basis set to compactly and accurately represent the response functions involved in the MP2 equations. Summations over the large number of virtual states are avoided by using a formalism inspired by density functional perturbation theory, and the Lanczos algorithm is used to include dynamical effects. To demonstrate this method, applications to three weakly interacting dimers are presented.

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.

PubMed

Bogdanowicz, Damian; Giaro, Krzysztof

2017-05-01

Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.

Multiparametric ultrasound in the detection of prostate cancer: a systematic review.

PubMed

Postema, Arnoud; Mischi, Massimo; de la Rosette, Jean; Wijkstra, Hessel

2015-11-01

To investigate the advances and clinical results of the different ultrasound modalities and the progress in combining them into multiparametric UltraSound (mpUS). A systematic literature search on mpUS and the different ultrasound modalities included: greyscale ultrasound, computerized transrectal ultrasound, Doppler and power Doppler techniques, dynamic contrast-enhanced ultrasound and (shear wave) elastography. Limited research available on combining ultrasound modalities has presented improvement in diagnostic performance. The data of two studies suggest that even adding a lower performing ultrasound modality to a better performing modality using crude methods can already improve the sensitivity by 13-51 %. The different modalities detect different tumours. No study has tried to combine ultrasound modalities employing a system similar to the PIRADS system used for mpMRI or more advanced classifying algorithms. Available evidence confirms that combining different ultrasound modalities significantly improves diagnostic performance.

Estimation of chirp rates of music-adapted prolate spheroidal atoms using reassignment

NASA Astrophysics Data System (ADS)

Mesz, Bruno; Serrano, Eduardo

2007-09-01

We introduce a modified Matching Pursuit algorithm for estimating frequency and frequency slope of FM-modulated music signals. The use of Matching Pursuit with constant frequency atoms provides coarse estimates which could be improved with chirped atoms, more suited in principle to this kind of signals. Application of the reassignment method is suggested by its good localization properties for chirps. We start considering a family of atoms generated by modulation and scaling of a prolate spheroidal wave function. These functions are concentrated in frequency on intervals of a semitone centered at the frequencies of the well-tempered scale. At each stage of the pursuit, we search the atom most correlated with the signal. We then consider the spectral peaks at each frame of the spectrogram and calculate a modified frequency and frequency slope using the derivatives of the reassignment operators; this is then used to estimate the parameters of a cubic interpolation polynomial that models local pitch fluctuations. We apply the method both to synthetic and music signals.

Spectral reconstruction of signals from periodic nonuniform subsampling based on a Nyquist folding scheme

NASA Astrophysics Data System (ADS)

Jiang, Kaili; Zhu, Jun; Tang, Bin

2017-12-01

Periodic nonuniform sampling occurs in many applications, and the Nyquist folding receiver (NYFR) is an efficient, low complexity, and broadband spectrum sensing architecture. In this paper, we first derive that the radio frequency (RF) sample clock function of NYFR is periodic nonuniform. Then, the classical results of periodic nonuniform sampling are applied to NYFR. We extend the spectral reconstruction algorithm of time series decomposed model to the subsampling case by using the spectrum characteristics of NYFR. The subsampling case is common for broadband spectrum surveillance. Finally, we take example for a LFM signal under large bandwidth to verify the proposed algorithm and compare the spectral reconstruction algorithm with orthogonal matching pursuit (OMP) algorithm.

Machine-learning in grading of gliomas based on multi-parametric magnetic resonance imaging at 3T.

PubMed

Citak-Er, Fusun; Firat, Zeynep; Kovanlikaya, Ilhami; Ture, Ugur; Ozturk-Isik, Esin

2018-06-15

The objective of this study was to assess the contribution of multi-parametric (mp) magnetic resonance imaging (MRI) quantitative features in the machine learning-based grading of gliomas with a multi-region-of-interests approach. Forty-three patients who were newly diagnosed as having a glioma were included in this study. The patients were scanned prior to any therapy using a standard brain tumor magnetic resonance (MR) imaging protocol that included T1 and T2-weighted, diffusion-weighted, diffusion tensor, MR perfusion and MR spectroscopic imaging. Three different regions-of-interest were drawn for each subject to encompass tumor, immediate tumor periphery, and distant peritumoral edema/normal. The normalized mp-MRI features were used to build machine-learning models for differentiating low-grade gliomas (WHO grades I and II) from high grades (WHO grades III and IV). In order to assess the contribution of regional mp-MRI quantitative features to the classification models, a support vector machine-based recursive feature elimination method was applied prior to classification. A machine-learning model based on support vector machine algorithm with linear kernel achieved an accuracy of 93.0%, a specificity of 86.7%, and a sensitivity of 96.4% for the grading of gliomas using ten-fold cross validation based on the proposed subset of the mp-MRI features. In this study, machine-learning based on multiregional and multi-parametric MRI data has proven to be an important tool in grading glial tumors accurately even in this limited patient population. Future studies are needed to investigate the use of machine learning algorithms for brain tumor classification in a larger patient cohort. Copyright © 2018. Published by Elsevier Ltd.

PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling

PubMed Central

Siddharthan, Rahul

2008-01-01

PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we widen the scope of the program, addressing two major problems in computational regulatory genomics. First, PhyloGibbs-MP can localise predictions to small, undetermined regions of a large input sequence, thus effectively predicting cis-regulatory modules (CRMs) ab initio while simultaneously predicting binding sites in those modules—tasks that are usually done by two separate programs. PhyloGibbs-MP's performance at such ab initio CRM prediction is comparable with or superior to dedicated module-prediction software that use prior knowledge of previously characterised transcription factors. Second, PhyloGibbs-MP can predict motifs that differentiate between two (or more) different groups of regulatory regions, that is, motifs that occur preferentially in one group over the others. While other “discriminative motif-finders” have been published in the literature, PhyloGibbs-MP's implementation has some unique features and flexibility. Benchmarks on synthetic and actual genomic data show that this algorithm is successful at enhancing predictions of differentiating sites and suppressing predictions of common sites and compares with or outperforms other discriminative motif-finders on actual genomic data. Additional enhancements include significant performance and speed improvements, the ability to use “informative priors” on known transcription factors, and the ability to output annotations in a format that can be visualised with the Generic Genome Browser. In stand-alone motif-finding, PhyloGibbs-MP remains competitive, outperforming PhyloGibbs-1.0 and other programs on benchmark data. PMID:18769735

Automatic Thread-Level Parallelization in the Chombo AMR Library

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

Christen, Matthias; Keen, Noel; Ligocki, Terry

2011-05-26

The increasing on-chip parallelism has some substantial implications for HPC applications. Currently, hybrid programming models (typically MPI+OpenMP) are employed for mapping software to the hardware in order to leverage the hardware?s architectural features. In this paper, we present an approach that automatically introduces thread level parallelism into Chombo, a parallel adaptive mesh refinement framework for finite difference type PDE solvers. In Chombo, core algorithms are specified in the ChomboFortran, a macro language extension to F77 that is part of the Chombo framework. This domain-specific language forms an already used target language for an automatic migration of the large number ofmore » existing algorithms into a hybrid MPI+OpenMP implementation. It also provides access to the auto-tuning methodology that enables tuning certain aspects of an algorithm to hardware characteristics. Performance measurements are presented for a few of the most relevant kernels with respect to a specific application benchmark using this technique as well as benchmark results for the entire application. The kernel benchmarks show that, using auto-tuning, up to a factor of 11 in performance was gained with 4 threads with respect to the serial reference implementation.« less

RF Pulse Design using Nonlinear Gradient Magnetic Fields

PubMed Central

Kopanoglu, Emre; Constable, R. Todd

2014-01-01

Purpose An iterative k-space trajectory and radio-frequency (RF) pulse design method is proposed for Excitation using Nonlinear Gradient Magnetic fields (ENiGMa). Theory and Methods The spatial encoding functions (SEFs) generated by nonlinear gradient fields (NLGFs) are linearly dependent in Cartesian-coordinates. Left uncorrected, this may lead to flip-angle variations in excitation profiles. In the proposed method, SEFs (k-space samples) are selected using a Matching-Pursuit algorithm, and the RF pulse is designed using a Conjugate-Gradient algorithm. Three variants of the proposed approach are given: the full-algorithm, a computationally-cheaper version, and a third version for designing spoke-based trajectories. The method is demonstrated for various target excitation profiles using simulations and phantom experiments. Results The method is compared to other iterative (Matching-Pursuit and Conjugate Gradient) and non-iterative (coordinate-transformation and Jacobian-based) pulse design methods as well as uniform density spiral and EPI trajectories. The results show that the proposed method can increase excitation fidelity significantly. Conclusion An iterative method for designing k-space trajectories and RF pulses using nonlinear gradient fields is proposed. The method can either be used for selecting the SEFs individually to guide trajectory design, or can be adapted to design and optimize specific trajectories of interest. PMID:25203286

Bearing fault diagnosis using a whale optimization algorithm-optimized orthogonal matching pursuit with a combined time-frequency atom dictionary

NASA Astrophysics Data System (ADS)

Zhang, Xin; Liu, Zhiwen; Miao, Qiang; Wang, Lei

2018-07-01

Condition monitoring and fault diagnosis of rolling element bearings are significant to guarantee the reliability and functionality of a mechanical system, production efficiency, and plant safety. However, this is almost invariably a formidable challenge because the fault features are often buried by strong background noises and other unstable interference components. To satisfactorily extract the bearing fault features, a whale optimization algorithm (WOA)-optimized orthogonal matching pursuit (OMP) with a combined time-frequency atom dictionary is proposed in this paper. Firstly, a combined time-frequency atom dictionary whose atom is a combination of Fourier dictionary atom and impact time-frequency dictionary atom is designed according to the properties of bearing fault vibration signal. Furthermore, to improve the efficiency and accuracy of signal sparse representation, the WOA is introduced into the OMP algorithm to optimize the atom parameters for best approximating the original signal with the dictionary atoms. The proposed method is validated through analyzing the bearing fault simulation signal and the real vibration signals collected from an experimental bearing and a wheelset bearing of high-speed trains. The comparisons with the respect to the state of the art in the field are illustrated in detail, which highlight the advantages of the proposed method.

Design and evaluation of a parametric model for cardiac sounds.

PubMed

Ibarra-Hernández, Roilhi F; Alonso-Arévalo, Miguel A; Cruz-Gutiérrez, Alejandro; Licona-Chávez, Ana L; Villarreal-Reyes, Salvador

2017-10-01

Heart sound analysis plays an important role in the auscultative diagnosis process to detect the presence of cardiovascular diseases. In this paper we propose a novel parametric heart sound model that accurately represents normal and pathological cardiac audio signals, also known as phonocardiograms (PCG). The proposed model considers that the PCG signal is formed by the sum of two parts: one of them is deterministic and the other one is stochastic. The first part contains most of the acoustic energy. This part is modeled by the Matching Pursuit (MP) algorithm, which performs an analysis-synthesis procedure to represent the PCG signal as a linear combination of elementary waveforms. The second part, also called residual, is obtained after subtracting the deterministic signal from the original heart sound recording and can be accurately represented as an autoregressive process using the Linear Predictive Coding (LPC) technique. We evaluate the proposed heart sound model by performing subjective and objective tests using signals corresponding to different pathological cardiac sounds. The results of the objective evaluation show an average Percentage of Root-Mean-Square Difference of approximately 5% between the original heart sound and the reconstructed signal. For the subjective test we conducted a formal methodology for perceptual evaluation of audio quality with the assistance of medical experts. Statistical results of the subjective evaluation show that our model provides a highly accurate approximation of real heart sound signals. We are not aware of any previous heart sound model rigorously evaluated as our proposal. Copyright © 2017 Elsevier Ltd. All rights reserved.

Geometry planning and image registration in magnetic particle imaging using bimodal fiducial markers

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

Werner, F., E-mail: f.werner@uke.de; Hofmann, M.; Them, K.

Purpose: Magnetic particle imaging (MPI) is a quantitative imaging modality that allows the distribution of superparamagnetic nanoparticles to be visualized. Compared to other imaging techniques like x-ray radiography, computed tomography (CT), and magnetic resonance imaging (MRI), MPI only provides a signal from the administered tracer, but no additional morphological information, which complicates geometry planning and the interpretation of MP images. The purpose of the authors’ study was to develop bimodal fiducial markers that can be visualized by MPI and MRI in order to create MP–MR fusion images. Methods: A certain arrangement of three bimodal fiducial markers was developed and usedmore » in a combined MRI/MPI phantom and also during in vivo experiments in order to investigate its suitability for geometry planning and image fusion. An algorithm for automated marker extraction in both MR and MP images and rigid registration was established. Results: The developed bimodal fiducial markers can be visualized by MRI and MPI and allow for geometry planning as well as automated registration and fusion of MR–MP images. Conclusions: To date, exact positioning of the object to be imaged within the field of view (FOV) and the assignment of reconstructed MPI signals to corresponding morphological regions has been difficult. The developed bimodal fiducial markers and the automated image registration algorithm help to overcome these difficulties.« less

Incorporating DSA in multipatterning semiconductor manufacturing technologies

NASA Astrophysics Data System (ADS)

Badr, Yasmine; Torres, J. A.; Ma, Yuansheng; Mitra, Joydeep; Gupta, Puneet

2015-03-01

Multi-patterning (MP) is the process of record for many sub-10nm process technologies. The drive to higher densities has required the use of double and triple patterning for several layers; but this increases the cost of the new processes especially for low volume products in which the mask set is a large percentage of the total cost. For that reason there has been a strong incentive to develop technologies like Directed Self Assembly (DSA), EUV or E-beam direct write to reduce the total number of masks needed in a new technology node. Because of the nature of the technology, DSA cylinder graphoepitaxy only allows single-size holes in a single patterning approach. However, by integrating DSA and MP into a hybrid DSA-MP process, it is possible to come up with decomposition approaches that increase the design flexibility, allowing different size holes or bar structures by independently changing the process for every patterning step. A simple approach to integrate multi-patterning with DSA is to perform DSA grouping and MP decomposition in sequence whether it is: grouping-then-decomposition or decomposition-then-grouping; and each of the two sequences has its pros and cons. However, this paper describes why these intuitive approaches do not produce results of acceptable quality from the point of view of design compliance and we highlight the need for custom DSA-aware MP algorithms.

Markov chain algorithms: a template for building future robust low-power systems

PubMed Central

Deka, Biplab; Birklykke, Alex A.; Duwe, Henry; Mansinghka, Vikash K.; Kumar, Rakesh

2014-01-01

Although computational systems are looking towards post CMOS devices in the pursuit of lower power, the expected inherent unreliability of such devices makes it difficult to design robust systems without additional power overheads for guaranteeing robustness. As such, algorithmic structures with inherent ability to tolerate computational errors are of significant interest. We propose to cast applications as stochastic algorithms based on Markov chains (MCs) as such algorithms are both sufficiently general and tolerant to transition errors. We show with four example applications—Boolean satisfiability, sorting, low-density parity-check decoding and clustering—how applications can be cast as MC algorithms. Using algorithmic fault injection techniques, we demonstrate the robustness of these implementations to transition errors with high error rates. Based on these results, we make a case for using MCs as an algorithmic template for future robust low-power systems. PMID:24842030

Prostate cancer: computer-aided diagnosis on multiparametric MRI

NASA Astrophysics Data System (ADS)

Marin, Laura; Racoceanu, Daniel; Renard Penna, Raphaele; Ezziane, Malek

2017-11-01

Prostate cancer (PCa) is one of the most common cancers in men, being also the second most deadly cancer after lung cancer. There is increasing interest in active surveillance and minimally invasive focal therapies in PCa to avoid morbidities associated with whole gland therapy. Tumor volume represents an essential prognostic factor of PCa and the definition of index lesion volume is critical for appropriate decision making, especially for image guide focal treatment or in case of active surveillance. Multi-parametric Magnetic Resonance Imaging (mp-MRI) is the modality of choice for the detection and the localization of PCa foci. However, little has been published on mp-MRI accuracy in determining PCa volume, especially at 3T. There is insufficient evidence and no consensus to determine which of the methods for measuring volume is optimal. The objective of this study concerns the elaboration of an algorithm for automatic interpretation of mp-MRI. We determine the accuracy of the proposed method by comparing the prostate tumor volume issued from the automated volumetric mp-MRI measurements of the tumoral region, with manual and semi-automated volumetric measurements done by and respectively with radiologists. Information issued from whole mount histopathology is used to validate the whole approach.

Speeding up local correlation methods

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

Kats, Daniel

2014-12-28

We present two techniques that can substantially speed up the local correlation methods. The first one allows one to avoid the expensive transformation of the electron-repulsion integrals from atomic orbitals to virtual space. The second one introduces an algorithm for the residual equations in the local perturbative treatment that, in contrast to the standard scheme, does not require holding the amplitudes or residuals in memory. It is shown that even an interpreter-based implementation of the proposed algorithm in the context of local MP2 method is faster and requires less memory than the highly optimized variants of conventional algorithms.

Analysis of the orbit distortion by the use of the wavelet transform

NASA Astrophysics Data System (ADS)

Matsushita, T.; Agui, A.; Yoshigoe, A.; Takao, M.; Aoyagi, H.; Takeuchi, M.; Nakatani, T.; Tanaka, H.

2004-05-01

We have adopted matching pursuit algorithm of discrete wavelet transform (DWT) for the analysis of the beam position shift correlated with the motion of insertion device(ID). The beam position data measured by the rf beam position monitors have included high-frequency `noises' and fluctuation of background level. Precise evaluation of the electron beam position shift correlated with the motion of the ID is required for estimation of the steering magnet currents in order to suppress the closed orbit distortion (COD). The DWT is a powerful tool for frequency analysis and data processing. The analysis of DWT was applied to the beam position shift correlated with the phase motion of APPLE-2 type undulator (ID23) in SPring-8. The result of the analysis indicated that `noises' are mainly composed of the components of 50 ˜ 6.25Hz and < 0.1Hz. We carried out the data processing to remove the `noises' by the matching pursuit algorithm. Then we have succeeded in suppressing the COD within 2 μm by the use of the steering magnet currents calculated from the processed data.

A geometric method for computing ocular kinematics and classifying gaze events using monocular remote eye tracking in a robotic environment.

PubMed

Singh, Tarkeshwar; Perry, Christopher M; Herter, Troy M

2016-01-26

Robotic and virtual-reality systems offer tremendous potential for improving assessment and rehabilitation of neurological disorders affecting the upper extremity. A key feature of these systems is that visual stimuli are often presented within the same workspace as the hands (i.e., peripersonal space). Integrating video-based remote eye tracking with robotic and virtual-reality systems can provide an additional tool for investigating how cognitive processes influence visuomotor learning and rehabilitation of the upper extremity. However, remote eye tracking systems typically compute ocular kinematics by assuming eye movements are made in a plane with constant depth (e.g. frontal plane). When visual stimuli are presented at variable depths (e.g. transverse plane), eye movements have a vergence component that may influence reliable detection of gaze events (fixations, smooth pursuits and saccades). To our knowledge, there are no available methods to classify gaze events in the transverse plane for monocular remote eye tracking systems. Here we present a geometrical method to compute ocular kinematics from a monocular remote eye tracking system when visual stimuli are presented in the transverse plane. We then use the obtained kinematics to compute velocity-based thresholds that allow us to accurately identify onsets and offsets of fixations, saccades and smooth pursuits. Finally, we validate our algorithm by comparing the gaze events computed by the algorithm with those obtained from the eye-tracking software and manual digitization. Within the transverse plane, our algorithm reliably differentiates saccades from fixations (static visual stimuli) and smooth pursuits from saccades and fixations when visual stimuli are dynamic. The proposed methods provide advancements for examining eye movements in robotic and virtual-reality systems. Our methods can also be used with other video-based or tablet-based systems in which eye movements are performed in a peripersonal plane with variable depth.

High dimensional feature reduction via projection pursuit

NASA Technical Reports Server (NTRS)

Jimenez, Luis; Landgrebe, David

1994-01-01

The recent development of more sophisticated remote sensing systems enables the measurement of radiation in many more spectral intervals than previously possible. An example of that technology is the AVIRIS system, which collects image data in 220 bands. As a result of this, new algorithms must be developed in order to analyze the more complex data effectively. Data in a high dimensional space presents a substantial challenge, since intuitive concepts valid in a 2-3 dimensional space to not necessarily apply in higher dimensional spaces. For example, high dimensional space is mostly empty. This results from the concentration of data in the corners of hypercubes. Other examples may be cited. Such observations suggest the need to project data to a subspace of a much lower dimension on a problem specific basis in such a manner that information is not lost. Projection Pursuit is a technique that will accomplish such a goal. Since it processes data in lower dimensions, it should avoid many of the difficulties of high dimensional spaces. In this paper, we begin the investigation of some of the properties of Projection Pursuit for this purpose.

Cooperative control of two active spacecraft during proximity operations. M.S. Thesis - MIT

NASA Technical Reports Server (NTRS)

Polutchko, Robert J.

1989-01-01

A cooperative autopilot is developed for the control of the relative attitude, relative position and absolute attitude of two maneuvering spacecraft during on orbit proximity operations. The autopilot consists of an open-loop trajectory solver which computes a nine dimensional linearized nominal state trajectory at the beginning of each maneuver and a phase space regulator which maintains the two spacecraft on the nominal trajectory during coast phases of the maneuver. A linear programming algorithm is used to perform jet selection. Simulation tests using a system of two space shuttle vehicles are performed to verify the performance of the cooperative controller and comparisons are made to a traditional passive target/active pursuit vehicle approach to proximity operations. The cooperative autopilot is shown to be able to control the two vehicle system when both the would be pursuit vehicle and the target vehicle are not completely controllable in six degrees of freedom. The cooperative controller is also shown to use as much as 37 percent less fuel and 57 percent fewer jet firings than a single pursuit vehicle during a simple docking approach maneuver.

Optimization of large matrix calculations for execution on the Cray X-MP vector supercomputer

NASA Technical Reports Server (NTRS)

Hornfeck, William A.

1988-01-01

A considerable volume of large computational computer codes were developed for NASA over the past twenty-five years. This code represents algorithms developed for machines of earlier generation. With the emergence of the vector supercomputer as a viable, commercially available machine, an opportunity exists to evaluate optimization strategies to improve the efficiency of existing software. This result is primarily due to architectural differences in the latest generation of large-scale machines and the earlier, mostly uniprocessor, machines. A sofware package being used by NASA to perform computations on large matrices is described, and a strategy for conversion to the Cray X-MP vector supercomputer is also described.

Ultra-low dose quantitative CT myocardial perfusion imaging with sparse-view dynamic acquisition and image reconstruction: A feasibility study.

PubMed

Enjilela, Esmaeil; Lee, Ting-Yim; Hsieh, Jiang; Wisenberg, Gerald; Teefy, Patrick; Yadegari, Andrew; Bagur, Rodrigo; Islam, Ali; Branch, Kelley; So, Aaron

2018-03-01

We implemented and validated a compressed sensing (CS) based algorithm for reconstructing dynamic contrast-enhanced (DCE) CT images of the heart from sparsely sampled X-ray projections. DCE CT imaging of the heart was performed on five normal and ischemic pigs after contrast injection. DCE images were reconstructed with filtered backprojection (FBP) and CS from all projections (984-view) and 1/3 of all projections (328-view), and with CS from 1/4 of all projections (246-view). Myocardial perfusion (MP) measurements with each protocol were compared to those with the reference 984-view FBP protocol. Both the 984-view CS and 328-view CS protocols were in good agreements with the reference protocol. The Pearson correlation coefficients of 984-view CS and 328-view CS determined from linear regression analyses were 0.98 and 0.99 respectively. The corresponding mean biases of MP measurement determined from Bland-Altman analyses were 2.7 and 1.2ml/min/100g. When only 328 projections were used for image reconstruction, CS was more accurate than FBP for MP measurement with respect to 984-view FBP. However, CS failed to generate MP maps comparable to those with 984-view FBP when only 246 projections were used for image reconstruction. DCE heart images reconstructed from one-third of a full projection set with CS were minimally affected by aliasing artifacts, leading to accurate MP measurements with the effective dose reduced to just 33% of conventional full-view FBP method. The proposed CS sparse-view image reconstruction method could facilitate the implementation of sparse-view dynamic acquisition for ultra-low dose CT MP imaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Pilot study for supervised target detection applied to spatially registered multiparametric MRI in order to non-invasively score prostate cancer.

PubMed

Mayer, Rulon; Simone, Charles B; Skinner, William; Turkbey, Baris; Choykey, Peter

2018-03-01

Gleason Score (GS) is a validated predictor of prostate cancer (PCa) disease progression and outcomes. GS from invasive needle biopsies suffers from significant inter-observer variability and possible sampling error, leading to underestimating disease severity ("underscoring") and can result in possible complications. A robust non-invasive image-based approach is, therefore, needed. Use spatially registered multi-parametric MRI (MP-MRI), signatures, and supervised target detection algorithms (STDA) to non-invasively GS PCa at the voxel level. This study retrospectively analyzed 26 MP-MRI from The Cancer Imaging Archive. The MP-MRI (T2, Diffusion Weighted, Dynamic Contrast Enhanced) were spatially registered to each other, combined into stacks, and stitched together to form hypercubes. Multi-parametric (or multi-spectral) signatures derived from a training set of registered MP-MRI were transformed using statistics-based Whitening-Dewhitening (WD). Transformed signatures were inserted into STDA (having conical decision surfaces) applied to registered MP-MRI determined the tumor GS. The MRI-derived GS was quantitatively compared to the pathologist's assessment of the histology of sectioned whole mount prostates from patients who underwent radical prostatectomy. In addition, a meta-analysis of 17 studies of needle biopsy determined GS with confusion matrices and was compared to the MRI-determined GS. STDA and histology determined GS are highly correlated (R = 0.86, p < 0.02). STDA more accurately determined GS and reduced GS underscoring of PCa relative to needle biopsy as summarized by meta-analysis (p < 0.05). This pilot study found registered MP-MRI, STDA, and WD transforms of signatures shows promise in non-invasively GS PCa and reducing underscoring with high spatial resolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of l₁-Norm SVR and Sparse Coding Algorithms for Linear Regression.

PubMed

Zhang, Qingtian; Hu, Xiaolin; Zhang, Bo

2015-08-01

Support vector regression (SVR) is a popular function estimation technique based on Vapnik's concept of support vector machine. Among many variants, the l1-norm SVR is known to be good at selecting useful features when the features are redundant. Sparse coding (SC) is a technique widely used in many areas and a number of efficient algorithms are available. Both l1-norm SVR and SC can be used for linear regression. In this brief, the close connection between the l1-norm SVR and SC is revealed and some typical algorithms are compared for linear regression. The results show that the SC algorithms outperform the Newton linear programming algorithm, an efficient l1-norm SVR algorithm, in efficiency. The algorithms are then used to design the radial basis function (RBF) neural networks. Experiments on some benchmark data sets demonstrate the high efficiency of the SC algorithms. In particular, one of the SC algorithms, the orthogonal matching pursuit is two orders of magnitude faster than a well-known RBF network designing algorithm, the orthogonal least squares algorithm.

Multiparametric Magnetic Resonance Imaging for Active Surveillance of Prostate Cancer.

PubMed

An, Julie Y; Sidana, Abhinav; Choyke, Peter L; Wood, Bradford J.; Pinto, Peter A; Türkbey, İsmail Barış

2017-09-29

Active surveillance has gained popularity as an acceptable management option for men with low-risk prostate cancer. Successful utilization of this strategy can delay or prevent unnecessary interventions - thereby reducing morbidity associated with overtreatment. The usefulness of active surveillance primarily depends on correct identification of patients with low-risk disease. However, current population-wide algorithms and tools do not adequately exclude high-risk disease, thereby limiting the confidence of clinicians and patients to go on active surveillance. Novel imaging tools such as mpMRI provide information about the size and location of potential cancers enabling more informed treatment decisions. The term "multiparametric" in prostate mpMRI refers to the summation of several MRI series into one examination whose initial goal is to identify potential clinically-significant lesions suitable for targeted biopsy. The main advantages of MRI are its superior anatomic resolution and the lack of ionizing radiation. Recently, the Prostate Imaging-Reporting and Data System has been instituted as an international standard for unifying mpMRI results. The imaging sequences in mpMRI defined by Prostate Imaging Reporting and Data System version 2 includes: T2-weighted MRI, diffusion-weighted MRI, derived apparent-diffusion coefficient from diffusion-weighted MRI, and dynamic contrast-enhanced MRI. The use of mpMRI prior to starting active surveillance could prevent those with missed, high-grade lesions from going on active surveillance, and reassure those with minimal disease who may be hesitant to take part in active surveillance. Although larger validation studies are still necessary, preliminary results suggest mpMRI has a role in selecting patients for active surveillance. Less certain is the role of mpMRI in monitoring patients on active surveillance, as data on this will take a long time to mature. The biggest obstacles to routine use of prostate MRI are quality control, cost, reproducibility, and access. Nevertheless, there is great a potential for mpMRI to improve outcomes and quality of treatment. The major roles of MRI will continue to expand and its emerging use in standard of care approaches becomes more clearly defined and supported by increasing levels of data.

Fall Detection Using Smartphone Audio Features.

PubMed

Cheffena, Michael

2016-07-01

An automated fall detection system based on smartphone audio features is developed. The spectrogram, mel frequency cepstral coefficents (MFCCs), linear predictive coding (LPC), and matching pursuit (MP) features of different fall and no-fall sound events are extracted from experimental data. Based on the extracted audio features, four different machine learning classifiers: k-nearest neighbor classifier (k-NN), support vector machine (SVM), least squares method (LSM), and artificial neural network (ANN) are investigated for distinguishing between fall and no-fall events. For each audio feature, the performance of each classifier in terms of sensitivity, specificity, accuracy, and computational complexity is evaluated. The best performance is achieved using spectrogram features with ANN classifier with sensitivity, specificity, and accuracy all above 98%. The classifier also has acceptable computational requirement for training and testing. The system is applicable in home environments where the phone is placed in the vicinity of the user.

Identification of Reference Genes for Real-Time Quantitative PCR Experiments in the Liverwort Marchantia polymorpha

PubMed Central

Dolan, Liam; Langdale, Jane A.

2015-01-01

Real-time quantitative polymerase chain reaction (qPCR) has become widely used as a method to compare gene transcript levels across different conditions. However, selection of suitable reference genes to normalize qPCR data is required for accurate transcript level analysis. Recently, Marchantia polymorpha has been adopted as a model for the study of liverwort development and land plant evolution. Identification of appropriate reference genes has therefore become a necessity for gene expression studies. In this study, transcript levels of eleven candidate reference genes have been analyzed across a range of biological contexts that encompass abiotic stress, hormone treatment and different developmental stages. The consistency of transcript levels was assessed using both geNorm and NormFinder algorithms, and a consensus ranking of the different candidate genes was then obtained. MpAPT and MpACT showed relatively constant transcript levels across all conditions tested whereas the transcript levels of other candidate genes were clearly influenced by experimental conditions. By analyzing transcript levels of phosphate and nitrate starvation reporter genes, we confirmed that MpAPT and MpACT are suitable reference genes in M. polymorpha and also demonstrated that normalization with an inappropriate gene can lead to erroneous analysis of qPCR data. PMID:25798897

Target Classification of Canonical Scatterers Using Classical Estimation and Dictionary Based Techniques

DTIC Science & Technology

2012-03-22

shapes tested , when the objective parameter set was confined to a dictionary’s de - fined parameter space. These physical characteristics included...8 2.3 Hypothesis Testing and Detection Theory . . . . . . . . . . . . . . . 8 2.4 3-D SAR Scattering Models...basis pursuit de -noising (BPDN) algorithm is chosen to perform extraction due to inherent efficiency and error tolerance. Multiple shape dictionaries

An orbital emulator for pursuit-evasion game theoretic sensor management

NASA Astrophysics Data System (ADS)

Shen, Dan; Wang, Tao; Wang, Gang; Jia, Bin; Wang, Zhonghai; Chen, Genshe; Blasch, Erik; Pham, Khanh

2017-05-01

This paper develops and evaluates an orbital emulator (OE) for space situational awareness (SSA). The OE can produce 3D satellite movements using capabilities generated from omni-wheeled robot and robotic arm motion methods. The 3D motion of a satellite is partitioned into the movements in the equatorial plane and the up-down motions in the vertical plane. The 3D actions are emulated by omni-wheeled robot models while the up-down motions are performed by a stepped-motor-controlled-ball along a rod (robotic arm), which is attached to the robot. For multiple satellites, a fast map-merging algorithm is integrated into the robot operating system (ROS) and simultaneous localization and mapping (SLAM) routines to locate the multiple robots in the scene. The OE is used to demonstrate a pursuit-evasion (PE) game theoretic sensor management algorithm, which models conflicts between a space-based-visible (SBV) satellite (as pursuer) and a geosynchronous (GEO) satellite (as evader). The cost function of the PE game is based on the informational entropy of the SBV-tracking-GEO scenario. GEO can maneuver using a continuous and low thruster. The hard-in-loop space emulator visually illustrates the SSA problem solution based PE game.

Reconstruction of finite-valued sparse signals

NASA Astrophysics Data System (ADS)

Keiper, Sandra; Kutyniok, Gitta; Lee, Dae Gwan; Pfander, Götz

2017-08-01

The need of reconstructing discrete-valued sparse signals from few measurements, that is solving an undetermined system of linear equations, appears frequently in science and engineering. Those signals appear, for example, in error correcting codes as well as massive Multiple-Input Multiple-Output (MIMO) channel and wideband spectrum sensing. A particular example is given by wireless communications, where the transmitted signals are sequences of bits, i.e., with entries in f0; 1g. Whereas classical compressed sensing algorithms do not incorporate the additional knowledge of the discrete nature of the signal, classical lattice decoding approaches do not utilize sparsity constraints. In this talk, we present an approach that incorporates a discrete values prior into basis pursuit. In particular, we address finite-valued sparse signals, i.e., sparse signals with entries in a finite alphabet. We will introduce an equivalent null space characterization and show that phase transition takes place earlier than when using the classical basis pursuit approach. We will further discuss robustness of the algorithm and show that the nonnegative case is very different from the bipolar one. One of our findings is that the positioning of the zero in the alphabet - i.e., whether it is a boundary element or not - is crucial.

Parallel transformation of K-SVD solar image denoising algorithm

NASA Astrophysics Data System (ADS)

Liang, Youwen; Tian, Yu; Li, Mei

2017-02-01

The images obtained by observing the sun through a large telescope always suffered with noise due to the low SNR. K-SVD denoising algorithm can effectively remove Gauss white noise. Training dictionaries for sparse representations is a time consuming task, due to the large size of the data involved and to the complexity of the training algorithms. In this paper, an OpenMP parallel programming language is proposed to transform the serial algorithm to the parallel version. Data parallelism model is used to transform the algorithm. Not one atom but multiple atoms updated simultaneously is the biggest change. The denoising effect and acceleration performance are tested after completion of the parallel algorithm. Speedup of the program is 13.563 in condition of using 16 cores. This parallel version can fully utilize the multi-core CPU hardware resources, greatly reduce running time and easily to transplant in multi-core platform.

Comparison and analysis of nonlinear algorithms for compressed sensing in MRI.

PubMed

Yu, Yeyang; Hong, Mingjian; Liu, Feng; Wang, Hua; Crozier, Stuart

2010-01-01

Compressed sensing (CS) theory has been recently applied in Magnetic Resonance Imaging (MRI) to accelerate the overall imaging process. In the CS implementation, various algorithms have been used to solve the nonlinear equation system for better image quality and reconstruction speed. However, there are no explicit criteria for an optimal CS algorithm selection in the practical MRI application. A systematic and comparative study of those commonly used algorithms is therefore essential for the implementation of CS in MRI. In this work, three typical algorithms, namely, the Gradient Projection For Sparse Reconstruction (GPSR) algorithm, Interior-point algorithm (l(1)_ls), and the Stagewise Orthogonal Matching Pursuit (StOMP) algorithm are compared and investigated in three different imaging scenarios, brain, angiogram and phantom imaging. The algorithms' performances are characterized in terms of image quality and reconstruction speed. The theoretical results show that the performance of the CS algorithms is case sensitive; overall, the StOMP algorithm offers the best solution in imaging quality, while the GPSR algorithm is the most efficient one among the three methods. In the next step, the algorithm performances and characteristics will be experimentally explored. It is hoped that this research will further support the applications of CS in MRI.

Empirical study of parallel LRU simulation algorithms

NASA Technical Reports Server (NTRS)

Carr, Eric; Nicol, David M.

1994-01-01

This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.

Robust High-Capacity Audio Watermarking Based on FFT Amplitude Modification

NASA Astrophysics Data System (ADS)

Fallahpour, Mehdi; Megías, David

This paper proposes a novel robust audio watermarking algorithm to embed data and extract it in a bit-exact manner based on changing the magnitudes of the FFT spectrum. The key point is selecting a frequency band for embedding based on the comparison between the original and the MP3 compressed/decompressed signal and on a suitable scaling factor. The experimental results show that the method has a very high capacity (about 5kbps), without significant perceptual distortion (ODG about -0.25) and provides robustness against common audio signal processing such as added noise, filtering and MPEG compression (MP3). Furthermore, the proposed method has a larger capacity (number of embedded bits to number of host bits rate) than recent image data hiding methods.

Channel Estimation and Pilot Design for Massive MIMO Systems with Block-Structured Compressive Sensing

NASA Astrophysics Data System (ADS)

Lv, ZhuoKai; Yang, Tiejun; Zhu, Chunhua

2018-03-01

Through utilizing the technology of compressive sensing (CS), the channel estimation methods can achieve the purpose of reducing pilots and improving spectrum efficiency. The channel estimation and pilot design scheme are explored during the correspondence under the help of block-structured CS in massive MIMO systems. The block coherence property of the aggregate system matrix can be minimized so that the pilot design scheme based on stochastic search is proposed. Moreover, the block sparsity adaptive matching pursuit (BSAMP) algorithm under the common sparsity model is proposed so that the channel estimation can be caught precisely. Simulation results are to be proved the proposed design algorithm with superimposed pilots design and the BSAMP algorithm can provide better channel estimation than existing methods.

An algorithm for the numerical solution of linear differential games

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

Polovinkin, E S; Ivanov, G E; Balashov, M V

2001-10-31

A numerical algorithm for the construction of stable Krasovskii bridges, Pontryagin alternating sets, and also of piecewise program strategies solving two-person linear differential (pursuit or evasion) games on a fixed time interval is developed on the basis of a general theory. The aim of the first player (the pursuer) is to hit a prescribed target (terminal) set by the phase vector of the control system at the prescribed time. The aim of the second player (the evader) is the opposite. A description of numerical algorithms used in the solution of differential games of the type under consideration is presented andmore » estimates of the errors resulting from the approximation of the game sets by polyhedra are presented.« less

Electroencephalographic profiles for differentiation of disorders of consciousness

PubMed Central

2013-01-01

Background Electroencephalography (EEG) is best suited for long-term monitoring of brain functions in patients with disorders of consciousness (DOC). Mathematical tools are needed to facilitate efficient interpretation of long-duration sleep-wake EEG recordings. Methods Starting with matching pursuit (MP) decomposition, we automatically detect and parametrize sleep spindles, slow wave activity, K-complexes and alpha, beta and theta waves present in EEG recordings, and automatically construct profiles of their time evolution, relevant to the assessment of residual brain function in patients with DOC. Results Above proposed EEG profiles were computed for 32 patients diagnosed as minimally conscious state (MCS, 20 patients), vegetative state/unresponsive wakefulness syndrome (VS/UWS, 11 patients) and Locked-in Syndrome (LiS, 1 patient). Their interpretation revealed significant correlations between patients’ behavioral diagnosis and: (a) occurrence of sleep EEG patterns including sleep spindles, slow wave activity and light/deep sleep cycles, (b) appearance and variability across time of alpha, beta, and theta rhythms. Discrimination between MCS and VS/UWS based upon prominent features of these profiles classified correctly 87% of cases. Conclusions Proposed EEG profiles offer user-independent, repeatable, comprehensive and continuous representation of relevant EEG characteristics, intended as an aid in differentiation between VS/UWS and MCS states and diagnostic prognosis. To enable further development of this methodology into clinically usable tests, we share user-friendly software for MP decomposition of EEG (http://braintech.pl/svarog) and scripts used for creation of the presented profiles (attached to this article). PMID:24143892

Synchronous Motions Across the Instrumental Climate Record

NASA Astrophysics Data System (ADS)

Carl, Peter

The Earth's climate system bears a rich variety of feedback mechanisms that may give rise to complex, evolving modal structures under internal and external control. Various types of synchronization may be identified in the system's motion when looking at representative time series of the instrumental period through the glasses of an advanced technique of sparse data approximation, the Matching Pursuit (MP) approach. To disentangle the emerging network of oscillatory modes to the degree that climate dynamics turns out to be separable, a large dictionary of "Gaussian logons," i.e. frequency modulated (FM) Gabor atoms, is applied. Though the extracted modes make up linear decompositions, this flexible analyzing signal matches highly nonlinear waveforms. Univariate analyses over the period 1870-1997 are presented of a set of customary time series in annual resolution, comprising global and regional climate, central European synoptic systems, German precipitation, and runoff of the Elbe river near Dresden. All the evidence from this first-generation MP-FM study, obtained in subsequent multivariate syntheses, points to dynamically excited regimes of an organized yet complex climate system under permanent change—perhaps a (pre)chaotic one at centennial timescales, suggesting a "chaos control" perspective on global climate dynamics and change. Findings and conclusions include, among others, internal structure of reconstructed insolation, the episodic nature of global warming as reflected in multidecadal temperature modes, their swarm of "interdomain" companions across the whole system that unveils an unknown regime character of interannual climate dynamics, and the apparent onset early in the 1990s of the present thermal stagnation.

An implementation of a tree code on a SIMD, parallel computer

NASA Technical Reports Server (NTRS)

Olson, Kevin M.; Dorband, John E.

1994-01-01

We describe a fast tree algorithm for gravitational N-body simulation on SIMD parallel computers. The tree construction uses fast, parallel sorts. The sorted lists are recursively divided along their x, y and z coordinates. This data structure is a completely balanced tree (i.e., each particle is paired with exactly one other particle) and maintains good spatial locality. An implementation of this tree-building algorithm on a 16k processor Maspar MP-1 performs well and constitutes only a small fraction (approximately 15%) of the entire cycle of finding the accelerations. Each node in the tree is treated as a monopole. The tree search and the summation of accelerations also perform well. During the tree search, node data that is needed from another processor is simply fetched. Roughly 55% of the tree search time is spent in communications between processors. We apply the code to two problems of astrophysical interest. The first is a simulation of the close passage of two gravitationally, interacting, disk galaxies using 65,636 particles. We also simulate the formation of structure in an expanding, model universe using 1,048,576 particles. Our code attains speeds comparable to one head of a Cray Y-MP, so single instruction, multiple data (SIMD) type computers can be used for these simulations. The cost/performance ratio for SIMD machines like the Maspar MP-1 make them an extremely attractive alternative to either vector processors or large multiple instruction, multiple data (MIMD) type parallel computers. With further optimizations (e.g., more careful load balancing), speeds in excess of today's vector processing computers should be possible.

New computing systems and their impact on structural analysis and design

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1989-01-01

A review is given of the recent advances in computer technology that are likely to impact structural analysis and design. The computational needs for future structures technology are described. The characteristics of new and projected computing systems are summarized. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed, and a novel partitioning strategy is outlined for maximizing the degree of parallelism. The strategy is designed for computers with a shared memory and a small number of powerful processors (or a small number of clusters of medium-range processors). It is based on approximating the response of the structure by a combination of symmetric and antisymmetric response vectors, each obtained using a fraction of the degrees of freedom of the original finite element model. The strategy was implemented on the CRAY X-MP/4 and the Alliant FX/8 computers. For nonlinear dynamic problems on the CRAY X-MP with four CPUs, it resulted in an order of magnitude reduction in total analysis time, compared with the direct analysis on a single-CPU CRAY X-MP machine.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

PubMed

Procacci, Piero

2016-06-27

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs

DOE PAGES

Azad, Ariful; Buluç, Aydın

2016-05-16

We describe parallel algorithms for computing maximal cardinality matching in a bipartite graph on distributed-memory systems. Unlike traditional algorithms that match one vertex at a time, our algorithms process many unmatched vertices simultaneously using a matrix-algebraic formulation of maximal matching. This generic matrix-algebraic framework is used to develop three efficient maximal matching algorithms with minimal changes. The newly developed algorithms have two benefits over existing graph-based algorithms. First, unlike existing parallel algorithms, cardinality of matching obtained by the new algorithms stays constant with increasing processor counts, which is important for predictable and reproducible performance. Second, relying on bulk-synchronous matrix operations,more » these algorithms expose a higher degree of parallelism on distributed-memory platforms than existing graph-based algorithms. We report high-performance implementations of three maximal matching algorithms using hybrid OpenMP-MPI and evaluate the performance of these algorithm using more than 35 real and randomly generated graphs. On real instances, our algorithms achieve up to 200 × speedup on 2048 cores of a Cray XC30 supercomputer. Even higher speedups are obtained on larger synthetically generated graphs where our algorithms show good scaling on up to 16,384 cores.« less

Application of composite dictionary multi-atom matching in gear fault diagnosis.

PubMed

Cui, Lingli; Kang, Chenhui; Wang, Huaqing; Chen, Peng

2011-01-01

The sparse decomposition based on matching pursuit is an adaptive sparse expression method for signals. This paper proposes an idea concerning a composite dictionary multi-atom matching decomposition and reconstruction algorithm, and the introduction of threshold de-noising in the reconstruction algorithm. Based on the structural characteristics of gear fault signals, a composite dictionary combining the impulse time-frequency dictionary and the Fourier dictionary was constituted, and a genetic algorithm was applied to search for the best matching atom. The analysis results of gear fault simulation signals indicated the effectiveness of the hard threshold, and the impulse or harmonic characteristic components could be separately extracted. Meanwhile, the robustness of the composite dictionary multi-atom matching algorithm at different noise levels was investigated. Aiming at the effects of data lengths on the calculation efficiency of the algorithm, an improved segmented decomposition and reconstruction algorithm was proposed, and the calculation efficiency of the decomposition algorithm was significantly enhanced. In addition it is shown that the multi-atom matching algorithm was superior to the single-atom matching algorithm in both calculation efficiency and algorithm robustness. Finally, the above algorithm was applied to gear fault engineering signals, and achieved good results.

A portable approach for PIC on emerging architectures

NASA Astrophysics Data System (ADS)

Decyk, Viktor

2016-03-01

A portable approach for designing Particle-in-Cell (PIC) algorithms on emerging exascale computers, is based on the recognition that 3 distinct programming paradigms are needed. They are: low level vector (SIMD) processing, middle level shared memory parallel programing, and high level distributed memory programming. In addition, there is a memory hierarchy associated with each level. Such algorithms can be initially developed using vectorizing compilers, OpenMP, and MPI. This is the approach recommended by Intel for the Phi processor. These algorithms can then be translated and possibly specialized to other programming models and languages, as needed. For example, the vector processing and shared memory programming might be done with CUDA instead of vectorizing compilers and OpenMP, but generally the algorithm itself is not greatly changed. The UCLA PICKSC web site at http://www.idre.ucla.edu/ contains example open source skeleton codes (mini-apps) illustrating each of these three programming models, individually and in combination. Fortran2003 now supports abstract data types, and design patterns can be used to support a variety of implementations within the same code base. Fortran2003 also supports interoperability with C so that implementations in C languages are also easy to use. Finally, main codes can be translated into dynamic environments such as Python, while still taking advantage of high performing compiled languages. Parallel languages are still evolving with interesting developments in co-Array Fortran, UPC, and OpenACC, among others, and these can also be supported within the same software architecture. Work supported by NSF and DOE Grants.

Massively parallel and linear-scaling algorithm for second-order Møller-Plesset perturbation theory applied to the study of supramolecular wires

NASA Astrophysics Data System (ADS)

Kjærgaard, Thomas; Baudin, Pablo; Bykov, Dmytro; Eriksen, Janus Juul; Ettenhuber, Patrick; Kristensen, Kasper; Larkin, Jeff; Liakh, Dmitry; Pawłowski, Filip; Vose, Aaron; Wang, Yang Min; Jørgensen, Poul

2017-03-01

We present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide-Expand-Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide-Expand-Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the "resolution of the identity second-order Møller-Plesset perturbation theory" (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

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

Pinski, Peter; Riplinger, Christoph; Neese, Frank, E-mail: evaleev@vt.edu, E-mail: frank.neese@cec.mpg.de

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implementsmore » sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.« less

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals.

PubMed

Pinski, Peter; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

Local pursuit strategy-inspired cooperative trajectory planning algorithm for a class of nonlinear constrained dynamical systems

NASA Astrophysics Data System (ADS)

Xu, Yunjun; Remeikas, Charles; Pham, Khanh

2014-03-01

Cooperative trajectory planning is crucial for networked vehicles to respond rapidly in cluttered environments and has a significant impact on many applications such as air traffic or border security monitoring and assessment. One of the challenges in cooperative planning is to find a computationally efficient algorithm that can accommodate both the complexity of the environment and real hardware and configuration constraints of vehicles in the formation. Inspired by a local pursuit strategy observed in foraging ants, feasible and optimal trajectory planning algorithms are proposed in this paper for a class of nonlinear constrained cooperative vehicles in environments with densely populated obstacles. In an iterative hierarchical approach, the local behaviours, such as the formation stability, obstacle avoidance, and individual vehicle's constraints, are considered in each vehicle's (i.e. follower's) decentralised optimisation. The cooperative-level behaviours, such as the inter-vehicle collision avoidance, are considered in the virtual leader's centralised optimisation. Early termination conditions are derived to reduce the computational cost by not wasting time in the local-level optimisation if the virtual leader trajectory does not satisfy those conditions. The expected advantages of the proposed algorithms are (1) the formation can be globally asymptotically maintained in a decentralised manner; (2) each vehicle decides its local trajectory using only the virtual leader and its own information; (3) the formation convergence speed is controlled by one single parameter, which makes it attractive for many practical applications; (4) nonlinear dynamics and many realistic constraints, such as the speed limitation and obstacle avoidance, can be easily considered; (5) inter-vehicle collision avoidance can be guaranteed in both the formation transient stage and the formation steady stage; and (6) the computational cost in finding both the feasible and optimal solutions is low. In particular, the feasible solution can be computed in a very quick fashion. The minimum energy trajectory planning for a group of robots in an obstacle-laden environment is simulated to showcase the advantages of the proposed algorithms.

Single image non-uniformity correction using compressive sensing

NASA Astrophysics Data System (ADS)

Jian, Xian-zhong; Lu, Rui-zhi; Guo, Qiang; Wang, Gui-pu

2016-05-01

A non-uniformity correction (NUC) method for an infrared focal plane array imaging system was proposed. The algorithm, based on compressive sensing (CS) of single image, overcame the disadvantages of "ghost artifacts" and bulk calculating costs in traditional NUC algorithms. A point-sampling matrix was designed to validate the measurements of CS on the time domain. The measurements were corrected using the midway infrared equalization algorithm, and the missing pixels were solved with the regularized orthogonal matching pursuit algorithm. Experimental results showed that the proposed method can reconstruct the entire image with only 25% pixels. A small difference was found between the correction results using 100% pixels and the reconstruction results using 40% pixels. Evaluation of the proposed method on the basis of the root-mean-square error, peak signal-to-noise ratio, and roughness index (ρ) proved the method to be robust and highly applicable.

Quantum image processing: A review of advances in its security technologies

NASA Astrophysics Data System (ADS)

Yan, Fei; Iliyasu, Abdullah M.; Le, Phuc Q.

In this review, we present an overview of the advances made in quantum image processing (QIP) comprising of the image representations, the operations realizable on them, and the likely protocols and algorithms for their applications. In particular, we focus on recent progresses on QIP-based security technologies including quantum watermarking, quantum image encryption, and quantum image steganography. This review is aimed at providing readers with a succinct, yet adequate compendium of the progresses made in the QIP sub-area. Hopefully, this effort will stimulate further interest aimed at the pursuit of more advanced algorithms and experimental validations for available technologies and extensions to other domains.

Photon-efficient super-resolution laser radar

NASA Astrophysics Data System (ADS)

Shin, Dongeek; Shapiro, Jeffrey H.; Goyal, Vivek K.

2017-08-01

The resolution achieved in photon-efficient active optical range imaging systems can be low due to non-idealities such as propagation through a diffuse scattering medium. We propose a constrained optimization-based frame- work to address extremes in scarcity of photons and blurring by a forward imaging kernel. We provide two algorithms for the resulting inverse problem: a greedy algorithm, inspired by sparse pursuit algorithms; and a convex optimization heuristic that incorporates image total variation regularization. We demonstrate that our framework outperforms existing deconvolution imaging techniques in terms of peak signal-to-noise ratio. Since our proposed method is able to super-resolve depth features using small numbers of photon counts, it can be useful for observing fine-scale phenomena in remote sensing through a scattering medium and through-the-skin biomedical imaging applications.

BCL::MP-Fold: membrane protein structure prediction guided by EPR restraints

PubMed Central

Fischer, Axel W.; Alexander, Nathan S.; Woetzel, Nils; Karakaş, Mert; Weiner, Brian E.; Meiler, Jens

2016-01-01

For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The protein-size-normalized root-mean-square-deviation (RMSD100) value of the most accurate model is better than 8 Å for twenty-seven, better than 6 Å for twenty-two, and better than 4 Å for fifteen out of twenty-nine proteins, demonstrating the algorithm’s ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data. PMID:25820805

Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

NASA Astrophysics Data System (ADS)

Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

2016-04-01

We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

Design and analysis of a model predictive controller for active queue management.

PubMed

Wang, Ping; Chen, Hong; Yang, Xiaoping; Ma, Yan

2012-01-01

Model predictive (MP) control as a novel active queue management (AQM) algorithm in dynamic computer networks is proposed. According to the predicted future queue length in the data buffer, early packets at the router are dropped reasonably by the MPAQM controller so that the queue length reaches the desired value with minimal tracking error. The drop probability is obtained by optimizing the network performance. Further, randomized algorithms are applied to analyze the robustness of MPAQM successfully, and also to provide the stability domain of systems with uncertain network parameters. The performances of MPAQM are evaluated through a series of simulations in NS2. The simulation results show that the MPAQM algorithm outperforms RED, PI, and REM algorithms in terms of stability, disturbance rejection, and robustness. Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.

Gaze control for an active camera system by modeling human pursuit eye movements

NASA Astrophysics Data System (ADS)

Toelg, Sebastian

1992-11-01

The ability to stabilize the image of one moving object in the presence of others by active movements of the visual sensor is an essential task for biological systems, as well as for autonomous mobile robots. An algorithm is presented that evaluates the necessary movements from acquired visual data and controls an active camera system (ACS) in a feedback loop. No a priori assumptions about the visual scene and objects are needed. The algorithm is based on functional models of human pursuit eye movements and is to a large extent influenced by structural principles of neural information processing. An intrinsic object definition based on the homogeneity of the optical flow field of relevant objects, i.e., moving mainly fronto- parallel, is used. Velocity and spatial information are processed in separate pathways, resulting in either smooth or saccadic sensor movements. The program generates a dynamic shape model of the moving object and focuses its attention to regions where the object is expected. The system proved to behave in a stable manner under real-time conditions in complex natural environments and manages general object motion. In addition it exhibits several interesting abilities well-known from psychophysics like: catch-up saccades, grouping due to coherent motion, and optokinetic nystagmus.

Decentralized indirect methods for learning automata games.

PubMed

Tilak, Omkar; Martin, Ryan; Mukhopadhyay, Snehasis

2011-10-01

We discuss the application of indirect learning methods in zero-sum and identical payoff learning automata games. We propose a novel decentralized version of the well-known pursuit learning algorithm. Such a decentralized algorithm has significant computational advantages over its centralized counterpart. The theoretical study of such a decentralized algorithm requires the analysis to be carried out in a nonstationary environment. We use a novel bootstrapping argument to prove the convergence of the algorithm. To our knowledge, this is the first time that such analysis has been carried out for zero-sum and identical payoff games. Extensive simulation studies are reported, which demonstrate the proposed algorithm's fast and accurate convergence in a variety of game scenarios. We also introduce the framework of partial communication in the context of identical payoff games of learning automata. In such games, the automata may not communicate with each other or may communicate selectively. This comprehensive framework has the capability to model both centralized and decentralized games discussed in this paper.

Median prior constrained TV algorithm for sparse view low-dose CT reconstruction.

PubMed

Liu, Yi; Shangguan, Hong; Zhang, Quan; Zhu, Hongqing; Shu, Huazhong; Gui, Zhiguo

2015-05-01

It is known that lowering the X-ray tube current (mAs) or tube voltage (kVp) and simultaneously reducing the total number of X-ray views (sparse view) is an effective means to achieve low-dose in computed tomography (CT) scan. However, the associated image quality by the conventional filtered back-projection (FBP) usually degrades due to the excessive quantum noise. Although sparse-view CT reconstruction algorithm via total variation (TV), in the scanning protocol of reducing X-ray tube current, has been demonstrated to be able to result in significant radiation dose reduction while maintain image quality, noticeable patchy artifacts still exist in reconstructed images. In this study, to address the problem of patchy artifacts, we proposed a median prior constrained TV regularization to retain the image quality by introducing an auxiliary vector m in register with the object. Specifically, the approximate action of m is to draw, in each iteration, an object voxel toward its own local median, aiming to improve low-dose image quality with sparse-view projection measurements. Subsequently, an alternating optimization algorithm is adopted to optimize the associative objective function. We refer to the median prior constrained TV regularization as "TV_MP" for simplicity. Experimental results on digital phantoms and clinical phantom demonstrated that the proposed TV_MP with appropriate control parameters can not only ensure a higher signal to noise ratio (SNR) of the reconstructed image, but also its resolution compared with the original TV method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cerenkov luminescence tomography based on preconditioning orthogonal matching pursuit

NASA Astrophysics Data System (ADS)

Liu, Haixiao; Hu, Zhenhua; Wang, Kun; Tian, Jie; Yang, Xin

2015-03-01

Cerenkov luminescence imaging (CLI) is a novel optical imaging method and has been proved to be a potential substitute of the traditional radionuclide imaging such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). This imaging method inherits the high sensitivity of nuclear medicine and low cost of optical molecular imaging. To obtain the depth information of the radioactive isotope, Cerenkov luminescence tomography (CLT) is established and the 3D distribution of the isotope is reconstructed. However, because of the strong absorption and scatter, the reconstruction of the CLT sources is always converted to an ill-posed linear system which is hard to be solved. In this work, the sparse nature of the light source was taken into account and the preconditioning orthogonal matching pursuit (POMP) method was established to effectively reduce the ill-posedness and obtain better reconstruction accuracy. To prove the accuracy and speed of this algorithm, a heterogeneous numerical phantom experiment and an in vivo mouse experiment were conducted. Both the simulation result and the mouse experiment showed that our reconstruction method can provide more accurate reconstruction result compared with the traditional Tikhonov regularization method and the ordinary orthogonal matching pursuit (OMP) method. Our reconstruction method will provide technical support for the biological application for Cerenkov luminescence.

Massively parallel and linear-scaling algorithm for second-order Moller–Plesset perturbation theory applied to the study of supramolecular wires

DOE PAGES

Kjaergaard, Thomas; Baudin, Pablo; Bykov, Dmytro; ...

2016-11-16

Here, we present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide–Expand–Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide–Expand–Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalabilitymore » of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the “resolution of the identity second-order Moller–Plesset perturbation theory” (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.« less

Early MIMD experience on the CRAY X-MP

NASA Astrophysics Data System (ADS)

Rhoades, Clifford E.; Stevens, K. G.

1985-07-01

This paper describes some early experience with converting four physics simulation programs to the CRAY X-MP, a current Multiple Instruction, Multiple Data (MIMD) computer consisting of two processors each with an architecture similar to that of the CRAY-1. As a multi-processor, the CRAY X-MP together with the high speed Solid-state Storage Device (SSD) in an ideal machine upon which to study MIMD algorithms for solving the equations of mathematical physics because it is fast enough to run real problems. The computer programs used in this study are all FORTRAN versions of original production codes. They range in sophistication from a one-dimensional numerical simulation of collisionless plasma to a two-dimensional hydrodynamics code with heat flow to a couple of three-dimensional fluid dynamics codes with varying degrees of viscous modeling. Early research with a dual processor configuration has shown speed-ups ranging from 1.55 to 1.98. It has been observed that a few simple extensions to FORTRAN allow a typical programmer to achieve a remarkable level of efficiency. These extensions involve the concept of memory local to a concurrent subprogram and memory common to all concurrent subprograms.

Severe forms of concealed penis without hypospadias: Surgical strategies

PubMed Central

de Jesus, Lisieux Eyer; Dekermacher, Samuel; Anderson, Kleber M.

2015-01-01

Introduction: Concealed penis (CP) may vary in severity and includes megaprepuce (MP) as a variant. Many different surgical strategies have been described in order to maximize penile exposure and to deal with skin deficiency. We describe the strategies that we use to overcome technical problems in severe cases of CP. Materials and Methods: Six consecutive cases of severe CP (including 3 with MP) were treated in a 2-year period between January 2011 and April 2013. These patients were treated using extensive degloving, removal of dysplastic dartos, Alexander's preputial flap, scrotal flaps and skin grafts. Three patients had been previously circumcised. Cases associated with hypospadias, obesity, disorders of sexual differentiation and micropenises were excluded. Results: All six patients attained good results, with good exposure of the penis, ability to void standing with a well-directed flow and reasonable esthetic results. A technical algorithm for the treatment of primary or recurring cases of CP is proposed. Conclusion: Alexander’ s distally based ventral preputial flap is a useful technical resource to treat MP cases. Free skin grafts and/or laterally based scrotal flaps may be used to cover the penis after release in severe cases of CP. PMID:26604447

Endangered Cultural Heritage: Global Mapping of Protected and Heritage Sites

DTIC Science & Technology

2017-07-01

the physical, ecologi - cal, and sociocultural attributes for transition into existing Programs of ERDC/CERL MP-17-1 12 Records. The development of...ENSITE’s Qualitative Assessment Frame- work allows physical, ecological , and sociocultural environmental attrib- utes to be spatially defined in...support of the commander’s intent. Furthermore, research as part of ENSITE develops a statistical algorithm to classify physical, ecological , and

Path Planning Algorithms for Autonomous Border Patrol Vehicles

NASA Astrophysics Data System (ADS)

Lau, George Tin Lam

This thesis presents an online path planning algorithm developed for unmanned vehicles in charge of autonomous border patrol. In this Pursuit-Evasion game, the unmanned vehicle is required to capture multiple trespassers on its own before any of them reach a target safe house where they are safe from capture. The problem formulation is based on Isaacs' Target Guarding problem, but extended to the case of multiple evaders. The proposed path planning method is based on Rapidly-exploring random trees (RRT) and is capable of producing trajectories within several seconds to capture 2 or 3 evaders. Simulations are carried out to demonstrate that the resulting trajectories approach the optimal solution produced by a nonlinear programming-based numerical optimal control solver. Experiments are also conducted on unmanned ground vehicles to show the feasibility of implementing the proposed online path planning algorithm on physical applications.

A novel speech watermarking algorithm by line spectrum pair modification

NASA Astrophysics Data System (ADS)

Zhang, Qian; Yang, Senbin; Chen, Guang; Zhou, Jun

2011-10-01

To explore digital watermarking specifically suitable for the speech domain, this paper experimentally investigates the properties of line spectrum pair (LSP) parameters firstly. The results show that the differences between contiguous LSPs are robust against common signal processing operations and small modifications of LSPs are imperceptible to the human auditory system (HAS). According to these conclusions, three contiguous LSPs of a speech frame are selected to embed a watermark bit. The middle LSP is slightly altered to modify the differences of these LSPs when embedding watermark. Correspondingly, the watermark is extracted by comparing these differences. The proposed algorithm's transparency is adjustable to meet the needs of different applications. The algorithm has good robustness against additive noise, quantization, amplitude scale and MP3 compression attacks, for the bit error rate (BER) is less than 5%. In addition, the algorithm allows a relatively low capacity, which approximates to 50 bps.

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

Collins, Benjamin S.

The Futility package contains the following: 1) Definition of the size of integers and real numbers; 2) A generic Unit test harness; 3) Definitions for some basic extensions to the Fortran language: arbitrary length strings, a parameter list construct, exception handlers, command line processor, timers; 4) Geometry definitions: point, line, plane, box, cylinder, polyhedron; 5) File wrapper functions: standard Fortran input/output files, Fortran binary files, HDF5 files; 6) Parallel wrapper functions: MPI, and Open MP abstraction layers, partitioning algorithms; 7) Math utilities: BLAS, Matrix and Vector definitions, Linear Solver methods and wrappers for other TPLs (PETSC, MKL, etc), preconditioner classes;more » 8) Misc: random number generator, water saturation properties, sorting algorithms.« less

spammpack, Version 2013-06-18

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

2014-01-17

This library is an implementation of the Sparse Approximate Matrix Multiplication (SpAMM) algorithm introduced. It provides a matrix data type, and an approximate matrix product, which exhibits linear scaling computational complexity for matrices with decay. The product error and the performance of the multiply can be tuned by choosing an appropriate tolerance. The library can be compiled for serial execution or parallel execution on shared memory systems with an OpenMP capable compiler

Parallel Algorithms for Computer Vision.

DTIC Science & Technology

1989-01-01

34 IEEE Tran. Pattern Ankyaij and Ma- Artifcial Intelligence , Tokyo, 1979. chine Intelligence , 6, 1984. Kirkpatrick, S., C.D. Gelatt, Jr. and M.P. Vecchi...MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB T P06010 JAN 89 ETL-0529 UNCLASSIFIED DACA76-85-C-0010 F.’G 12/1I N mommiimmmiiso...PoggioI Massachusetts Institute of Technology i Artificial Intelligence Laboratory 545 Technology Square Cambridge, Massachusetts 02139 DTIC January

An Integrated Framework Advancing Membrane Protein Modeling and Design

PubMed Central

Weitzner, Brian D.; Duran, Amanda M.; Tilley, Drew C.; Elazar, Assaf; Gray, Jeffrey J.

2015-01-01

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design. PMID:26325167

A Gradient-Based Multistart Algorithm for Multimodal Aerodynamic Shape Optimization Problems Based on Free-Form Deformation

NASA Astrophysics Data System (ADS)

Streuber, Gregg Mitchell

Environmental and economic factors motivate the pursuit of more fuel-efficient aircraft designs. Aerodynamic shape optimization is a powerful tool in this effort, but is hampered by the presence of multimodality in many design spaces. Gradient-based multistart optimization uses a sampling algorithm and multiple parallel optimizations to reliably apply fast gradient-based optimization to moderately multimodal problems. Ensuring that the sampled geometries remain physically realizable requires manually developing specialized linear constraints for each class of problem. Utilizing free-form deformation geometry control allows these linear constraints to be written in a geometry-independent fashion, greatly easing the process of applying the algorithm to new problems. This algorithm was used to assess the presence of multimodality when optimizing a wing in subsonic and transonic flows, under inviscid and viscous conditions, and a blended wing-body under transonic, viscous conditions. Multimodality was present in every wing case, while the blended wing-body was found to be generally unimodal.

Eye-Pursuit and Reafferent Head Movement Signals Carried by Pursuit Neurons in the Caudal Part of the Frontal Eye Fields during Head-Free Pursuit

PubMed Central

Kasahara, Satoshi; Akao, Teppei; Kurkin, Sergei; Peterson, Barry W.

2009-01-01

Eye and head movements are coordinated during head-free pursuit. To examine whether pursuit neurons in frontal eye fields (FEF) carry gaze-pursuit commands that drive both eye-pursuit and head-pursuit, monkeys whose heads were free to rotate about a vertical axis were trained to pursue a juice feeder with their head and a target with their eyes. Initially the feeder and target moved synchronously with the same visual angle. FEF neurons responding to this gaze-pursuit were tested for eye-pursuit of target motion while the feeder was stationary and for head-pursuit while the target was stationary. The majority of pursuit neurons exhibited modulation during head-pursuit, but their preferred directions during eye-pursuit and head-pursuit were different. Although peak modulation occurred during head movements, the onset of discharge usually was not aligned with the head movement onset. The minority of neurons whose discharge onset was so aligned discharged after the head movement onset. These results do not support the idea that the head-pursuit–related modulation reflects head-pursuit commands. Furthermore, modulation similar to that during head-pursuit was obtained by passive head rotation on stationary trunk. Our results suggest that FEF pursuit neurons issue gaze or eye movement commands during gaze-pursuit and that the head-pursuit–related modulation primarily reflects reafferent signals resulting from head movements. PMID:18483002

Quantization of Motor Activity into Primitives and Time-Frequency Atoms Using Independent Component Analysis and Matching Pursuit Algorithms

DTIC Science & Technology

2001-10-25

form: (1) A is a scaling factor, t is time and r a coordinate vector describing the limb configuration. We...combination of limb state and EMG. In our early examination of EMG we detected underlying groups of muscles and phases of activity by inspection and...representations of EEG or other biological signals has been thoroughly explored. Such components might be used as a basis for neuroprosthetic control

Volitional and Real-Time Control Cursor Based on Eye Movement Decoding Using a Linear Decoding Model

PubMed Central

Zhang, Cheng

2016-01-01

The aim of this study is to build a linear decoding model that reveals the relationship between the movement information and the EOG (electrooculogram) data to online control a cursor continuously with blinks and eye pursuit movements. First of all, a blink detection method is proposed to reject a voluntary single eye blink or double-blink information from EOG. Then, a linear decoding model of time series is developed to predict the position of gaze, and the model parameters are calibrated by the RLS (Recursive Least Square) algorithm; besides, the assessment of decoding accuracy is assessed through cross-validation procedure. Additionally, the subsection processing, increment control, and online calibration are presented to realize the online control. Finally, the technology is applied to the volitional and online control of a cursor to hit the multiple predefined targets. Experimental results show that the blink detection algorithm performs well with the voluntary blink detection rate over 95%. Through combining the merits of blinks and smooth pursuit movements, the movement information of eyes can be decoded in good conformity with the average Pearson correlation coefficient which is up to 0.9592, and all signal-to-noise ratios are greater than 0. The novel system allows people to successfully and economically control a cursor online with a hit rate of 98%. PMID:28058044

One algorithm to rule them all? An evaluation and discussion of ten eye movement event-detection algorithms.

PubMed

Andersson, Richard; Larsson, Linnea; Holmqvist, Kenneth; Stridh, Martin; Nyström, Marcus

2017-04-01

Almost all eye-movement researchers use algorithms to parse raw data and detect distinct types of eye movement events, such as fixations, saccades, and pursuit, and then base their results on these. Surprisingly, these algorithms are rarely evaluated. We evaluated the classifications of ten eye-movement event detection algorithms, on data from an SMI HiSpeed 1250 system, and compared them to manual ratings of two human experts. The evaluation focused on fixations, saccades, and post-saccadic oscillations. The evaluation used both event duration parameters, and sample-by-sample comparisons to rank the algorithms. The resulting event durations varied substantially as a function of what algorithm was used. This evaluation differed from previous evaluations by considering a relatively large set of algorithms, multiple events, and data from both static and dynamic stimuli. The main conclusion is that current detectors of only fixations and saccades work reasonably well for static stimuli, but barely better than chance for dynamic stimuli. Differing results across evaluation methods make it difficult to select one winner for fixation detection. For saccade detection, however, the algorithm by Larsson, Nyström and Stridh (IEEE Transaction on Biomedical Engineering, 60(9):2484-2493,2013) outperforms all algorithms in data from both static and dynamic stimuli. The data also show how improperly selected algorithms applied to dynamic data misestimate fixation and saccade properties.

An autonomous robot inspired by insect neurophysiology pursues moving features in natural environments

NASA Astrophysics Data System (ADS)

Bagheri, Zahra M.; Cazzolato, Benjamin S.; Grainger, Steven; O'Carroll, David C.; Wiederman, Steven D.

2017-08-01

Objective. Many computer vision and robotic applications require the implementation of robust and efficient target-tracking algorithms on a moving platform. However, deployment of a real-time system is challenging, even with the computational power of modern hardware. Lightweight and low-powered flying insects, such as dragonflies, track prey or conspecifics within cluttered natural environments, illustrating an efficient biological solution to the target-tracking problem. Approach. We used our recent recordings from ‘small target motion detector’ neurons in the dragonfly brain to inspire the development of a closed-loop target detection and tracking algorithm. This model exploits facilitation, a slow build-up of response to targets which move along long, continuous trajectories, as seen in our electrophysiological data. To test performance in real-world conditions, we implemented this model on a robotic platform that uses active pursuit strategies based on insect behaviour. Main results. Our robot performs robustly in closed-loop pursuit of targets, despite a range of challenging conditions used in our experiments; low contrast targets, heavily cluttered environments and the presence of distracters. We show that the facilitation stage boosts responses to targets moving along continuous trajectories, improving contrast sensitivity and detection of small moving targets against textured backgrounds. Moreover, the temporal properties of facilitation play a useful role in handling vibration of the robotic platform. We also show that the adoption of feed-forward models which predict the sensory consequences of self-movement can significantly improve target detection during saccadic movements. Significance. Our results provide insight into the neuronal mechanisms that underlie biological target detection and selection (from a moving platform), as well as highlight the effectiveness of our bio-inspired algorithm in an artificial visual system.

Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity.

PubMed

Jung, Yousung; Shao, Yihan; Head-Gordon, Martin

2007-09-01

The scaled opposite spin Møller-Plesset method (SOS-MP2) is an economical way of obtaining correlation energies that are computationally cheaper, and yet, in a statistical sense, of higher quality than standard MP2 theory, by introducing one empirical parameter. But SOS-MP2 still has a fourth-order scaling step that makes the method inapplicable to very large molecular systems. We reduce the scaling of SOS-MP2 by exploiting the sparsity of expansion coefficients and local integral matrices, by performing local auxiliary basis expansions for the occupied-virtual product distributions. To exploit sparsity of 3-index local quantities, we use a blocking scheme in which entire zero-rows and columns, for a given third global index, are deleted by comparison against a numerical threshold. This approach minimizes sparse matrix book-keeping overhead, and also provides sufficiently large submatrices after blocking, to allow efficient matrix-matrix multiplies. The resulting algorithm is formally cubic scaling, and requires only moderate computational resources (quadratic memory and disk space) and, in favorable cases, is shown to yield effective quadratic scaling behavior in the size regime we can apply it to. Errors associated with local fitting using the attenuated Coulomb metric and numerical thresholds in the blocking procedure are found to be insignificant in terms of the predicted relative energies. A diverse set of test calculations shows that the size of system where significant computational savings can be achieved depends strongly on the dimensionality of the system, and the extent of localizability of the molecular orbitals. Copyright 2007 Wiley Periodicals, Inc.

A Subconscious Interaction between Fixation and Anticipatory Pursuit

PubMed Central

Bal, Japjot; Heinen, Stephen J.

2017-01-01

Ocular smooth pursuit and fixation are typically viewed as separate systems, yet there is evidence that the brainstem fixation system inhibits pursuit. Here we present behavioral evidence that the fixation system modulates pursuit behavior outside of conscious awareness. Human observers (male and female) either pursued a small spot that translated across a screen, or fixated it as it remained stationary. As shown previously, pursuit trials potentiated the oculomotor system, producing anticipatory eye velocity on the next trial before the target moved that mimicked the stimulus-driven velocity. Randomly interleaving fixation trials reduced anticipatory pursuit, suggesting that a potentiated fixation system interacted with pursuit to suppress eye velocity in upcoming pursuit trials. The reduction was not due to passive decay of the potentiated pursuit signal because interleaving “blank” trials in which no target appeared did not reduce anticipatory pursuit. Interspersed short fixation trials reduced anticipation on long pursuit trials, suggesting that fixation potentiation was stronger than pursuit potentiation. Furthermore, adding more pursuit trials to a block did not restore anticipatory pursuit, suggesting that fixation potentiation was not overridden by certainty of an imminent pursuit trial but rather was immune to conscious intervention. To directly test whether cognition can override fixation suppression, we alternated pursuit and fixation trials to perfectly specify trial identity. Still, anticipatory pursuit did not rise above that observed with an equal number of random fixation trials. The results suggest that potentiated fixation circuitry interacts with pursuit circuitry at a subconscious level to inhibit pursuit. SIGNIFICANCE STATEMENT When an object moves, we view it with smooth pursuit eye movements. When an object is stationary, we view it with fixational eye movements. Pursuit and fixation are historically regarded as controlled by different neural circuitry, and alternating between invoking them is thought to be guided by a conscious decision. However, our results show that pursuit is actively suppressed by prior fixation of a stationary object. This suppression is involuntary, and cannot be avoided even if observers are certain that the object will move. The results suggest that the neural fixation circuitry is potentiated by engaging stationary objects, and interacts with pursuit outside of conscious awareness. PMID:29061701

A Subconscious Interaction between Fixation and Anticipatory Pursuit.

PubMed

Watamaniuk, Scott N J; Bal, Japjot; Heinen, Stephen J

2017-11-22

Ocular smooth pursuit and fixation are typically viewed as separate systems, yet there is evidence that the brainstem fixation system inhibits pursuit. Here we present behavioral evidence that the fixation system modulates pursuit behavior outside of conscious awareness. Human observers (male and female) either pursued a small spot that translated across a screen, or fixated it as it remained stationary. As shown previously, pursuit trials potentiated the oculomotor system, producing anticipatory eye velocity on the next trial before the target moved that mimicked the stimulus-driven velocity. Randomly interleaving fixation trials reduced anticipatory pursuit, suggesting that a potentiated fixation system interacted with pursuit to suppress eye velocity in upcoming pursuit trials. The reduction was not due to passive decay of the potentiated pursuit signal because interleaving "blank" trials in which no target appeared did not reduce anticipatory pursuit. Interspersed short fixation trials reduced anticipation on long pursuit trials, suggesting that fixation potentiation was stronger than pursuit potentiation. Furthermore, adding more pursuit trials to a block did not restore anticipatory pursuit, suggesting that fixation potentiation was not overridden by certainty of an imminent pursuit trial but rather was immune to conscious intervention. To directly test whether cognition can override fixation suppression, we alternated pursuit and fixation trials to perfectly specify trial identity. Still, anticipatory pursuit did not rise above that observed with an equal number of random fixation trials. The results suggest that potentiated fixation circuitry interacts with pursuit circuitry at a subconscious level to inhibit pursuit. SIGNIFICANCE STATEMENT When an object moves, we view it with smooth pursuit eye movements. When an object is stationary, we view it with fixational eye movements. Pursuit and fixation are historically regarded as controlled by different neural circuitry, and alternating between invoking them is thought to be guided by a conscious decision. However, our results show that pursuit is actively suppressed by prior fixation of a stationary object. This suppression is involuntary, and cannot be avoided even if observers are certain that the object will move. The results suggest that the neural fixation circuitry is potentiated by engaging stationary objects, and interacts with pursuit outside of conscious awareness. Copyright © 2017 the authors 0270-6474/17/3711424-07$15.00/0.

The proinflammatory environment in potential heart and lung donors: prevalence and impact of donor management and hormonal therapy.

PubMed

Venkateswaran, Rajamiyer V; Dronavalli, Vamsidhar; Lambert, Peter A; Steeds, Richard P; Wilson, Ian C; Thompson, Richard D; Mascaro, Jorge G; Bonser, Robert S

2009-08-27

Brain stem death can elicit a potentially manipulable cardiotoxic proinflammatory cytokine response. We investigated the prevalence of this response, the impact of donor management with tri-iodothyronine (T3) and methylprednisolone (MP) administration, and the relationship of biomarkers to organ function and transplant suitability. In a prospective randomized double-blinded factorially designed study of T3 and MP therapy, we measured serum levels of interleukin-1 and -6 (IL-1 and IL-6), tumor necrosis factor-alpha (TNF-alpha), C-reactive protein, and procalcitonin (PCT) levels in 79 potential heart or lung donors. Measurements were performed before and after 4 hr of algorithm-based donor management to optimize cardiorespiratory function and +/-hormone treatment. Donors were assigned to receive T3, MP, both drugs, or placebo. Initial IL-1 was elevated in 16% donors, IL-6 in 100%, TNF-alpha in 28%, CRP in 98%, and PCT in 87%. Overall biomarker concentrations did not change between initial and later measurements and neither T3 nor MP effected any change. Both PCT (P =0.02) and TNF-alpha (P =0.044) levels were higher in donor hearts with marginal hemodynamics at initial assessment. Higher PCT levels were related to worse cardiac index and right and left ventricular ejection fractions and a PCT level more than 2 ng x mL(-1) may attenuate any improvement in cardiac index gained by donor management. No differences were observed between initially marginal and nonmarginal donor lungs. A PCT level less than or equal to 2 ng x mL(-1) but not other biomarkers predicted transplant suitability following management. There is high prevalence of a proinflammatory environment in the organ donor that is not affected by tri-iodothyronine or MP therapy. High PCT and TNF-alpha levels are associated with donor heart dysfunction.

Application of a hybrid MPI/OpenMP approach for parallel groundwater model calibration using multi-core computers

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

Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

2010-01-01

Calibration of groundwater models involves hundreds to thousands of forward solutions, each of which may solve many transient coupled nonlinear partial differential equations, resulting in a computationally intensive problem. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelisms in software and hardware to reduce calibration time on multi-core computers. HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for direct solutions for a reactive transport model application, and a field-scale coupled flow and transport model application. In the reactive transport model, a single parallelizable loop is identified to account for over 97% of the total computational time using GPROF.more » Addition of a few lines of OpenMP compiler directives to the loop yields a speedup of about 10 on a 16-core compute node. For the field-scale model, parallelizable loops in 14 of 174 HGC5 subroutines that require 99% of the execution time are identified. As these loops are parallelized incrementally, the scalability is found to be limited by a loop where Cray PAT detects over 90% cache missing rates. With this loop rewritten, similar speedup as the first application is achieved. The OpenMP-parallelized code can be run efficiently on multiple workstations in a network or multiple compute nodes on a cluster as slaves using parallel PEST to speedup model calibration. To run calibration on clusters as a single task, the Levenberg Marquardt algorithm is added to HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, 100 200 compute cores are used to reduce the calibration time from weeks to a few hours for these two applications. This approach is applicable to most of the existing groundwater model codes for many applications.« less

Normal aging affects movement execution but not visual motion working memory and decision-making delay during cue-dependent memory-based smooth-pursuit.

PubMed

Fukushima, Kikuro; Barnes, Graham R; Ito, Norie; Olley, Peter M; Warabi, Tateo

2014-07-01

Aging affects virtually all functions including sensory/motor and cognitive activities. While retinal image motion is the primary input for smooth-pursuit, its efficiency/accuracy depends on cognitive processes. Elderly subjects exhibit gain decrease during initial and steady-state pursuit, but reports on latencies are conflicting. Using a cue-dependent memory-based smooth-pursuit task, we identified important extra-retinal mechanisms for initial pursuit in young adults including cue information priming and extra-retinal drive components (Ito et al. in Exp Brain Res 229:23-35, 2013). We examined aging effects on parameters for smooth-pursuit using the same tasks. Elderly subjects were tested during three task conditions as previously described: memory-based pursuit, simple ramp-pursuit just to follow motion of a single spot, and popping-out of the correct spot during memory-based pursuit to enhance retinal image motion. Simple ramp-pursuit was used as a task that did not require visual motion working memory. To clarify aging effects, we then compared the results with the previous young subject data. During memory-based pursuit, elderly subjects exhibited normal working memory of cue information. Most movement-parameters including pursuit latencies differed significantly between memory-based pursuit and simple ramp-pursuit and also between young and elderly subjects. Popping-out of the correct spot motion was ineffective for enhancing initial pursuit in elderly subjects. However, the latency difference between memory-based pursuit and simple ramp-pursuit in individual subjects, which includes decision-making delay in the memory task, was similar between the two groups. Our results suggest that smooth-pursuit latencies depend on task conditions and that, although the extra-retinal mechanisms were functional for initial pursuit in elderly subjects, they were less effective.

The Process of Parallelizing the Conjunction Prediction Algorithm of ESA's SSA Conjunction Prediction Service Using GPGPU

NASA Astrophysics Data System (ADS)

Fehr, M.; Navarro, V.; Martin, L.; Fletcher, E.

2013-08-01

Space Situational Awareness[8] (SSA) is defined as the comprehensive knowledge, understanding and maintained awareness of the population of space objects, the space environment and existing threats and risks. As ESA's SSA Conjunction Prediction Service (CPS) requires the repetitive application of a processing algorithm against a data set of man-made space objects, it is crucial to exploit the highly parallelizable nature of this problem. Currently the CPS system makes use of OpenMP[7] for parallelization purposes using CPU threads, but only a GPU with its hundreds of cores can fully benefit from such high levels of parallelism. This paper presents the adaptation of several core algorithms[5] of the CPS for general-purpose computing on graphics processing units (GPGPU) using NVIDIAs Compute Unified Device Architecture (CUDA).

Beyond union of subspaces: Subspace pursuit on Grassmann manifold for data representation

DOE PAGES

Shen, Xinyue; Krim, Hamid; Gu, Yuantao

2016-03-01

Discovering the underlying structure of a high-dimensional signal or big data has always been a challenging topic, and has become harder to tackle especially when the observations are exposed to arbitrary sparse perturbations. Here in this paper, built on the model of a union of subspaces (UoS) with sparse outliers and inspired by a basis pursuit strategy, we exploit the fundamental structure of a Grassmann manifold, and propose a new technique of pursuing the subspaces systematically by solving a non-convex optimization problem using the alternating direction method of multipliers. This problem as noted is further complicated by non-convex constraints onmore » the Grassmann manifold, as well as the bilinearity in the penalty caused by the subspace bases and coefficients. Nevertheless, numerical experiments verify that the proposed algorithm, which provides elegant solutions to the sub-problems in each step, is able to de-couple the subspaces and pursue each of them under time-efficient parallel computation.« less

Crystal Structure Predictions Using Adaptive Genetic Algorithm and Motif Search methods

NASA Astrophysics Data System (ADS)

Ho, K. M.; Wang, C. Z.; Zhao, X.; Wu, S.; Lyu, X.; Zhu, Z.; Nguyen, M. C.; Umemoto, K.; Wentzcovitch, R. M. M.

2017-12-01

Material informatics is a new initiative which has attracted a lot of attention in recent scientific research. The basic strategy is to construct comprehensive data sets and use machine learning to solve a wide variety of problems in material design and discovery. In pursuit of this goal, a key element is the quality and completeness of the databases used. Recent advance in the development of crystal structure prediction algorithms has made it a complementary and more efficient approach to explore the structure/phase space in materials using computers. In this talk, we discuss the importance of the structural motifs and motif-networks in crystal structure predictions. Correspondingly, powerful methods are developed to improve the sampling of the low-energy structure landscape.

A parallel finite-difference method for computational aerodynamics

NASA Technical Reports Server (NTRS)

Swisshelm, Julie M.

1989-01-01

A finite-difference scheme for solving complex three-dimensional aerodynamic flow on parallel-processing supercomputers is presented. The method consists of a basic flow solver with multigrid convergence acceleration, embedded grid refinements, and a zonal equation scheme. Multitasking and vectorization have been incorporated into the algorithm. Results obtained include multiprocessed flow simulations from the Cray X-MP and Cray-2. Speedups as high as 3.3 for the two-dimensional case and 3.5 for segments of the three-dimensional case have been achieved on the Cray-2. The entire solver attained a factor of 2.7 improvement over its unitasked version on the Cray-2. The performance of the parallel algorithm on each machine is analyzed.

An efficient three-dimensional Poisson solver for SIMD high-performance-computing architectures

NASA Technical Reports Server (NTRS)

Cohl, H.

1994-01-01

We present an algorithm that solves the three-dimensional Poisson equation on a cylindrical grid. The technique uses a finite-difference scheme with operator splitting. This splitting maps the banded structure of the operator matrix into a two-dimensional set of tridiagonal matrices, which are then solved in parallel. Our algorithm couples FFT techniques with the well-known ADI (Alternating Direction Implicit) method for solving Elliptic PDE's, and the implementation is extremely well suited for a massively parallel environment like the SIMD architecture of the MasPar MP-1. Due to the highly recursive nature of our problem, we believe that our method is highly efficient, as it avoids excessive interprocessor communication.

A vectorized Lanczos eigensolver for high-performance computers

NASA Technical Reports Server (NTRS)

Bostic, Susan W.

1990-01-01

The computational strategies used to implement a Lanczos-based-method eigensolver on the latest generation of supercomputers are described. Several examples of structural vibration and buckling problems are presented that show the effects of using optimization techniques to increase the vectorization of the computational steps. The data storage and access schemes and the tools and strategies that best exploit the computer resources are presented. The method is implemented on the Convex C220, the Cray 2, and the Cray Y-MP computers. Results show that very good computation rates are achieved for the most computationally intensive steps of the Lanczos algorithm and that the Lanczos algorithm is many times faster than other methods extensively used in the past.

Time-frequency techniques in biomedical signal analysis. a tutorial review of similarities and differences.

PubMed

Wacker, M; Witte, H

2013-01-01

This review outlines the methodological fundamentals of the most frequently used non-parametric time-frequency analysis techniques in biomedicine and their main properties, as well as providing decision aids concerning their applications. The short-term Fourier transform (STFT), the Gabor transform (GT), the S-transform (ST), the continuous Morlet wavelet transform (CMWT), and the Hilbert transform (HT) are introduced as linear transforms by using a unified concept of the time-frequency representation which is based on a standardized analytic signal. The Wigner-Ville distribution (WVD) serves as an example of the 'quadratic transforms' class. The combination of WVD and GT with the matching pursuit (MP) decomposition and that of the HT with the empirical mode decomposition (EMD) are explained; these belong to the class of signal-adaptive approaches. Similarities between linear transforms are demonstrated and differences with regard to the time-frequency resolution and interference (cross) terms are presented in detail. By means of simulated signals the effects of different time-frequency resolutions of the GT, CMWT, and WVD as well as the resolution-related properties of the interference (cross) terms are shown. The method-inherent drawbacks and their consequences for the application of the time-frequency techniques are demonstrated by instantaneous amplitude, frequency and phase measures and related time-frequency representations (spectrogram, scalogram, time-frequency distribution, phase-locking maps) of measured magnetoencephalographic (MEG) signals. The appropriate selection of a method and its parameter settings will ensure readability of the time-frequency representations and reliability of results. When the time-frequency characteristics of a signal strongly correspond with the time-frequency resolution of the analysis then a method may be considered 'optimal'. The MP-based signal-adaptive approaches are preferred as these provide an appropriate time-frequency resolution for all frequencies while simultaneously reducing interference (cross) terms.

Cue-dependent memory-based smooth-pursuit in normal human subjects: importance of extra-retinal mechanisms for initial pursuit.

PubMed

Ito, Norie; Barnes, Graham R; Fukushima, Junko; Fukushima, Kikuro; Warabi, Tateo

2013-08-01

Using a cue-dependent memory-based smooth-pursuit task previously applied to monkeys, we examined the effects of visual motion-memory on smooth-pursuit eye movements in normal human subjects and compared the results with those of the trained monkeys. These results were also compared with those during simple ramp-pursuit that did not require visual motion-memory. During memory-based pursuit, all subjects exhibited virtually no errors in either pursuit-direction or go/no-go selection. Tracking eye movements of humans and monkeys were similar in the two tasks, but tracking eye movements were different between the two tasks; latencies of the pursuit and corrective saccades were prolonged, initial pursuit eye velocity and acceleration were lower, peak velocities were lower, and time to reach peak velocities lengthened during memory-based pursuit. These characteristics were similar to anticipatory pursuit initiated by extra-retinal components during the initial extinction task of Barnes and Collins (J Neurophysiol 100:1135-1146, 2008b). We suggest that the differences between the two tasks reflect differences between the contribution of extra-retinal and retinal components. This interpretation is supported by two further studies: (1) during popping out of the correct spot to enhance retinal image-motion inputs during memory-based pursuit, pursuit eye velocities approached those during simple ramp-pursuit, and (2) during initial blanking of spot motion during memory-based pursuit, pursuit components appeared in the correct direction. Our results showed the importance of extra-retinal mechanisms for initial pursuit during memory-based pursuit, which include priming effects and extra-retinal drive components. Comparison with monkey studies on neuronal responses and model analysis suggested possible pathways for the extra-retinal mechanisms.

Vestibular-Related Frontal Cortical Areas and Their Roles in Smooth-Pursuit Eye Movements: Representation of Neck Velocity, Neck-Vestibular Interactions, and Memory-Based Smooth-Pursuit

PubMed Central

Fukushima, Kikuro; Fukushima, Junko; Warabi, Tateo

2011-01-01

Smooth-pursuit eye movements are voluntary responses to small slow-moving objects in the fronto-parallel plane. They evolved in primates, who possess high-acuity foveae, to ensure clear vision about the moving target. The primate frontal cortex contains two smooth-pursuit related areas; the caudal part of the frontal eye fields (FEF) and the supplementary eye fields (SEF). Both areas receive vestibular inputs. We review functional differences between the two areas in smooth-pursuit. Most FEF pursuit neurons signal pursuit parameters such as eye velocity and gaze-velocity, and are involved in canceling the vestibulo-ocular reflex by linear addition of vestibular and smooth-pursuit responses. In contrast, gaze-velocity signals are rarely represented in the SEF. Most FEF pursuit neurons receive neck velocity inputs, while discharge modulation during pursuit and trunk-on-head rotation adds linearly. Linear addition also occurs between neck velocity responses and vestibular responses during head-on-trunk rotation in a task-dependent manner. During cross-axis pursuit–vestibular interactions, vestibular signals effectively initiate predictive pursuit eye movements. Most FEF pursuit neurons discharge during the interaction training after the onset of pursuit eye velocity, making their involvement unlikely in the initial stages of generating predictive pursuit. Comparison of representative signals in the two areas and the results of chemical inactivation during a memory-based smooth-pursuit task indicate they have different roles; the SEF plans smooth-pursuit including working memory of motion–direction, whereas the caudal FEF generates motor commands for pursuit eye movements. Patients with idiopathic Parkinson’s disease were asked to perform this task, since impaired smooth-pursuit and visual working memory deficit during cognitive tasks have been reported in most patients. Preliminary results suggested specific roles of the basal ganglia in memory-based smooth-pursuit. PMID:22174706

Forces and stress in second order Møller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach

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

Del Ben, Mauro, E-mail: mauro.delben@chem.uzh.ch; Hutter, Jürg, E-mail: hutter@chem.uzh.ch; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch

The forces acting on the atoms as well as the stress tensor are crucial ingredients for calculating the structural and dynamical properties of systems in the condensed phase. Here, these derivatives of the total energy are evaluated for the second-order Møller-Plesset perturbation energy (MP2) in the framework of the resolution of identity Gaussian and plane waves method, in a way that is fully consistent with how the total energy is computed. This consistency is non-trivial, given the different ways employed to compute Coulomb, exchange, and canonical four center integrals, and allows, for example, for energy conserving dynamics in various ensembles.more » Based on this formalism, a massively parallel algorithm has been developed for finite and extended system. The designed parallel algorithm displays, with respect to the system size, cubic, quartic, and quintic requirements, respectively, for the memory, communication, and computation. All these requirements are reduced with an increasing number of processes, and the measured performance shows excellent parallel scalability and efficiency up to thousands of nodes. Additionally, the computationally more demanding quintic scaling steps can be accelerated by employing graphics processing units (GPU’s) showing, for large systems, a gain of almost a factor two compared to the standard central processing unit-only case. In this way, the evaluation of the derivatives of the RI-MP2 energy can be performed within a few minutes for systems containing hundreds of atoms and thousands of basis functions. With good time to solution, the implementation thus opens the possibility to perform molecular dynamics (MD) simulations in various ensembles (microcanonical ensemble and isobaric-isothermal ensemble) at the MP2 level of theory. Geometry optimization, full cell relaxation, and energy conserving MD simulations have been performed for a variety of molecular crystals including NH{sub 3}, CO{sub 2}, formic acid, and benzene.« less

Multitasking the Davidson algorithm for the large, sparse eigenvalue problem

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

Umar, V.M.; Fischer, C.F.

1989-01-01

The authors report how the Davidson algorithm, developed for handling the eigenvalue problem for large and sparse matrices arising in quantum chemistry, was modified for use in atomic structure calculations. To date these calculations have used traditional eigenvalue methods, which limit the range of feasible calculations because of their excessive memory requirements and unsatisfactory performance attributed to time-consuming and costly processing of zero valued elements. The replacement of a traditional matrix eigenvalue method by the Davidson algorithm reduced these limitations. Significant speedup was found, which varied with the size of the underlying problem and its sparsity. Furthermore, the range ofmore » matrix sizes that can be manipulated efficiently was expended by more than one order or magnitude. On the CRAY X-MP the code was vectorized and the importance of gather/scatter analyzed. A parallelized version of the algorithm obtained an additional 35% reduction in execution time. Speedup due to vectorization and concurrency was also measured on the Alliant FX/8.« less

Gaze pursuit responses in nucleus reticularis tegmenti pontis of head-unrestrained macaques.

PubMed

Suzuki, David A; Betelak, Kathleen F; Yee, Robert D

2009-01-01

Eye-head gaze pursuit-related activity was recorded in rostral portions of the nucleus reticularis tegmenti pontis (rNRTP) in alert macaques. The head was unrestrained in the horizontal plane, and macaques were trained to pursue a moving target either with their head, with the eyes stationary in the orbits, or with their eyes, with their head voluntarily held stationary in space. Head-pursuit-related modulations in rNRTP activity were observed with some cells exhibiting increases in firing rate with increases in head-pursuit frequency. For many units, this head-pursuit response appeared to saturate at higher frequencies (>0.6 Hz). The response phase re:peak head-pursuit velocity formed a continuum, containing cells that could encode head-pursuit velocity and those encoding head-pursuit acceleration. The latter cells did not exhibit head position-related activity. Sensitivities were calculated with respect to peak head-pursuit velocity and averaged 1.8 spikes/s/deg/s. Of the cells that were tested for both head- and eye-pursuit-related activity, 86% exhibited responses to both head- and eye-pursuit and therefore carried a putative gaze-pursuit signal. For these gaze-pursuit units, the ratio of head to eye response sensitivities averaged approximately 1.4. Pursuit eccentricity seemed to affect head-pursuit response amplitude even in the absence of a head position response per se. The results indicated that rNRTP is a strong candidate for the source of an active head-pursuit signal that projects to the cerebellum, specifically to the target-velocity and gaze-velocity Purkinje cells that have been observed in vermal lobules VI and VII.

SDN based millimetre wave radio over fiber (RoF) network

NASA Astrophysics Data System (ADS)

Amate, Ahmed; Milosavljevic, Milos; Kourtessis, Pandelis; Robinson, Matthew; Senior, John M.

2015-01-01

This paper introduces software-defined, millimeter Wave (mm-Wave) networks with Radio over Fiber (RoF) for the delivery of gigabit connectivity required to develop fifth generation (5G) mobile. This network will enable an effective open access system allowing providers to manage and lease the infrastructure to service providers through unbundling new business models. Exploiting the inherited benefits of RoF, complete base station functionalities are centralized at the edges of the metro and aggregation network, leaving remote radio heads (RRHs) with only tunable filtering and amplification. A Software Defined Network (SDN) Central Controller (SCC) is responsible for managing the resource across several mm-Wave Radio Access Networks (RANs) providing a global view of the several network segments. This ensures flexible resource allocation for reduced overall latency and increased throughput. The SDN based mm-Wave RAN also allows for inter edge node communication. Therefore, certain packets can be routed between different RANs supported by the same edge node, reducing latency. System level simulations of the complete network have shown significant improvement of the overall throughput and SINR for wireless users by providing effective resource allocation and coordination among interfering cells. A new Coordinated Multipoint (CoMP) algorithm exploiting the benefits of the SCC global network view for reduced delay in control message exchange is presented, accounting for a minimum packet delay and limited Channel State Information (CSI) in a Long Term Evolution-Advanced (LTE-A), Cloud RAN (CRAN) configuration. The algorithm does not require detailed CSI feedback from UEs but it rather considers UE location (determined by the eNB) as the required parameter. UE throughput in the target sector is represented using a Cumulative Distributive Function (CDF). The drawn characteristics suggest that there is a significant 60% improvement in UE cell edge throughput following the application, in the coordinating cells, of the new CoMP algorithm. Results also show a further improvement of 36% in cell edge UE throughput when eNBs are centralized in a CRAN backhaul architecture. The SINR distribution of UEs in the cooperating cells has also been evaluated using a box plot. As expected, UEs with CoMP perform better demonstrating an increase of over 2 dB at the median between the transmission scenarios.

Multi-GPU parallel algorithm design and analysis for improved inversion of probability tomography with gravity gradiometry data

NASA Astrophysics Data System (ADS)

Hou, Zhenlong; Huang, Danian

2017-09-01

In this paper, we make a study on the inversion of probability tomography (IPT) with gravity gradiometry data at first. The space resolution of the results is improved by multi-tensor joint inversion, depth weighting matrix and the other methods. Aiming at solving the problems brought by the big data in the exploration, we present the parallel algorithm and the performance analysis combining Compute Unified Device Architecture (CUDA) with Open Multi-Processing (OpenMP) based on Graphics Processing Unit (GPU) accelerating. In the test of the synthetic model and real data from Vinton Dome, we get the improved results. It is also proved that the improved inversion algorithm is effective and feasible. The performance of parallel algorithm we designed is better than the other ones with CUDA. The maximum speedup could be more than 200. In the performance analysis, multi-GPU speedup and multi-GPU efficiency are applied to analyze the scalability of the multi-GPU programs. The designed parallel algorithm is demonstrated to be able to process larger scale of data and the new analysis method is practical.

Smooth-pursuit eye-movement-related neuronal activity in macaque nucleus reticularis tegmenti pontis.

PubMed

Suzuki, David A; Yamada, Tetsuto; Yee, Robert D

2003-04-01

Neuronal responses that were observed during smooth-pursuit eye movements were recorded from cells in rostral portions of the nucleus reticularis tegmenti pontis (rNRTP). The responses were categorized as smooth-pursuit eye velocity (78%) or eye acceleration (22%). A separate population of rNRTP cells encoded static eye position. The sensitivity to pursuit eye velocity averaged 0.81 spikes/s per degrees /s, whereas the average sensitivity to pursuit eye acceleration was 0.20 spikes/s per degrees /s(2). Of the eye-velocity cells with horizontal preferences for pursuit responses, 56% were optimally responsive to contraversive smooth-pursuit eye movements and 44% preferred ipsiversive pursuit. For cells with vertical pursuit preferences, 61% preferred upward pursuit and 39% preferred downward pursuit. The direction selectivity was broad with 50% of the maximal response amplitude observed for directions of smooth pursuit up to +/-85 degrees away from the optimal direction. The activities of some rNRTP cells were linearly related to eye position with an average sensitivity of 2.1 spikes/s per deg. In some cells, the magnitude of the response during smooth-pursuit eye movements was affected by the position of the eyes even though these cells did not encode eye position. On average, pursuit centered to one side of screen center elicited a response that was 73% of the response amplitude obtained with tracking centered at screen center. For pursuit centered on the opposite side, the average response was 127% of the response obtained at screen center. The results provide a neuronal rationale for the slow, pursuit-like eye movements evoked with rNRTP microstimulation and for the deficits in smooth-pursuit eye movements observed with ibotenic acid injection into rNRTP. More globally, the results support the notion of a frontal and supplementary eye field-rNRTP-cerebellum pathway involved with controlling smooth-pursuit eye movements.

A novel method for extraction of neural response from single channel cochlear implant auditory evoked potentials.

PubMed

Sinkiewicz, Daniel; Friesen, Lendra; Ghoraani, Behnaz

2017-02-01

Cortical auditory evoked potentials (CAEP) are used to evaluate cochlear implant (CI) patient auditory pathways, but the CI device produces an electrical artifact, which obscures the relevant information in the neural response. Currently there are multiple methods, which attempt to recover the neural response from the contaminated CAEP, but there is no gold standard, which can quantitatively confirm the effectiveness of these methods. To address this crucial shortcoming, we develop a wavelet-based method to quantify the amount of artifact energy in the neural response. In addition, a novel technique for extracting the neural response from single channel CAEPs is proposed. The new method uses matching pursuit (MP) based feature extraction to represent the contaminated CAEP in a feature space, and support vector machines (SVM) to classify the components as normal hearing (NH) or artifact. The NH components are combined to recover the neural response without artifact energy, as verified using the evaluation tool. Although it needs some further evaluation, this approach is a promising method of electrical artifact removal from CAEPs. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Membrane proteins structures: A review on computational modeling tools.

PubMed

Almeida, Jose G; Preto, Antonio J; Koukos, Panagiotis I; Bonvin, Alexandre M J J; Moreira, Irina S

2017-10-01

Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Model-Based Individualized Treatment of Chemotherapeutics: Bayesian Population Modeling and Dose Optimization

PubMed Central

Jayachandran, Devaraj; Laínez-Aguirre, José; Rundell, Ann; Vik, Terry; Hannemann, Robert; Reklaitis, Gintaras; Ramkrishna, Doraiswami

2015-01-01

6-Mercaptopurine (6-MP) is one of the key drugs in the treatment of many pediatric cancers, auto immune diseases and inflammatory bowel disease. 6-MP is a prodrug, converted to an active metabolite 6-thioguanine nucleotide (6-TGN) through enzymatic reaction involving thiopurine methyltransferase (TPMT). Pharmacogenomic variation observed in the TPMT enzyme produces a significant variation in drug response among the patient population. Despite 6-MP’s widespread use and observed variation in treatment response, efforts at quantitative optimization of dose regimens for individual patients are limited. In addition, research efforts devoted on pharmacogenomics to predict clinical responses are proving far from ideal. In this work, we present a Bayesian population modeling approach to develop a pharmacological model for 6-MP metabolism in humans. In the face of scarcity of data in clinical settings, a global sensitivity analysis based model reduction approach is used to minimize the parameter space. For accurate estimation of sensitive parameters, robust optimal experimental design based on D-optimality criteria was exploited. With the patient-specific model, a model predictive control algorithm is used to optimize the dose scheduling with the objective of maintaining the 6-TGN concentration within its therapeutic window. More importantly, for the first time, we show how the incorporation of information from different levels of biological chain-of response (i.e. gene expression-enzyme phenotype-drug phenotype) plays a critical role in determining the uncertainty in predicting therapeutic target. The model and the control approach can be utilized in the clinical setting to individualize 6-MP dosing based on the patient’s ability to metabolize the drug instead of the traditional standard-dose-for-all approach. PMID:26226448

A new procedure for dynamic adaption of three-dimensional unstructured grids

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Strawn, Roger

1993-01-01

A new procedure is presented for the simultaneous coarsening and refinement of three-dimensional unstructured tetrahedral meshes. This algorithm allows for localized grid adaption that is used to capture aerodynamic flow features such as vortices and shock waves in helicopter flowfield simulations. The mesh-adaption algorithm is implemented in the C programming language and uses a data structure consisting of a series of dynamically-allocated linked lists. These lists allow the mesh connectivity to be rapidly reconstructed when individual mesh points are added and/or deleted. The algorithm allows the mesh to change in an anisotropic manner in order to efficiently resolve directional flow features. The procedure has been successfully implemented on a single processor of a Cray Y-MP computer. Two sample cases are presented involving three-dimensional transonic flow. Computed results show good agreement with conventional structured-grid solutions for the Euler equations.

Impaired smooth-pursuit in Parkinson's disease: normal cue-information memory, but dysfunction of extra-retinal mechanisms for pursuit preparation and execution

PubMed Central

Fukushima, Kikuro; Ito, Norie; Barnes, Graham R; Onishi, Sachiyo; Kobayashi, Nobuyoshi; Takei, Hidetoshi; Olley, Peter M; Chiba, Susumu; Inoue, Kiyoharu; Warabi, Tateo

2015-01-01

While retinal image motion is the primary input for smooth-pursuit, its efficiency depends on cognitive processes including prediction. Reports are conflicting on impaired prediction during pursuit in Parkinson's disease. By separating two major components of prediction (image motion direction memory and movement preparation) using a memory-based pursuit task, and by comparing tracking eye movements with those during a simple ramp-pursuit task that did not require visual memory, we examined smooth-pursuit in 25 patients with Parkinson's disease and compared the results with 14 age-matched controls. In the memory-based pursuit task, cue 1 indicated visual motion direction, whereas cue 2 instructed the subjects to prepare to pursue or not to pursue. Based on the cue-information memory, subjects were asked to pursue the correct spot from two oppositely moving spots or not to pursue. In 24/25 patients, the cue-information memory was normal, but movement preparation and execution were impaired. Specifically, unlike controls, most of the patients (18/24 = 75%) lacked initial pursuit during the memory task and started tracking the correct spot by saccades. Conversely, during simple ramp-pursuit, most patients (83%) exhibited initial pursuit. Popping-out of the correct spot motion during memory-based pursuit was ineffective for enhancing initial pursuit. The results were similar irrespective of levodopa/dopamine agonist medication. Our results indicate that the extra-retinal mechanisms of most patients are dysfunctional in initiating memory-based (not simple ramp) pursuit. A dysfunctional pursuit loop between frontal eye fields (FEF) and basal ganglia may contribute to the impairment of extra-retinal mechanisms, resulting in deficient pursuit commands from the FEF to brainstem. PMID:25825544

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics

NASA Technical Reports Server (NTRS)

Farhat, Charbel; Crivelli, Luis; Roux, Francois-Xavier

1992-01-01

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallelize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet -- and perhaps will never -- be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Evaluation of water resources system vulnerability based on co-operative co-evolutionary genetic algorithm and projection pursuit model under the DPSIR framework

NASA Astrophysics Data System (ADS)

Zhao, Y.; Su, X. H.; Wang, M. H.; Li, Z. Y.; Li, E. K.; Xu, X.

2017-08-01

Water resources vulnerability control management is essential because it is related to the benign evolution of socio-economic, environmental and water resources system. Research on water resources system vulnerability is helpful to realization of water resources sustainable utilization. In this study, the DPSIR framework of driving forces-pressure-state-impact-response was adopted to construct the evaluation index system of water resources system vulnerability. Then the co-evolutionary genetic algorithm and projection pursuit were used to establish evaluation model of water resources system vulnerability. Tengzhou City in Shandong Province was selected as a study area. The system vulnerability was analyzed in terms of driving forces, pressure, state, impact and response on the basis of the projection value calculated by the model. The results show that the five components all belong to vulnerability Grade II, the vulnerability degree of impact and state were higher than other components due to the fierce imbalance in supply-demand and the unsatisfied condition of water resources utilization. It is indicated that the influence of high speed socio-economic development and the overuse of the pesticides have already disturbed the benign development of water environment to some extents. While the indexes in response represented lower vulnerability degree than the other components. The results of the evaluation model are coincident with the status of water resources system in the study area, which indicates that the model is feasible and effective.

A Two-Stage Reconstruction Processor for Human Detection in Compressive Sensing CMOS Radar.

PubMed

Tsao, Kuei-Chi; Lee, Ling; Chu, Ta-Shun; Huang, Yuan-Hao

2018-04-05

Complementary metal-oxide-semiconductor (CMOS) radar has recently gained much research attraction because small and low-power CMOS devices are very suitable for deploying sensing nodes in a low-power wireless sensing system. This study focuses on the signal processing of a wireless CMOS impulse radar system that can detect humans and objects in the home-care internet-of-things sensing system. The challenges of low-power CMOS radar systems are the weakness of human signals and the high computational complexity of the target detection algorithm. The compressive sensing-based detection algorithm can relax the computational costs by avoiding the utilization of matched filters and reducing the analog-to-digital converter bandwidth requirement. The orthogonal matching pursuit (OMP) is one of the popular signal reconstruction algorithms for compressive sensing radar; however, the complexity is still very high because the high resolution of human respiration leads to high-dimension signal reconstruction. Thus, this paper proposes a two-stage reconstruction algorithm for compressive sensing radar. The proposed algorithm not only has lower complexity than the OMP algorithm by 75% but also achieves better positioning performance than the OMP algorithm especially in noisy environments. This study also designed and implemented the algorithm by using Vertex-7 FPGA chip (Xilinx, San Jose, CA, USA). The proposed reconstruction processor can support the 256 × 13 real-time radar image display with a throughput of 28.2 frames per second.

The vestibular-related frontal cortex and its role in smooth-pursuit eye movements and vestibular-pursuit interactions

PubMed Central

Fukushima, Junko; Akao, Teppei; Kurkin, Sergei; Kaneko, Chris R.S.; Fukushima, Kikuro

2006-01-01

In order to see clearly when a target is moving slowly, primates with high acuity foveae use smooth-pursuit and vergence eye movements. The former rotates both eyes in the same direction to track target motion in frontal planes, while the latter rotates left and right eyes in opposite directions to track target motion in depth. Together, these two systems pursue targets precisely and maintain their images on the foveae of both eyes. During head movements, both systems must interact with the vestibular system to minimize slip of the retinal images. The primate frontal cortex contains two pursuit-related areas; the caudal part of the frontal eye fields (FEF) and supplementary eye fields (SEF). Evoked potential studies have demonstrated vestibular projections to both areas and pursuit neurons in both areas respond to vestibular stimulation. The majority of FEF pursuit neurons code parameters of pursuit such as pursuit and vergence eye velocity, gaze velocity, and retinal image motion for target velocity in frontal and depth planes. Moreover, vestibular inputs contribute to the predictive pursuit responses of FEF neurons. In contrast, the majority of SEF pursuit neurons do not code pursuit metrics and many SEF neurons are reported to be active in more complex tasks. These results suggest that FEF- and SEF-pursuit neurons are involved in different aspects of vestibular-pursuit interactions and that eye velocity coding of SEF pursuit neurons is specialized for the task condition. PMID:16917164

Multi-linear sparse reconstruction for SAR imaging based on higher-order SVD

NASA Astrophysics Data System (ADS)

Gao, Yu-Fei; Gui, Guan; Cong, Xun-Chao; Yang, Yue; Zou, Yan-Bin; Wan, Qun

2017-12-01

This paper focuses on the spotlight synthetic aperture radar (SAR) imaging for point scattering targets based on tensor modeling. In a real-world scenario, scatterers usually distribute in the block sparse pattern. Such a distribution feature has been scarcely utilized by the previous studies of SAR imaging. Our work takes advantage of this structure property of the target scene, constructing a multi-linear sparse reconstruction algorithm for SAR imaging. The multi-linear block sparsity is introduced into higher-order singular value decomposition (SVD) with a dictionary constructing procedure by this research. The simulation experiments for ideal point targets show the robustness of the proposed algorithm to the noise and sidelobe disturbance which always influence the imaging quality of the conventional methods. The computational resources requirement is further investigated in this paper. As a consequence of the algorithm complexity analysis, the present method possesses the superiority on resource consumption compared with the classic matching pursuit method. The imaging implementations for practical measured data also demonstrate the effectiveness of the algorithm developed in this paper.

A compressed sensing method with analytical results for lidar feature classification

NASA Astrophysics Data System (ADS)

Allen, Josef D.; Yuan, Jiangbo; Liu, Xiuwen; Rahmes, Mark

2011-04-01

We present an innovative way to autonomously classify LiDAR points into bare earth, building, vegetation, and other categories. One desirable product of LiDAR data is the automatic classification of the points in the scene. Our algorithm automatically classifies scene points using Compressed Sensing Methods via Orthogonal Matching Pursuit algorithms utilizing a generalized K-Means clustering algorithm to extract buildings and foliage from a Digital Surface Models (DSM). This technology reduces manual editing while being cost effective for large scale automated global scene modeling. Quantitative analyses are provided using Receiver Operating Characteristics (ROC) curves to show Probability of Detection and False Alarm of buildings vs. vegetation classification. Histograms are shown with sample size metrics. Our inpainting algorithms then fill the voids where buildings and vegetation were removed, utilizing Computational Fluid Dynamics (CFD) techniques and Partial Differential Equations (PDE) to create an accurate Digital Terrain Model (DTM) [6]. Inpainting preserves building height contour consistency and edge sharpness of identified inpainted regions. Qualitative results illustrate other benefits such as Terrain Inpainting's unique ability to minimize or eliminate undesirable terrain data artifacts.

Joint time-frequency analysis of EEG signals based on a phase-space interpretation of the recording process

NASA Astrophysics Data System (ADS)

Testorf, M. E.; Jobst, B. C.; Kleen, J. K.; Titiz, A.; Guillory, S.; Scott, R.; Bujarski, K. A.; Roberts, D. W.; Holmes, G. L.; Lenck-Santini, P.-P.

2012-10-01

Time-frequency transforms are used to identify events in clinical EEG data. Data are recorded as part of a study for correlating the performance of human subjects during a memory task with pathological events in the EEG, called spikes. The spectrogram and the scalogram are reviewed as tools for evaluating spike activity. A statistical evaluation of the continuous wavelet transform across trials is used to quantify phase-locking events. For simultaneously improving the time and frequency resolution, and for representing the EEG of several channels or trials in a single time-frequency plane, a multichannel matching pursuit algorithm is used. Fundamental properties of the algorithm are discussed as well as preliminary results, which were obtained with clinical EEG data.

An efficient dictionary learning algorithm and its application to 3-D medical image denoising.

PubMed

Li, Shutao; Fang, Leyuan; Yin, Haitao

2012-02-01

In this paper, we propose an efficient dictionary learning algorithm for sparse representation of given data and suggest a way to apply this algorithm to 3-D medical image denoising. Our learning approach is composed of two main parts: sparse coding and dictionary updating. On the sparse coding stage, an efficient algorithm named multiple clusters pursuit (MCP) is proposed. The MCP first applies a dictionary structuring strategy to cluster the atoms with high coherence together, and then employs a multiple-selection strategy to select several competitive atoms at each iteration. These two strategies can greatly reduce the computation complexity of the MCP and assist it to obtain better sparse solution. On the dictionary updating stage, the alternating optimization that efficiently approximates the singular value decomposition is introduced. Furthermore, in the 3-D medical image denoising application, a joint 3-D operation is proposed for taking the learning capabilities of the presented algorithm to simultaneously capture the correlations within each slice and correlations across the nearby slices, thereby obtaining better denoising results. The experiments on both synthetically generated data and real 3-D medical images demonstrate that the proposed approach has superior performance compared to some well-known methods. © 2011 IEEE

Accelerating the reconstruction of magnetic resonance imaging by three-dimensional dual-dictionary learning using CUDA.

PubMed

Jiansen Li; Jianqi Sun; Ying Song; Yanran Xu; Jun Zhao

2014-01-01

An effective way to improve the data acquisition speed of magnetic resonance imaging (MRI) is using under-sampled k-space data, and dictionary learning method can be used to maintain the reconstruction quality. Three-dimensional dictionary trains the atoms in dictionary in the form of blocks, which can utilize the spatial correlation among slices. Dual-dictionary learning method includes a low-resolution dictionary and a high-resolution dictionary, for sparse coding and image updating respectively. However, the amount of data is huge for three-dimensional reconstruction, especially when the number of slices is large. Thus, the procedure is time-consuming. In this paper, we first utilize the NVIDIA Corporation's compute unified device architecture (CUDA) programming model to design the parallel algorithms on graphics processing unit (GPU) to accelerate the reconstruction procedure. The main optimizations operate in the dictionary learning algorithm and the image updating part, such as the orthogonal matching pursuit (OMP) algorithm and the k-singular value decomposition (K-SVD) algorithm. Then we develop another version of CUDA code with algorithmic optimization. Experimental results show that more than 324 times of speedup is achieved compared with the CPU-only codes when the number of MRI slices is 24.

Perceptual control models of pursuit manual tracking demonstrate individual specificity and parameter consistency.

PubMed

Parker, Maximilian G; Tyson, Sarah F; Weightman, Andrew P; Abbott, Bruce; Emsley, Richard; Mansell, Warren

2017-11-01

Computational models that simulate individuals' movements in pursuit-tracking tasks have been used to elucidate mechanisms of human motor control. Whilst there is evidence that individuals demonstrate idiosyncratic control-tracking strategies, it remains unclear whether models can be sensitive to these idiosyncrasies. Perceptual control theory (PCT) provides a unique model architecture with an internally set reference value parameter, and can be optimized to fit an individual's tracking behavior. The current study investigated whether PCT models could show temporal stability and individual specificity over time. Twenty adults completed three blocks of 15 1-min, pursuit-tracking trials. Two blocks (training and post-training) were completed in one session and the third was completed after 1 week (follow-up). The target moved in a one-dimensional, pseudorandom pattern. PCT models were optimized to the training data using a least-mean-squares algorithm, and validated with data from post-training and follow-up. We found significant inter-individual variability (partial η 2 : .464-.697) and intra-individual consistency (Cronbach's α: .880-.976) in parameter estimates. Polynomial regression revealed that all model parameters, including the reference value parameter, contribute to simulation accuracy. Participants' tracking performances were significantly more accurately simulated by models developed from their own tracking data than by models developed from other participants' data. We conclude that PCT models can be optimized to simulate the performance of an individual and that the test-retest reliability of individual models is a necessary criterion for evaluating computational models of human performance.

Smooth-pursuit eye-movement deficits with chemical lesions in macaque nucleus reticularis tegmenti pontis.

PubMed

Suzuki, D A; Yamada, T; Hoedema, R; Yee, R D

1999-09-01

Anatomic and neuronal recordings suggest that the nucleus reticularis tegmenti pontis (NRTP) of macaques may be a major pontine component of a cortico-ponto-cerebellar pathway that subserves the control of smooth-pursuit eye movements. The existence of such a pathway was implicated by the lack of permanent pursuit impairment after bilateral lesions in the dorsolateral pontine nucleus. To provide more direct evidence that NRTP is involved with regulating smooth-pursuit eye movements, chemical lesions were made in macaque NRTP by injecting either lidocaine or ibotenic acid. Injection sites first were identified by the recording of smooth-pursuit-related modulations in neuronal activity. The resulting lesions caused significant deficits in both the maintenance and the initiation of smooth-pursuit eye movements. After lesion formation, the gain of constant-velocity, maintained smooth-pursuit eye movements decreased, on the average, by 44%. Recovery of the ability to maintain smooth-pursuit eye movements occurred over approximately 3 days when maintained pursuit gains attained normal values. The step-ramp, "Rashbass" task was used to investigate the effects of the lesions on the initiation of smooth-pursuit eye movements. Eye accelerations averaged over the initial 80 ms of pursuit initiation were determined and found to be decremented, on the average, by 48% after the administration of ibotenic acid. Impairments in the initiation and maintenance of smooth-pursuit eye movements were directional in nature. Upward pursuit seemed to be the most vulnerable and was impaired in all cases independent of lesioning agent and type of pursuit investigated. Downward smooth pursuit seemed more resistant to the effects of chemical lesions in NRTP. Impairments in horizontal tracking were observed with examples of deficits in ipsilaterally and contralaterally directed pursuit. The results provide behavioral support for the physiologically and anatomic-based conclusion that NRTP is a component of a cortico-ponto-cerebellar circuit that presumably involves the pursuit area of the frontal eye field (FEF) and projects to ocular motor-related areas of the cerebellum. This FEF-NRTP-cerebellum path would parallel a middle and medial superior temporal cerebral cortical area-dorsolateral pontine nucleus-cerebellum pathway also known to be involved with regulating smooth-pursuit eye movements.

Exact diagonalization of quantum lattice models on coprocessors

NASA Astrophysics Data System (ADS)

Siro, T.; Harju, A.

2016-10-01

We implement the Lanczos algorithm on an Intel Xeon Phi coprocessor and compare its performance to a multi-core Intel Xeon CPU and an NVIDIA graphics processor. The Xeon and the Xeon Phi are parallelized with OpenMP and the graphics processor is programmed with CUDA. The performance is evaluated by measuring the execution time of a single step in the Lanczos algorithm. We study two quantum lattice models with different particle numbers, and conclude that for small systems, the multi-core CPU is the fastest platform, while for large systems, the graphics processor is the clear winner, reaching speedups of up to 7.6 compared to the CPU. The Xeon Phi outperforms the CPU with sufficiently large particle number, reaching a speedup of 2.5.

Integrated detection, estimation, and guidance in pursuit of a maneuvering target

NASA Astrophysics Data System (ADS)

Dionne, Dany

The thesis focuses on efficient solutions of non-cooperative pursuit-evasion games with imperfect information on the state of the system. This problem is important in the context of interception of future maneuverable ballistic missiles. However, the theoretical developments are expected to find application to a broad class of hybrid control and estimation problems in industry. The validity of the results is nevertheless confirmed using a benchmark problem in the area of terminal guidance. A specific interception scenario between an incoming target with no information and a single interceptor missile with noisy measurements is analyzed in the form of a linear hybrid system subject to additive abrupt changes. The general research is aimed to achieve improved homing accuracy by integrating ideas from detection theory, state estimation theory and guidance. The results achieved can be summarized as follows. (i) Two novel maneuver detectors are developed to diagnose abrupt changes in a class of hybrid systems (detection and isolation of evasive maneuvers): a new implementation of the GLR detector and the novel adaptive- H0 GLR detector. (ii) Two novel state estimators for target tracking are derived using the novel maneuver detectors. The state estimators employ parameterized family of functions to described possible evasive maneuvers. (iii) A novel adaptive Bayesian multiple model predictor of the ballistic miss is developed which employs semi-Markov models and ideas from detection theory. (iv) A novel integrated estimation and guidance scheme that significantly improves the homing accuracy is also presented. The integrated scheme employs banks of estimators and guidance laws, a maneuver detector, and an on-line governor; the scheme is adaptive with respect to the uncertainty affecting the probability density function of the filtered state. (v) A novel discretization technique for the family of continuous-time, game theoretic, bang-bang guidance laws is introduced. The performance of the novel algorithms is assessed for the scenario of a pursuit-evasion engagement between a randomly maneuvering ballistic missile and an interceptor. Extensive Monte Carlo simulations are employed to evaluate the main statistical properties of the algorithms. (Abstract shortened by UMI.)

Method of transmission of dynamic multibit digital images from micro-unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Petrov, E. P.; Kharina, N. L.

2018-01-01

In connection with successful usage of nanotechnologies in remote sensing great attention is paid to the systems in micro-unmanned aerial vehicles (MUAVs) capable to provide high spatial resolution of dynamic multibit digital images (MDI). Limited energy resources on board the MUAV do not allow transferring a large amount of video information in the shortest possible time. It keeps back the broad development of MUAV. The search for methods to shorten the transmission time of dynamic MDIs from MUAV over the radio channel leads to the methods of MDI compression without computational operations onboard the MUAV. The known compression codecs of video information can not be applied because of the limited energy resources. In this paper we propose a method for reducing the transmission time of dynamic MDIs without computational operations and distortions onboard the MUAV. To develop the method a mathematical apparatus of the theory of conditional Markov processes with discrete arguments was used. On its basis a mathematical model for the transformation of the MDI represented by binary images (BI) in the MDI, consisting of groups of neighboring BIs (GBI) transmitted by multiphase (MP) signals, is constructed. The algorithm for multidimensional nonlinear filtering of MP signals is synthesized, realizing the statistical redundancy of the MDI to compensate for the noise stability losses caused by the use of MP signals.

Innovative Approach to Validation of Ultraviolet (UV) Reactors ...

EPA Pesticide Factsheets

Slide presentation at Conference: ASCE 7th Civil Engineering Conference in the Asian Region. USEPA in partnership with the Cadmus Group, Carollo Engineers, and other State & Industry collaborators, are evaluating new approaches for validating UV reactors to meet groundwater & surface water pathogen inactivation including viruses for low-pressure and medium-pressure UV systems. Evaluation objectives of the study: Practical approach for validating LP and MP UV reactors for virus & cryptosporidium inactivation using various test microbes, i.e., MS2, B. pumilus, AD2, T1; Apply UV dose algorithms based on theory vs empirical that predict log-I and RED as a function of the UV sensitivity of the microbe (combined variable criteria), flow, lamp-sensor output, DL-ASCFs, w/wo UVT; Assess capabilities of test microbe for predicting target pathogen, assess credibility with second test microbe vs bracketing; Evaluate UV lamp sensor technology that accounts for germicidal contributions of low-and high-wavelength UV light within MP reactors; Address approaches for propagating and assaying AD2, B. pumilus, MS2, and methods for determining low and high wavelength ASCFs using collimated beam LP & MP UV lamps; Determine & apply low and high wavelength ASCFs to predict cryptosporidium and adenovirus credit using MS2, or B. pumilus, T1 test data; Simplify Validation-Factor (VF) analysis of uncertainties/biases; Develop recommendations document from recent lessons learned applicabl

Advances in Mössbauer data analysis

NASA Astrophysics Data System (ADS)

de Souza, Paulo A.

1998-08-01

The whole Mössbauer community generates a huge amount of data in several fields of human knowledge since the first publication of Rudolf Mössbauer. Interlaboratory measurements of the same substance may result in minor differences in the Mössbauer Parameters (MP) of isomer shift, quadrupole splitting and internal magnetic field. Therefore, a conventional data bank of published MP will be of limited help in identification of substances. Data bank search for exact information became incapable to differentiate the values of Mössbauer parameters within the experimental errors (e.g., IS = 0.22 mm/s from IS = 0.23 mm/s), but physically both values may be considered the same. An artificial neural network (ANN) is able to identify a substance and its crystalline structure from measured MP, and its slight variations do not represent an obstacle for the ANN identification. A barrier to the popularization of Mössbauer spectroscopy as an analytical technique is the absence of a full automated equipment, since the analysis of a Mössbauer spectrum normally is time-consuming and requires a specialist. In this work, the fitting process of a Mössbauer spectrum was completely automated through the use of genetic algorithms and fuzzy logic. Both software and hardware systems were implemented turning out to be a fully automated Mössbauer data analysis system. The developed system will be presented.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments.

PubMed

Roy, Tapta Kanchan; Sharma, Rahul; Gerber, R Benny

2016-01-21

First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.

Stochastic, real-space, imaginary-time evaluation of third-order Feynman-Goldstone diagrams

NASA Astrophysics Data System (ADS)

Willow, Soohaeng Yoo; Hirata, So

2014-01-01

A new, alternative set of interpretation rules of Feynman-Goldstone diagrams for many-body perturbation theory is proposed, which translates diagrams into algebraic expressions suitable for direct Monte Carlo integrations. A vertex of a diagram is associated with a Coulomb interaction (rather than a two-electron integral) and an edge with the trace of a Green's function in real space and imaginary time. With these, 12 diagrams of third-order many-body perturbation (MP3) theory are converted into 20-dimensional integrals, which are then evaluated by a Monte Carlo method. It uses redundant walkers for convergence acceleration and a weight function for importance sampling in conjunction with the Metropolis algorithm. The resulting Monte Carlo MP3 method has low-rank polynomial size dependence of the operation cost, a negligible memory cost, and a naturally parallel computational kernel, while reproducing the correct correlation energies of small molecules within a few mEh after 106 Monte Carlo steps.

Impaired smooth-pursuit in Parkinson's disease: normal cue-information memory, but dysfunction of extra-retinal mechanisms for pursuit preparation and execution.

PubMed

Fukushima, Kikuro; Ito, Norie; Barnes, Graham R; Onishi, Sachiyo; Kobayashi, Nobuyoshi; Takei, Hidetoshi; Olley, Peter M; Chiba, Susumu; Inoue, Kiyoharu; Warabi, Tateo

2015-03-01

While retinal image motion is the primary input for smooth-pursuit, its efficiency depends on cognitive processes including prediction. Reports are conflicting on impaired prediction during pursuit in Parkinson's disease. By separating two major components of prediction (image motion direction memory and movement preparation) using a memory-based pursuit task, and by comparing tracking eye movements with those during a simple ramp-pursuit task that did not require visual memory, we examined smooth-pursuit in 25 patients with Parkinson's disease and compared the results with 14 age-matched controls. In the memory-based pursuit task, cue 1 indicated visual motion direction, whereas cue 2 instructed the subjects to prepare to pursue or not to pursue. Based on the cue-information memory, subjects were asked to pursue the correct spot from two oppositely moving spots or not to pursue. In 24/25 patients, the cue-information memory was normal, but movement preparation and execution were impaired. Specifically, unlike controls, most of the patients (18/24 = 75%) lacked initial pursuit during the memory task and started tracking the correct spot by saccades. Conversely, during simple ramp-pursuit, most patients (83%) exhibited initial pursuit. Popping-out of the correct spot motion during memory-based pursuit was ineffective for enhancing initial pursuit. The results were similar irrespective of levodopa/dopamine agonist medication. Our results indicate that the extra-retinal mechanisms of most patients are dysfunctional in initiating memory-based (not simple ramp) pursuit. A dysfunctional pursuit loop between frontal eye fields (FEF) and basal ganglia may contribute to the impairment of extra-retinal mechanisms, resulting in deficient pursuit commands from the FEF to brainstem. © 2015 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

40 CFR 86.145-82 - Calculations; particulate emissions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... final reported test results for the mass particulate (Mp) in grams/mile shall be computed as follows. Mp = 0.43(Mp1 + Mp2)/(Dct + Ds) + 0.57(Mp3 + Mp2)/(Dht = Ds) where: (1) Mp1 = Mass of particulate...) for determination.) (2) Mp2 = Mass of particulate determined from the “stabilized” phase of the cold...

40 CFR 86.145-82 - Calculations; particulate emissions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... final reported test results for the mass particulate (Mp) in grams/mile shall be computed as follows. Mp = 0.43(Mp1 + Mp2)/(Dct + Ds) + 0.57(Mp3 + Mp2)/(Dht = Ds) where: (1) Mp1 = Mass of particulate...) for determination.) (2) Mp2 = Mass of particulate determined from the “stabilized” phase of the cold...

Computational Performance of Intel MIC, Sandy Bridge, and GPU Architectures: Implementation of a 1D c++/OpenMP Electrostatic Particle-In-Cell Code

DTIC Science & Technology

2014-05-01

fusion, space and astrophysical plasmas, but still the general picture can be presented quite well with the fluid approach [6, 7]. The microscopic...purpose computing CPU for algorithms where processing of large blocks of data is done in parallel. The reason for that is the GPU’s highly effective...parallel structure. Most of the image and video processing computations involve heavy matrix and vector op- erations over large amounts of data and

OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms

DTIC Science & Technology

2016-05-01

composed of hyper - spectral video sequences recording the release of chemical plumes at the Dugway Proving Ground. We use the 329 frames of the...video. Each frame is a hyper - spectral image with dimension 128 × 320 × 129, where 129 is the dimension of the channel of each pixel. The total number of...j=1 . Then we use the nested for- loop to calculate the values of WXY by the formula (1). We then put the corresponding value in an array which

Two-Dimensional Signal Processing and Storage and Theory and Applications of Electromagnetic Measurements.

DTIC Science & Technology

1984-06-01

and shift varying deblurring of images. mui W AcCOan~MP ins Several of the techniques which have been investigated under this work unit are based upon...concern with the use of these iterative algorithms for deconvolution is the effect of noise on the restoration. In the absence of constraints on the...perform badly in the presence of broadband noise . An ad A hoc procedure which improves performance is to prefilter the data to enhance the signal-to

Role of retinal slip in the prediction of target motion during smooth and saccadic pursuit.

PubMed

de Brouwer, S; Missal, M; Lefèvre, P

2001-08-01

Visual tracking of moving targets requires the combination of smooth pursuit eye movements with catch-up saccades. In primates, catch-up saccades usually take place only during pursuit initiation because pursuit gain is close to unity. This contrasts with the lower and more variable gain of smooth pursuit in cats, where smooth eye movements are intermingled with catch-up saccades during steady-state pursuit. In this paper, we studied in detail the role of retinal slip in the prediction of target motion during smooth and saccadic pursuit in the cat. We found that the typical pattern of pursuit in the cat was a combination of smooth eye movements with saccades. During smooth pursuit initiation, there was a correlation between peak eye acceleration and target velocity. During pursuit maintenance, eye velocity oscillated at approximately 3 Hz around a steady-state value. The average gain of smooth pursuit was approximately 0.5. Trained cats were able to continue pursuing in the absence of a visible target, suggesting a role of the prediction of future target motion in this species. The analysis of catch-up saccades showed that the smooth-pursuit motor command is added to the saccadic command during catch-up saccades and that both position error and retinal slip are taken into account in their programming. The influence of retinal slip on catch-up saccades showed that prediction about future target motion is used in the programming of catch-up saccades. Altogether, these results suggest that pursuit systems in primates and cats are qualitatively similar, with a lower average gain in the cat and that prediction affects both saccades and smooth eye movements during pursuit.

Changing Hot Pursuit Policy: An Empirical Assessment of the Impact on Pursuit Behavior.

ERIC Educational Resources Information Center

Crew, Robert E., Jr.; And Others

1994-01-01

Using a two-year time series, the impact on law enforcement pursuit behavior of two changes in pursuit policy in a police department was studied using the ARIMA computer program and Tobit analysis. Each policy change produced significant reductions in pursuits engaged in by police officers. (SLD)

Preparation and Evaluation of a Modified Mohs Paste Mixed with Zinc Oxide 10% Topical Oil-Based Ointment.

PubMed

Tsuruta, Minako; Miyoshi, Takanori; Tsuruyama, Moeko; Matsumoto, Saori; Yamashina, Takuya; Irie, Kenji; Matsuo, Naomi; Itonaga, Tomomi; Hiraki, Yoichi; Kawamata, Yosei

2018-05-01

The skin fixative used in Mohs chemosurgery contains zinc chloride and is referred to as Mohs paste (MP). However, MP shows a remarkable change in rheological characteristics after its preparation. To prepare an MP with stable rheological characteristics, we prepared a modified MP (mMP) using zinc oxide 10% single ointment (Zn _ointment ), which is an oil-based ointment. We evaluated mMP by determining its rheological characteristics, depth of tissue fixation, and observation of the tissue surface after treatment. The viscosity of mMP increased after three months. However, the treatment-dependent viscosity of mMP could be obtained by mixing with glycerin. The viscosity and spreadability of mMP _3mth , which was three months after preparation, were 1992.0 ± 376.5 Pa·s and 2.1 ± 0.1 cm, respectively. In contrast, the viscosity and spreadability of MP mixed with glycerin were 436.9 ± 0.0 Pa·s and 2.8 ± 0.0 cm, respectively. The fixed invasion depth of MP was significantly higher than that of mMP (p < 0.05). This study of a mixture of MP and Zn _ointment showed that the viscosity of mMP could be adjusted with glycerin. Also, the tissue fixation of mMP progressed slowly compared with that of MP. This finding suggests that mMP is effective and safe for Mohs treatment.

Efference Copy Failure during Smooth Pursuit Eye Movements in Schizophrenia

PubMed Central

Dias, Elisa C.; Sanchez, Jamie L.; Schütz, Alexander C.; Javitt, Daniel C.

2013-01-01

Abnormal smooth pursuit eye movements in patients with schizophrenia are often considered a consequence of impaired motion perception. Here we used a novel motion prediction task to assess the effects of abnormal pursuit on perception in human patients. Schizophrenia patients (n = 15) and healthy controls (n = 16) judged whether a briefly presented moving target (“ball”) would hit/miss a stationary vertical line segment (“goal”). To relate prediction performance and pursuit directly, we manipulated eye movements: in half of the trials, observers smoothly tracked the ball; in the other half, they fixated on the goal. Strict quality criteria ensured that pursuit was initiated and that fixation was maintained. Controls were significantly better in trajectory prediction during pursuit than during fixation, their performance increased with presentation duration, and their pursuit gain and perceptual judgments were correlated. Such perceptual benefits during pursuit may be due to the use of extraretinal motion information estimated from an efference copy signal. With an overall lower performance in pursuit and perception, patients showed no such pursuit advantage and no correlation between pursuit gain and perception. Although patients' pursuit showed normal improvement with longer duration, their prediction performance failed to benefit from duration increases. This dissociation indicates relatively intact early visual motion processing, but a failure to use efference copy information. Impaired efference function in the sensory system may represent a general deficit in schizophrenia and thus contribute to symptoms and functional outcome impairments associated with the disorder. PMID:23864667

Efference copy failure during smooth pursuit eye movements in schizophrenia.

PubMed

Spering, Miriam; Dias, Elisa C; Sanchez, Jamie L; Schütz, Alexander C; Javitt, Daniel C

2013-07-17

Abnormal smooth pursuit eye movements in patients with schizophrenia are often considered a consequence of impaired motion perception. Here we used a novel motion prediction task to assess the effects of abnormal pursuit on perception in human patients. Schizophrenia patients (n = 15) and healthy controls (n = 16) judged whether a briefly presented moving target ("ball") would hit/miss a stationary vertical line segment ("goal"). To relate prediction performance and pursuit directly, we manipulated eye movements: in half of the trials, observers smoothly tracked the ball; in the other half, they fixated on the goal. Strict quality criteria ensured that pursuit was initiated and that fixation was maintained. Controls were significantly better in trajectory prediction during pursuit than during fixation, their performance increased with presentation duration, and their pursuit gain and perceptual judgments were correlated. Such perceptual benefits during pursuit may be due to the use of extraretinal motion information estimated from an efference copy signal. With an overall lower performance in pursuit and perception, patients showed no such pursuit advantage and no correlation between pursuit gain and perception. Although patients' pursuit showed normal improvement with longer duration, their prediction performance failed to benefit from duration increases. This dissociation indicates relatively intact early visual motion processing, but a failure to use efference copy information. Impaired efference function in the sensory system may represent a general deficit in schizophrenia and thus contribute to symptoms and functional outcome impairments associated with the disorder.

Parallelization strategies for continuum-generalized method of moments on the multi-thread systems

NASA Astrophysics Data System (ADS)

Bustamam, A.; Handhika, T.; Ernastuti, Kerami, D.

2017-07-01

Continuum-Generalized Method of Moments (C-GMM) covers the Generalized Method of Moments (GMM) shortfall which is not as efficient as Maximum Likelihood estimator by using the continuum set of moment conditions in a GMM framework. However, this computation would take a very long time since optimizing regularization parameter. Unfortunately, these calculations are processed sequentially whereas in fact all modern computers are now supported by hierarchical memory systems and hyperthreading technology, which allowing for parallel computing. This paper aims to speed up the calculation process of C-GMM by designing a parallel algorithm for C-GMM on the multi-thread systems. First, parallel regions are detected for the original C-GMM algorithm. There are two parallel regions in the original C-GMM algorithm, that are contributed significantly to the reduction of computational time: the outer-loop and the inner-loop. Furthermore, this parallel algorithm will be implemented with standard shared-memory application programming interface, i.e. Open Multi-Processing (OpenMP). The experiment shows that the outer-loop parallelization is the best strategy for any number of observations.

Gaze Pursuit Responses in Nucleus Reticularis Tegmenti Pontis of Head-Unrestrained Macaques

PubMed Central

Suzuki, David A.; Betelak, Kathleen F.; Yee, Robert D.

2009-01-01

Eye-head gaze pursuit–related activity was recorded in rostral portions of the nucleus reticularis tegmenti pontis (rNRTP) in alert macaques. The head was unrestrained in the horizontal plane, and macaques were trained to pursue a moving target either with their head, with the eyes stationary in the orbits, or with their eyes, with their head voluntarily held stationary in space. Head-pursuit–related modulations in rNRTP activity were observed with some cells exhibiting increases in firing rate with increases in head-pursuit frequency. For many units, this head-pursuit response appeared to saturate at higher frequencies (>0.6 Hz). The response phase re:peak head-pursuit velocity formed a continuum, containing cells that could encode head-pursuit velocity and those encoding head-pursuit acceleration. The latter cells did not exhibit head position–related activity. Sensitivities were calculated with respect to peak head-pursuit velocity and averaged 1.8 spikes/s/deg/s. Of the cells that were tested for both head- and eye-pursuit–related activity, 86% exhibited responses to both head- and eye-pursuit and therefore carried a putative gaze-pursuit signal. For these gaze-pursuit units, the ratio of head to eye response sensitivities averaged ∼1.4. Pursuit eccentricity seemed to affect head-pursuit response amplitude even in the absence of a head position response per se. The results indicated that rNRTP is a strong candidate for the source of an active head-pursuit signal that projects to the cerebellum, specifically to the target-velocity and gaze-velocity Purkinje cells that have been observed in vermal lobules VI and VII. PMID:18987125

A Two-Stage Reconstruction Processor for Human Detection in Compressive Sensing CMOS Radar

PubMed Central

Tsao, Kuei-Chi; Lee, Ling; Chu, Ta-Shun

2018-01-01

Complementary metal-oxide-semiconductor (CMOS) radar has recently gained much research attraction because small and low-power CMOS devices are very suitable for deploying sensing nodes in a low-power wireless sensing system. This study focuses on the signal processing of a wireless CMOS impulse radar system that can detect humans and objects in the home-care internet-of-things sensing system. The challenges of low-power CMOS radar systems are the weakness of human signals and the high computational complexity of the target detection algorithm. The compressive sensing-based detection algorithm can relax the computational costs by avoiding the utilization of matched filters and reducing the analog-to-digital converter bandwidth requirement. The orthogonal matching pursuit (OMP) is one of the popular signal reconstruction algorithms for compressive sensing radar; however, the complexity is still very high because the high resolution of human respiration leads to high-dimension signal reconstruction. Thus, this paper proposes a two-stage reconstruction algorithm for compressive sensing radar. The proposed algorithm not only has lower complexity than the OMP algorithm by 75% but also achieves better positioning performance than the OMP algorithm especially in noisy environments. This study also designed and implemented the algorithm by using Vertex-7 FPGA chip (Xilinx, San Jose, CA, USA). The proposed reconstruction processor can support the 256×13 real-time radar image display with a throughput of 28.2 frames per second. PMID:29621170

Low-order auditory Zernike moment: a novel approach for robust music identification in the compressed domain

NASA Astrophysics Data System (ADS)

Li, Wei; Xiao, Chuan; Liu, Yaduo

2013-12-01

Audio identification via fingerprint has been an active research field for years. However, most previously reported methods work on the raw audio format in spite of the fact that nowadays compressed format audio, especially MP3 music, has grown into the dominant way to store music on personal computers and/or transmit it over the Internet. It will be interesting if a compressed unknown audio fragment could be directly recognized from the database without decompressing it into the wave format at first. So far, very few algorithms run directly on the compressed domain for music information retrieval, and most of them take advantage of the modified discrete cosine transform coefficients or derived cepstrum and energy type of features. As a first attempt, we propose in this paper utilizing compressed domain auditory Zernike moment adapted from image processing techniques as the key feature to devise a novel robust audio identification algorithm. Such fingerprint exhibits strong robustness, due to its statistically stable nature, against various audio signal distortions such as recompression, noise contamination, echo adding, equalization, band-pass filtering, pitch shifting, and slight time scale modification. Experimental results show that in a music database which is composed of 21,185 MP3 songs, a 10-s long music segment is able to identify its original near-duplicate recording, with average top-5 hit rate up to 90% or above even under severe audio signal distortions.

Phylogenomic analyses data of the avian phylogenomics project.

PubMed

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Narula, Nitish; Liu, Liang; Burt, Dave; Ellegren, Hans; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas Pius; Zhang, Guojie

2015-01-01

Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

Discrimination of curvature from motion during smooth pursuit eye movements and fixation.

PubMed

Ross, Nicholas M; Goettker, Alexander; Schütz, Alexander C; Braun, Doris I; Gegenfurtner, Karl R

2017-09-01

Smooth pursuit and motion perception have mainly been investigated with stimuli moving along linear trajectories. Here we studied the quality of pursuit movements to curved motion trajectories in human observers and examined whether the pursuit responses would be sensitive enough to discriminate various degrees of curvature. In a two-interval forced-choice task subjects pursued a Gaussian blob moving along a curved trajectory and then indicated in which interval the curve was flatter. We also measured discrimination thresholds for the same curvatures during fixation. Motion curvature had some specific effects on smooth pursuit properties: trajectories with larger amounts of curvature elicited lower open-loop acceleration, lower pursuit gain, and larger catch-up saccades compared with less curved trajectories. Initially, target motion curvatures were underestimated; however, ∼300 ms after pursuit onset pursuit responses closely matched the actual curved trajectory. We calculated perceptual thresholds for curvature discrimination, which were on the order of 1.5 degrees of visual angle (°) for a 7.9° curvature standard. Oculometric sensitivity to curvature discrimination based on the whole pursuit trajectory was quite similar to perceptual performance. Oculometric thresholds based on smaller time windows were higher. Thus smooth pursuit can quite accurately follow moving targets with curved trajectories, but temporal integration over longer periods is necessary to reach perceptual thresholds for curvature discrimination. NEW & NOTEWORTHY Even though motion trajectories in the real world are frequently curved, most studies of smooth pursuit and motion perception have investigated linear motion. We show that pursuit initially underestimates the curvature of target motion and is able to reproduce the target curvature ∼300 ms after pursuit onset. Temporal integration of target motion over longer periods is necessary for pursuit to reach the level of precision found in perceptual discrimination of curvature. Copyright © 2017 the American Physiological Society.

Effects of vehicles and prodrug properties and their interactions on the delivery of 6-mercaptopurine through skin: S6-acyloxymethyl-6-mercaptopurine prodrugs.

PubMed

Waranis, R P; Sloan, K B

1988-03-01

A homologous series of S6-acyloxymethyl-6-mercaptopurine (6-mono-6-MP) and two 9-acyloxymethyl-6-mercaptopurine (9-mono-6-MP) prodrugs have been synthesized and characterized. The ability of the 6-mono-6-MP prodrugs to deliver 6-mercaptopurine (6-MP) through hairless mouse skin from isopropyl myristate (IPM) and propylene glycol (PG) has been evaluated. There was a good correlation between the log experimental permeability coefficients from the diffusion data and calculated solubility parameters of the prodrugs. Although there was no statistical difference between the rates of delivery of 6-MP by the acetyl through valeryl 6-mono-6-MP prodrugs from IPM, the butyryl and valeryl prodrugs were significantly better at delivering 6-MP from PG. For a given solubility parameter value, the 6-mono-6-MP prodrugs were less soluble in water and IPM, and more soluble in PG than the previously studied S6,9-bisacyloxymethyl-6-MP (6,9-bis-6-MP) prodrugs. On the other hand, for a given solubility parameter, the 6,9-bis-6-MP prodrugs were generally more effective at delivering 6-MP from IPM and PG. The single 9-mono-6-MP prodrug that was evaluated was much less effective at delivering 6-MP than either the 6-mono- or 6,9-bis-6-MP prodrugs. Thus, it is much less important to mask the imidazole than the thionamide functional group in 6-MP to enhance the topical delivery of 6-MP using a prodrug approach.

Modifying mesoporous silica nanoparticles to avoid the metabolic deactivation of 6-mercaptopurine and methotrexate in combinatorial chemotherapy

NASA Astrophysics Data System (ADS)

Wang, Wenjing; Fang, Chenjie; Wang, Xiaozhu; Chen, Yuxi; Wang, Yaonan; Feng, Wei; Yan, Chunhua; Zhao, Ming; Peng, Shiqi

2013-06-01

Mesoporous silica nanoparticles with amino and thiol groups (MSNSN) were prepared and covalently modified with methotrexate and 6-mercaptopurine to form 6-MP-MSNSN-MTX. In the presence of DTT, 6-MP-MSNSN-MTX gradually releases 6-MP. In rat plasma, 6-MP-MSNSN-MTX effectively inhibits the metabolic deactivation of 6-MP and MTX. 6-MP-MSNSN-MTX could be an agent for long-acting chemotherapy.Mesoporous silica nanoparticles with amino and thiol groups (MSNSN) were prepared and covalently modified with methotrexate and 6-mercaptopurine to form 6-MP-MSNSN-MTX. In the presence of DTT, 6-MP-MSNSN-MTX gradually releases 6-MP. In rat plasma, 6-MP-MSNSN-MTX effectively inhibits the metabolic deactivation of 6-MP and MTX. 6-MP-MSNSN-MTX could be an agent for long-acting chemotherapy. Electronic supplementary information (ESI) available: Experimental details of the synthesis and in vitro and in vivo assays. See DOI: 10.1039/c3nr00227f

Functions of the nucleus of the optic tract (NOT)

PubMed Central

Yakushin, Sergei B.; Gizzi, Martin; Reisine, Harvey; Raphan, Theodore; Büttner-Ennever, Jean; Cohen, Bernard

2007-01-01

Ocular pursuit in monkeys, elicited by sinusoidal and triangular (constant velocity) stimuli, was studied before and after lesions of the nucleus of the optic tract (NOT). Before NOT lesions, pursuit gains (eye velocity/target velocity) were close to unity for sinusoidal and constant-velocity stimuli at frequencies up to 1 Hz. In this range, retinal slip was less than 2°. Electrode tracks made to identify the location of NOT caused deficits in ipsilateral pursuit, which later recovered. Small electrolytic lesions of NOT reduced ipsilateral pursuit gains to below 0.5 in all tested conditions. Pursuit was better, however, when the eyes moved from the contra-lateral side toward the center (centripetal pursuit) than from the center ipsilaterally (centrifugal pursuit), although the eyes remained in close proximity to the target with saccadic tracking. Effects of lesions on ipsilateral pursuit were not permanent, and pursuit gains had generally recovered to 60–80% of baseline after about 2 weeks. One animal had bilateral NOT lesions and lost pursuit for 4 days. Thereafter, it had a centrifugal pursuit deficit that lasted for more than 2 months. Vertical pursuit and visually guided saccades were not affected by the bilateral NOT lesions in this animal. We also compared effects of these and similar NOT lesions on opto-kinetic nystagmus (OKN) and optokinetic after-nystagmus (OKAN). Correlation of functional deficits with NOT lesions from this and previous studies showed that rostral lesions of NOT in and around the pretectal oli-vary nucleus, which interrupted cortical input through the brachium of the superior colliculus (BSC), affected both smooth pursuit and OKN. In two animals in which it was tested, NOT lesions that caused a deficit in pursuit also decreased the rapid and slow components of OKN slow-phase velocity and affected OKAN. It was previously shown that slightly more caudal NOT lesions were more effective in altering gain adaptation of the angular vestibulo-ocular relfex (aVOR). The present findings suggest that cortical pathways through rostral NOT play an important role in maintenance of ipsilateral ocular pursuit. Since lesions that affected ocular pursuit had similar effects on ipsilateral OKN, processing for these two functions is probably closely linked in NOT, as it is elsewhere. PMID:10803412

Application of a sparse representation method using K-SVD to data compression of experimental ambient vibration data for SHM

NASA Astrophysics Data System (ADS)

Noh, Hae Young; Kiremidjian, Anne S.

2011-04-01

This paper introduces a data compression method using the K-SVD algorithm and its application to experimental ambient vibration data for structural health monitoring purposes. Because many damage diagnosis algorithms that use system identification require vibration measurements of multiple locations, it is necessary to transmit long threads of data. In wireless sensor networks for structural health monitoring, however, data transmission is often a major source of battery consumption. Therefore, reducing the amount of data to transmit can significantly lengthen the battery life and reduce maintenance cost. The K-SVD algorithm was originally developed in information theory for sparse signal representation. This algorithm creates an optimal over-complete set of bases, referred to as a dictionary, using singular value decomposition (SVD) and represents the data as sparse linear combinations of these bases using the orthogonal matching pursuit (OMP) algorithm. Since ambient vibration data are stationary, we can segment them and represent each segment sparsely. Then only the dictionary and the sparse vectors of the coefficients need to be transmitted wirelessly for restoration of the original data. We applied this method to ambient vibration data measured from a four-story steel moment resisting frame. The results show that the method can compress the data efficiently and restore the data with very little error.

Characterization of microparticles in patients with venous malformations of the head and neck.

PubMed

Zhu, J-Y; Ren, J-G; Zhang, W; Wang, F-Q; Cai, Y; Zhao, J-H; Chen, G; Zhao, Y-F

2017-01-01

To determine the basic biochemical features of microparticles (MP) in patients with venous malformation (VM) of the head and neck. Microparticles were isolated from peripheral venous blood of VM patients or healthy subjects and from lesional fluid of VM patients. Flow cytometry and real-time polymerase chain reaction were employed to determine the concentration, cellular origin, and RNA expression of obtained MP. A functional coagulation test was applied to measure the coagulant activity of MP. Circulating levels of total MP, platelet-derived MP, and endothelial MP were significantly elevated in VM patients and were consistently increased in VM patients with more extensive lesions. Lesional MP (MP from lesional fluid of VM) in VM patients were more abundant than circulating MP from VM patients or healthy subjects. Moreover, MP from VM patients displayed markedly distinct mRNA and microRNA expression compared with healthy subjects. Furthermore, MP from VM patients exhibited enhanced procoagulant activity, as evidenced by significantly shorter coagulation time. This study demonstrates for the first time that patients with VM have an altered MP profile and MP may be associated with VM-associated thrombogenesis. Further studies are required to explore the precise pathophysiological roles of MP in VM. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

An efficient parallel algorithm: Poststack and prestack Kirchhoff 3D depth migration using flexi-depth iterations

NASA Astrophysics Data System (ADS)

Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh

2015-07-01

This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.

Pharmacokinetic and pharmacodynamic assessment of bioavailability for two prodrugs of methylprednisolone

PubMed Central

Daley-Yates, P. T.; Gregory, A. J.; Brooks, C. D.

1997-01-01

Aims The aim of this study was to establish whether pharmacokinetic differences between two pro-drugs of methylprednisolone (MP) are likely to be of clinical significance. Methods This study was a single-blind, randomized, crossover design comparing the bioequivalence of MP released from the pro-drugs Promedrol (MP suleptanate) and Solu-Medrol (MP succinate) after a single 250 mg (MP equivalent) intramuscular injection to 20 healthy male volunteers. Bioequivalence was assessed by conventional pharmacokinetic analysis, by measuring pharmacodynamic responses plus a novel approach using pharmacokinetic/pharmacodynamic modeling. The main measure of pharmacodynamic response was whole blood histamine (WBH), a measure of basophil numbers. Results The MP Cmax was less for MP suleptanate due to a longer absorption half-life of the prodrug from the intramuscular injection site. The bioavailability of MP was equivalent when based on AUC with a MP suleptanate median 108% of the MP succinate value (90% CI: 102–114%). For Cmax the MP suleptanate median was 81% of the MP succinate value (90% CI: 75–88%). The tmax for MP from MP suleptanate was delayed relative to MP succinate. The median difference was 200% (90% non-parametric CI: 141–283%). The area under the WBH effect-time curve (AUEC) and the maximum response (Emax ) were found to be equivalent (90% CI: 98–113% and 93–109% respectively). The maximum changes in other white blood cell counts, blood glucose concentration and the parameters of the pharmacodynamic sigmoid Emax model (EC50, Emax and γ) were also not significantly different between prodrugs. Conclusions MP suleptanate is an acceptable pharmaceutical alternative to MP succinate. The use of both pharmacokinetic and pharmacodynamic response data together gives greater confidence in the conclusions compared with those based only on conventional pharmacokinetic bioequivalence analysis. PMID:9205819

[Preliminary results of noncontact temperature measuring using an infrared thermometer on the tarsus pf swine with osteoarthrosis tarsi deformans].

PubMed

Sabec, D; Lazar, P

1990-01-01

The surface temperature on tarsus of 54 performance tested boars of about 60 kg of Swedish Landrace was measured by means of infra-red thermometer at three measuring points (MP1, MP2 and MP3). MP1 was situated above the tuberculum of os metatarsale III or, as visualised in 21 slaughtered boars, above pathoanatomical alterations of osteoarthrosis tarsi deformans (OATD). MP2 was located directly medially and MP3 laterally from MP1. A clear palpatory symptom was found only with 10 boars, while all 21 slaughtered boars showed different morphological lesions of OATD. The average temperature at MP1 was 35.69 degrees C and was significantly higher (P = .01) than at MP2 (35.34) and MP3 (35.30). The temperature differences between MP1 and MP2 or MP3 were statistically reliable. Boars, who had a clear palpatory symptoms at tuberculum, showed an average temperature at MT1 of 36.27 degrees C, which was higher (P = .0114) than of those with an unclear palpatory symptom (35.64 degrees C). The results show that the temperature differences are the consequence of OATD.

Smooth pursuit eye movements and schizophrenia: literature review.

PubMed

Franco, J G; de Pablo, J; Gaviria, A M; Sepúlveda, E; Vilella, E

2014-09-01

To review the scientific literature about the relationship between impairment on smooth pursuit eye movements and schizophrenia. Narrative review that includes historical articles, reports about basic and clinical investigation, systematic reviews, and meta-analysis on the topic. Up to 80% of schizophrenic patients have impairment of smooth pursuit eye movements. Despite the diversity of test protocols, 65% of patients and controls are correctly classified by their overall performance during this pursuit. The smooth pursuit eye movements depend on the ability to anticipate the target's velocity and the visual feedback, as well as on learning and attention. The neuroanatomy implicated in smooth pursuit overlaps to some extent with certain frontal cortex zones associated with some clinical and neuropsychological characteristics of the schizophrenia, therefore some specific components of smooth pursuit anomalies could serve as biomarkers of the disease. Due to their sedative effect, antipsychotics have a deleterious effect on smooth pursuit eye movements, thus these movements cannot be used to evaluate the efficacy of the currently available treatments. Standardized evaluation of smooth pursuit eye movements on schizophrenia will allow to use specific aspects of that pursuit as biomarkers for the study of its genetics, psychopathology, or neuropsychology. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

Characterization of Rift Valley Fever Virus MP-12 Strain Encoding NSs of Punta Toro Virus or Sandfly Fever Sicilian Virus

PubMed Central

Lihoradova, Olga A.; Indran, Sabarish V.; Kalveram, Birte; Lokugamage, Nandadeva; Head, Jennifer A.; Gong, Bin; Tigabu, Bersabeh; Juelich, Terry L.; Freiberg, Alexander N.; Ikegami, Tetsuro

2013-01-01

Rift Valley fever virus (RVFV; genus Phlebovirus, family Bunyaviridae) is a mosquito-borne zoonotic pathogen which can cause hemorrhagic fever, neurological disorders or blindness in humans, and a high rate of abortion in ruminants. MP-12 strain, a live-attenuated candidate vaccine, is attenuated in the M- and L-segments, but the S-segment retains the virulent phenotype. MP-12 was manufactured as an Investigational New Drug vaccine by using MRC-5 cells and encodes a functional NSs gene, the major virulence factor of RVFV which 1) induces a shutoff of the host transcription, 2) inhibits interferon (IFN)-β promoter activation, and 3) promotes the degradation of dsRNA-dependent protein kinase (PKR). MP-12 lacks a marker for differentiation of infected from vaccinated animals (DIVA). Although MP-12 lacking NSs works for DIVA, it does not replicate efficiently in type-I IFN-competent MRC-5 cells, while the use of type-I IFN-incompetent cells may negatively affect its genetic stability. To generate modified MP-12 vaccine candidates encoding a DIVA marker, while still replicating efficiently in MRC-5 cells, we generated recombinant MP-12 encoding Punta Toro virus Adames strain NSs (rMP12-PTNSs) or Sandfly fever Sicilian virus NSs (rMP12-SFSNSs) in place of MP-12 NSs. We have demonstrated that those recombinant MP-12 viruses inhibit IFN-β mRNA synthesis, yet do not promote the degradation of PKR. The rMP12-PTNSs, but not rMP12-SFSNSs, replicated more efficiently than recombinant MP-12 lacking NSs in MRC-5 cells. Mice vaccinated with rMP12-PTNSs or rMP12-SFSNSs induced neutralizing antibodies at a level equivalent to those vaccinated with MP-12, and were efficiently protected from wild-type RVFV challenge. The rMP12-PTNSs and rMP12-SFSNSs did not induce antibodies cross-reactive to anti-RVFV NSs antibody and are therefore applicable to DIVA. Thus, rMP12-PTNSs is highly efficacious, replicates efficiently in MRC-5 cells, and encodes a DIVA marker, all of which are important for vaccine development for Rift Valley fever. PMID:23638202

Characterization of Rift Valley fever virus MP-12 strain encoding NSs of Punta Toro virus or sandfly fever Sicilian virus.

PubMed

Lihoradova, Olga A; Indran, Sabarish V; Kalveram, Birte; Lokugamage, Nandadeva; Head, Jennifer A; Gong, Bin; Tigabu, Bersabeh; Juelich, Terry L; Freiberg, Alexander N; Ikegami, Tetsuro

2013-01-01

Rift Valley fever virus (RVFV; genus Phlebovirus, family Bunyaviridae) is a mosquito-borne zoonotic pathogen which can cause hemorrhagic fever, neurological disorders or blindness in humans, and a high rate of abortion in ruminants. MP-12 strain, a live-attenuated candidate vaccine, is attenuated in the M- and L-segments, but the S-segment retains the virulent phenotype. MP-12 was manufactured as an Investigational New Drug vaccine by using MRC-5 cells and encodes a functional NSs gene, the major virulence factor of RVFV which 1) induces a shutoff of the host transcription, 2) inhibits interferon (IFN)-β promoter activation, and 3) promotes the degradation of dsRNA-dependent protein kinase (PKR). MP-12 lacks a marker for differentiation of infected from vaccinated animals (DIVA). Although MP-12 lacking NSs works for DIVA, it does not replicate efficiently in type-I IFN-competent MRC-5 cells, while the use of type-I IFN-incompetent cells may negatively affect its genetic stability. To generate modified MP-12 vaccine candidates encoding a DIVA marker, while still replicating efficiently in MRC-5 cells, we generated recombinant MP-12 encoding Punta Toro virus Adames strain NSs (rMP12-PTNSs) or Sandfly fever Sicilian virus NSs (rMP12-SFSNSs) in place of MP-12 NSs. We have demonstrated that those recombinant MP-12 viruses inhibit IFN-β mRNA synthesis, yet do not promote the degradation of PKR. The rMP12-PTNSs, but not rMP12-SFSNSs, replicated more efficiently than recombinant MP-12 lacking NSs in MRC-5 cells. Mice vaccinated with rMP12-PTNSs or rMP12-SFSNSs induced neutralizing antibodies at a level equivalent to those vaccinated with MP-12, and were efficiently protected from wild-type RVFV challenge. The rMP12-PTNSs and rMP12-SFSNSs did not induce antibodies cross-reactive to anti-RVFV NSs antibody and are therefore applicable to DIVA. Thus, rMP12-PTNSs is highly efficacious, replicates efficiently in MRC-5 cells, and encodes a DIVA marker, all of which are important for vaccine development for Rift Valley fever.

Infrared super-resolution imaging based on compressed sensing

NASA Astrophysics Data System (ADS)

Sui, Xiubao; Chen, Qian; Gu, Guohua; Shen, Xuewei

2014-03-01

The theoretical basis of traditional infrared super-resolution imaging method is Nyquist sampling theorem. The reconstruction premise is that the relative positions of the infrared objects in the low-resolution image sequences should keep fixed and the image restoration means is the inverse operation of ill-posed issues without fixed rules. The super-resolution reconstruction ability of the infrared image, algorithm's application area and stability of reconstruction algorithm are limited. To this end, we proposed super-resolution reconstruction method based on compressed sensing in this paper. In the method, we selected Toeplitz matrix as the measurement matrix and realized it by phase mask method. We researched complementary matching pursuit algorithm and selected it as the recovery algorithm. In order to adapt to the moving target and decrease imaging time, we take use of area infrared focal plane array to acquire multiple measurements at one time. Theoretically, the method breaks though Nyquist sampling theorem and can greatly improve the spatial resolution of the infrared image. The last image contrast and experiment data indicate that our method is effective in improving resolution of infrared images and is superior than some traditional super-resolution imaging method. The compressed sensing super-resolution method is expected to have a wide application prospect.

Parallel k-means++

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

A parallelization of the k-means++ seed selection algorithm on three distinct hardware platforms: GPU, multicore CPU, and multithreaded architecture. K-means++ was developed by David Arthur and Sergei Vassilvitskii in 2007 as an extension of the k-means data clustering technique. These algorithms allow people to cluster multidimensional data, by attempting to minimize the mean distance of data points within a cluster. K-means++ improved upon traditional k-means by using a more intelligent approach to selecting the initial seeds for the clustering process. While k-means++ has become a popular alternative to traditional k-means clustering, little work has been done to parallelize this technique.more » We have developed original C++ code for parallelizing the algorithm on three unique hardware architectures: GPU using NVidia's CUDA/Thrust framework, multicore CPU using OpenMP, and the Cray XMT multithreaded architecture. By parallelizing the process for these platforms, we are able to perform k-means++ clustering much more quickly than it could be done before.« less

An Automated Parallel Image Registration Technique Based on the Correlation of Wavelet Features

NASA Technical Reports Server (NTRS)

LeMoigne, Jacqueline; Campbell, William J.; Cromp, Robert F.; Zukor, Dorothy (Technical Monitor)

2001-01-01

With the increasing importance of multiple platform/multiple remote sensing missions, fast and automatic integration of digital data from disparate sources has become critical to the success of these endeavors. Our work utilizes maxima of wavelet coefficients to form the basic features of a correlation-based automatic registration algorithm. Our wavelet-based registration algorithm is tested successfully with data from the National Oceanic and Atmospheric Administration (NOAA) Advanced Very High Resolution Radiometer (AVHRR) and the Landsat/Thematic Mapper(TM), which differ by translation and/or rotation. By the choice of high-frequency wavelet features, this method is similar to an edge-based correlation method, but by exploiting the multi-resolution nature of a wavelet decomposition, our method achieves higher computational speeds for comparable accuracies. This algorithm has been implemented on a Single Instruction Multiple Data (SIMD) massively parallel computer, the MasPar MP-2, as well as on the CrayT3D, the Cray T3E and a Beowulf cluster of Pentium workstations.

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales.

PubMed

Huebsch, Nathaniel; Loskill, Peter; Mandegar, Mohammad A; Marks, Natalie C; Sheehan, Alice S; Ma, Zhen; Mathur, Anurag; Nguyen, Trieu N; Yoo, Jennie C; Judge, Luke M; Spencer, C Ian; Chukka, Anand C; Russell, Caitlin R; So, Po-Lin; Conklin, Bruce R; Healy, Kevin E

2015-05-01

Contractile motion is the simplest metric of cardiomyocyte health in vitro, but unbiased quantification is challenging. We describe a rapid automated method, requiring only standard video microscopy, to analyze the contractility of human-induced pluripotent stem cell-derived cardiomyocytes (iPS-CM). New algorithms for generating and filtering motion vectors combined with a newly developed isogenic iPSC line harboring genetically encoded calcium indicator, GCaMP6f, allow simultaneous user-independent measurement and analysis of the coupling between calcium flux and contractility. The relative performance of these algorithms, in terms of improving signal to noise, was tested. Applying these algorithms allowed analysis of contractility in iPS-CM cultured over multiple spatial scales from single cells to three-dimensional constructs. This open source software was validated with analysis of isoproterenol response in these cells, and can be applied in future studies comparing the drug responsiveness of iPS-CM cultured in different microenvironments in the context of tissue engineering.

TMVOC-MP: a parallel numerical simulator for Three-PhaseNon-isothermal Flows of Multicomponent Hydrocarbon Mixtures inporous/fractured media

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

Zhang, Keni; Yamamoto, Hajime; Pruess, Karsten

2008-02-15

TMVOC-MP is a massively parallel version of the TMVOC code (Pruess and Battistelli, 2002), a numerical simulator for three-phase non-isothermal flow of water, gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous/fractured media. TMVOC-MP was developed by introducing massively parallel computing techniques into TMVOC. It retains the physical process model of TMVOC, designed for applications to contamination problems that involve hydrocarbon fuels or organic solvents in saturated and unsaturated zones. TMVOC-MP can model contaminant behavior under 'natural' environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted sourcemore » remediation. With its sophisticated parallel computing techniques, TMVOC-MP can handle much larger problems than TMVOC, and can be much more computationally efficient. TMVOC-MP models multiphase fluid systems containing variable proportions of water, non-condensible gases (NCGs), and water-soluble volatile organic chemicals (VOCs). The user can specify the number and nature of NCGs and VOCs. There are no intrinsic limitations to the number of NCGs or VOCs, although the arrays for fluid components are currently dimensioned as 20, accommodating water plus 19 components that may be either NCGs or VOCs. Among them, NCG arrays are dimensioned as 10. The user may select NCGs from a data bank provided in the software. The currently available choices include O{sub 2}, N{sub 2}, CO{sub 2}, CH{sub 4}, ethane, ethylene, acetylene, and air (a pseudo-component treated with properties averaged from N{sub 2} and O{sub 2}). Thermophysical property data of VOCs can be selected from a chemical data bank, included with TMVOC-MP, that provides parameters for 26 commonly encountered chemicals. Users also can input their own data for other fluids. The fluid components may partition (volatilize and/or dissolve) among gas, aqueous, and NAPL phases. Any combination of the three phases may present, and phases may appear and disappear in the course of a simulation. In addition, VOCs may be adsorbed by the porous medium, and may biodegrade according to a simple half-life model. Detailed discussion of physical processes, assumptions, and fluid properties used in TMVOC-MP can be found in the TMVOC user's guide (Pruess and Battistelli, 2002). TMVOC-MP was developed based on the parallel framework of the TOUGH2-MP code (Zhang et al. 2001, Wu et al. 2002). It uses the MPI (Message Passing Forum, 1994) for parallel implementation. A domain decomposition approach is adopted for the parallelization. The code partitions a simulation domain, defined by an unstructured grid, using partitioning algorithm from the METIS software package (Karypsis and Kumar, 1998). In parallel simulation, each processor is in charge of one part of the simulation domain for assembling mass and energy balance equations, solving linear equation systems, updating thermophysical properties, and performing other local computations. The local linear-equation systems are solved in parallel by multiple processors with the Aztec linear solver package (Tuminaro et al., 1999). Although each processor solves the linearized equations of subdomains independently, the entire linear equation system is solved together by all processors collaboratively via communication between neighboring processors during each iteration. Detailed discussion of the prototype of the data-exchange scheme can be found in Elmroth et al. (2001). In addition, FORTRAN 90 features are introduced to TMVOC-MP, such as dynamic memory allocation, array operation, matrix manipulation, and replacing 'common blocks' (used in the original TMVOC) with modules. All new subroutines are written in FORTRAN 90. Program units imported from the original TMVOC remain in standard FORTRAN 77. This report provides a quick starting guide for using the TMVOC-MP program. We suppose that the users have basic knowledge of using the original TMVOC code. The users can find the detailed technical description of the physical processes modeled, and the mathematical and numerical methods in the user's guide for TMVOC (Pruess and Battistelli, 2002).« less

Embrittlement phenomenon of Ag core MP35N cable as lead conductor in medical device.

PubMed

Wang, Ling; Li, Bernie; Zhang, Haitao

2013-02-01

Ag core MP35N (Ag/MP35N) wire has been used in lead electric conductor wires in the medical device industry for many years. Recently it was noticed that the combination of silver and MP35N restricts its wire drawing process. The annealing temperature in Ag/MP35N has to be lower than the melting temperature of pure Ag (960 °C), which cannot fully anneal MP35N. The lower annealing temperature results in a highly cold worked MP35N, which significantly reduces Ag/MP35N ductility. The embrittlement phenomenon of Ag/MP35N cable was observed in tension and bending deformation. The effect of the embrittlement on the wire flex fatigue life was evaluated using a newly developed flex fatigue testing method. The Ag/MP35N cable fatigue results was analyzed with a Coffin-Manson approach and compared to the MP35N cable fatigue results. The root causes of the Ag/Mp35N embrittlement phenomenon are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature

NASA Astrophysics Data System (ADS)

Dick, Jeffrey M.; Evans, Katy A.; Holman, Alex I.; Jaraula, Caroline M. B.; Grice, Kliti

2013-12-01

Estimates of standard molal Gibbs energy (ΔGf°) and enthalpy (ΔHf°) of formation, entropy (S°), heat capacity (CP°) and volume (V°) at 25 °C and 1 bar of aqueous phenanthrene (P) and 1-, 2-, 3-, 4- and 9-methylphenanthrene (1-MP, 2-MP, 3-MP, 4-MP, 9-MP) were made by combining reported standard-state properties of the crystalline compounds, solubilities and enthalpies of phenanthrene and 1-MP, and relative Gibbs energies, enthalpies and entropies of aqueous MP isomers from published quantum chemical simulations. The calculated properties are consistent with greater stabilities of the β isomers (2-MP and 3-MP) relative to the α isomers (1-MP and 9-MP) at 25 °C. However, the metastable equilibrium values of the abundance ratios 2-MP/1-MP (MPR) and (2-MP + 3-MP)/(1-MP + 9-MP) (MPI-3) decrease with temperature, becoming <1 at ∼375-455 °C. The thermodynamic model is consistent with observations of reversals of these organic maturity parameters at high temperature in hydrothermal and metamorphic settings. Application of the model to data reported for the Paleoproterozoic Here’s Your Chance (HYC) Pb-Zn-Ag ore deposit (McArthur River, Northern Territory, Australia) indicates a likely effect of high-temperature equilibration on reported values of MPR and MPI-3, but this finding is contingent on the location within the deposit. If metastable equilibrium holds, a third aromatic maturity ratio, 1.5 × (2-MP + 3-MP)/(P + 1-MP + 9-MP) (MPI-1), can be used as a proxy for oxidation potential. Values of logaH2aq determined from data reported for HYC and for a sequence of deeply buried source rocks are indicative of more reducing conditions at a given temperature than those inferred from data reported for two sets of samples exposed to contact or regional metamorphism. These results are limiting-case scenarios for the modeled systems that do not account for effects of non-ideal mixing or kinetics, or external sources or transport of the organic matter. Nevertheless, quantifying the temperature dependence of equilibrium constants of organic reactions enables the utilization of organic maturity parameters as relative geothermometers at temperatures higher than the nominal limits of the oil window.

Illusory motion reveals velocity matching, not foveation, drives smooth pursuit of large objects

PubMed Central

Ma, Zheng; Watamaniuk, Scott N. J.; Heinen, Stephen J.

2017-01-01

When small objects move in a scene, we keep them foveated with smooth pursuit eye movements. Although large objects such as people and animals are common, it is nonetheless unknown how we pursue them since they cannot be foveated. It might be that the brain calculates an object's centroid, and then centers the eyes on it during pursuit as a foveation mechanism might. Alternatively, the brain merely matches the velocity by motion integration. We test these alternatives with an illusory motion stimulus that translates at a speed different from its retinal motion. The stimulus was a Gabor array that translated at a fixed velocity, with component Gabors that drifted with motion consistent or inconsistent with the translation. Velocity matching predicts different pursuit behaviors across drift conditions, while centroid matching predicts no difference. We also tested whether pursuit can segregate and ignore irrelevant local drifts when motion and centroid information are consistent by surrounding the Gabors with solid frames. Finally, observers judged the global translational speed of the Gabors to determine whether smooth pursuit and motion perception share mechanisms. We found that consistent Gabor motion enhanced pursuit gain while inconsistent, opposite motion diminished it, drawing the eyes away from the center of the stimulus and supporting a motion-based pursuit drive. Catch-up saccades tended to counter the position offset, directing the eyes opposite to the deviation caused by the pursuit gain change. Surrounding the Gabors with visible frames canceled both the gain increase and the compensatory saccades. Perceived speed was modulated analogous to pursuit gain. The results suggest that smooth pursuit of large stimuli depends on the magnitude of integrated retinal motion information, not its retinal location, and that the position system might be unnecessary for generating smooth velocity to large pursuit targets. PMID:29090315

Microplastic in Aquatic Ecosystems.

PubMed

Ivleva, Natalia P; Wiesheu, Alexandra C; Niessner, Reinhard

2017-02-06

The contamination of marine and freshwater ecosystems with plastic, and especially with microplastic (MP), is a global ecological problem of increasing scientific concern. This has stimulated a great deal of research on the occurrence of MP, interaction of MP with chemical pollutants, the uptake of MP by aquatic organisms, and the resulting (negative) impact of MP. Herein, we review the major issues of MP in aquatic environments, with the principal aims 1) to characterize the methods applied for MP analysis (including sampling, processing, identification and quantification), indicate the most reliable techniques, and discuss the required further improvements; 2) to estimate the abundance of MP in marine/freshwater ecosystems and clarify the problems that hamper the comparability of such results; and 3) to summarize the existing literature on the uptake of MP by living organisms. Finally, we identify knowledge gaps, suggest possible strategies to assess environmental risks arising from MP, and discuss prospects to minimize MP abundance in aquatic ecosystems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Competition between color and luminance for target selection in smooth pursuit and saccadic eye movements.

PubMed

Spering, Miriam; Montagnini, Anna; Gegenfurtner, Karl R

2008-11-24

Visual processing of color and luminance for smooth pursuit and saccadic eye movements was investigated using a target selection paradigm. In two experiments, stimuli were varied along the dimensions color and luminance, and selection of the more salient target was compared in pursuit and saccades. Initial pursuit was biased in the direction of the luminance component whereas saccades showed a relative preference for color. An early pursuit response toward luminance was often reversed to color by a later saccade. Observers' perceptual judgments of stimulus salience, obtained in two control experiments, were clearly biased toward luminance. This choice bias in perceptual data implies that the initial short-latency pursuit response agrees with perceptual judgments. In contrast, saccades, which have a longer latency than pursuit, do not seem to follow the perceptual judgment of salience but instead show a stronger relative preference for color. These substantial differences in target selection imply that target selection processes for pursuit and saccadic eye movements use distinctly different weights for color and luminance stimuli.

Tycho 2: A Proxy Application for Kinetic Transport Sweeps

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

Garrett, Charles Kristopher; Warsa, James S.

2016-09-14

Tycho 2 is a proxy application that implements discrete ordinates (SN) kinetic transport sweeps on unstructured, 3D, tetrahedral meshes. It has been designed to be small and require minimal dependencies to make collaboration and experimentation as easy as possible. Tycho 2 has been released as open source software. The software is currently in a beta release with plans for a stable release (version 1.0) before the end of the year. The code is parallelized via MPI across spatial cells and OpenMP across angles. Currently, several parallelization algorithms are implemented.

Alkylation of 6-mercaptopurine (6-MP) with N-alkyl-N-alkoxycarbonylaminomethyl chlorides: S6-(N-alkyl-N-alkoxycarbonyl)aminomethyl-6-MP prodrug structure effect on the dermal delivery of 6-MP.

PubMed

Siver, K G; Sloan, K B

1990-01-01

The S6-(N-alkyl-N-alkoxycarbonyl)aminomethyl-6-MP (6-CARB-6-MP) prodrugs 5-20 were synthesized from the reaction of 6-MP with N-alkyl-N-alkyoxycarbonylaminomethyl chlorides (4) in dimethyl sulfoxide in overall yields of 5-62%, depending on the N-alkyl and the alkoxy groups involved. The derivatives were fully characterized by spectral and microanalyses. The assignment of the substitution pattern as S6-alkyl was based on comparisons of the UV, 1H NMR and 13C NMR spectra with model compounds. A S6, 9-bis-alkyl derivative was obtained from the reaction of 2 equivalents of 4 with 6-MP but the product was unstable and decomposed on standing to a 9-alkyl derivative. The 6-CARB-6-MP prodrugs reverted to 6-MP in water by an SN1-type mechanism involving unimolecular charge separation in the transition state of the rate determining step. There was no effect of dermal enzymes on the rate of hydrolysis. The solubilities in isopropyl myristate (IPM) for all of the 6-CARB-6-MP prodrugs were significantly greater than the solubility of 6-MP in IPM but only one prodrug (5) was apparently even as soluble as 6-MP in water. Selected 6-CARB-6-MP prodrugs were examined in diffusion cell experiments. Only the N-methyl-N-methoxycarbonyl derivative 5 gave a steady-state rate of delivery of 6-MP from IPM that was significantly greater than the steady-state rate of delivery of 6-MP from 6-MP in IPM. All the other derivatives gave steady-state rates of delivery of 6-MP from IPM that were either not significantly different, or were significantly lower than the rate obtained from 6-MP in IPM. In all cases, the effect of the 6-CARB-6-MP:IPM suspensions on the permeability of the skin, as determined by the second application flux of theophylline:propylene glycol, was of the same magnitude as the effect of IPM alone.

Methylphenidate side effects in advanced cancer: a retrospective analysis.

PubMed

Lasheen, Wael; Walsh, Declan; Mahmoud, Fade; Davis, Mellar P; Rivera, Nilo; Khoshknabi, Dilara Seyidova

2010-02-01

Methylphenidate (MP) is often recommended for symptom control in advanced cancer. Little is known about its side effects in frail adults. To evaluate MP-associated symptoms or side effects (S/E). Data was collected from 2 published prospective cohort series and a phase 2 study of MP for symptom control in advanced cancer. All 3 reports had identical dosing schedules and symptom assessments. Initial MP doses were 10 mg/d (5 mg at 8 AM and at 12 noon) titrated up to a maximum of 30 mg/d. Depression, fatigue, and symptoms identified as possible MP S/E were evaluated for presence (prevalence) and for severity (using categorical scales) before MP (day 0) and on days 3, 5, and 7 thereafter. The categorical scale used was none, mild, moderate, and severe. 62 patients were enrolled. Fifty completed 7 days of MP with a median age of 69 (range 30-90) years. Thirty-five received MP 10 mg/day. Most (96%) had improvement in depression and/or fatigue. Among the 62 patients, new symptom prevalence throughout the study was agitation (16%), insomnia (16%), dry mouth (15%), nausea (10%), tremors (6%), anorexia (5%), headache (3%), palpitations (2%), and vomiting (2%). Patients could have more than 1 symptom simultaneously. Seven (11%) withdrew due to MP S/E. Some symptoms present before MP showed significant improvement during MP therapy. (1) Treatment with MP (10-20 mg/d) in advanced cancer is well tolerated. (2) S/E symptoms with MP appeared to improve spontaneously despite continued MP therapy. (3) Depression and fatigue improved at doses lower than those recommended in other clinical conditions. (4) MP improved depression and fatigue, and some secondary symptoms associated with them. Methylphenidate (MP) appears safe when used in the treatment of depression and fatigue in advanced cancer.

Thinking About Better Speech: Mental Practice for Stroke-Induced Motor Speech Impairments

PubMed Central

Page, Stephen J.; Harnish, Stacy

2012-01-01

Background Mental practice (MP) is a mind-body technique in which physical movements are cognitively rehearsed. It has shown efficacy in reducing the severity of a number of neurological impairments. Aims In the present review, we highlight recent developments in MP research, and the basis for MP use after stroke-induced motor speech disorders. Main Contribution In this review, we: (a) propose a novel conceptual model regarding the development of learned nonuse in people with motor speech impairments; (b) review the rationale and efficacy of MP for reducing the severity of stroke-induced impairments; (c) review evidence demonstrating muscular and neural activations during and following MP use; (d) review evidence showing that MP increases skill acquisition, use, and function in stroke; (e) review literature regarding neuroplasticity after stroke, including MP-induced neuroplasticity and the neural substrates underlying motor and language reacquisition; and (f) based on the above, review the rationale and clinical application of MP for stroke-induced motor speech impairments. Conclusions Support for MP use includes decades of MP neurobiological and behavioral efficacy data in a number of populations. Most recently, these data have expanded to the application of MP in neurological populations. Given increasingly demanding managed care environments, efficacious strategies that can be easily administered are needed. We also encounter clinicians who aspire to use MP, but their protocols do not contain several of the elements shown to be fundamental to effective MP implementation. Given shortfalls of some conventional aphasia and motor speech rehabilitative techniques, and uncertainty regarding optimal MP implementation, this paper introduces the neurophysiologic bases for MP, the evidence for MP use in stroke rehabilitation, and discusses its applications and considerations in patients with stroke-induced motor speech impairments. PMID:22308050

Survey of college students' MP3 listening: Habits, safety issues, attitudes, and education.

PubMed

Hoover, Alicia; Krishnamurti, Sridhar

2010-06-01

To survey listening habits and attitudes of typical college students who use MP3 players and to investigate possible safety issues related to MP3 player listening. College students who were frequent MP3 player users (N = 428) filled out a 30-item online survey. Specific areas probed by the present survey included frequency and duration of MP3 player use, MP3 player volume levels used, types of earphones used, typical environments in which MP3 player was worn, specific activities related to safety while listening to MP3 players, and attitudes toward MP3 player use. The majority of listeners wore MP3 players for less than 2 hr daily at safe volume levels. About one third of respondents reported being distracted while wearing an MP3 player, and more than one third of listeners experienced soreness in their ears after a listening session. About one third of respondents reported occasionally using their MP3 players at maximum volume levels. Listeners indicated willingness to (a) reduce volume levels, (b) decrease listening duration, and (c) buy specialized earphones to conserve their hearing. The study found concerns regarding the occasional use of MP3 players at full volume and reduced environmental awareness among some college student users.

A Hybrid MPI/OpenMP Approach for Parallel Groundwater Model Calibration on Multicore Computers

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

Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

2010-01-01

Groundwater model calibration is becoming increasingly computationally time intensive. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelism in software and hardware to reduce calibration time on multicore computers with minimal parallelization effort. At first, HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for a uranium transport model with over a hundred species involving nearly a hundred reactions, and a field scale coupled flow and transport model. In the first application, a single parallelizable loop is identified to consume over 97% of the total computational time. With a few lines of OpenMP compiler directives inserted into the code,more » the computational time reduces about ten times on a compute node with 16 cores. The performance is further improved by selectively parallelizing a few more loops. For the field scale application, parallelizable loops in 15 of the 174 subroutines in HGC5 are identified to take more than 99% of the execution time. By adding the preconditioned conjugate gradient solver and BICGSTAB, and using a coloring scheme to separate the elements, nodes, and boundary sides, the subroutines for finite element assembly, soil property update, and boundary condition application are parallelized, resulting in a speedup of about 10 on a 16-core compute node. The Levenberg-Marquardt (LM) algorithm is added into HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, compute nodes at the number of adjustable parameters (when the forward difference is used for Jacobian approximation), or twice that number (if the center difference is used), are used to reduce the calibration time from days and weeks to a few hours for the two applications. This approach can be extended to global optimization scheme and Monte Carol analysis where thousands of compute nodes can be efficiently utilized.« less

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

PubMed

Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

2016-08-09

Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance progress in elucidating transcription regulation mechanism, thus provide benefit to the genomic research community and prokaryotic genome researchers in particular.

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 10 : OR\\0x2010217 NB ramp flow & ML speed-flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ramp flow and ML speed-flow plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2....

Smooth Pursuit Eye Movements: Is Perceived Motion Necessary?

ERIC Educational Resources Information Center

Mack, Arien; And Others

1979-01-01

It has recently been shown that perceived motion, in the absence of any appropriate retinal motion, is a sufficient stimulus to generate smooth pursuit eye motions. However, three experiments show that perceived motion is not necessary for pursuit, but that retinal motion always governs pursuit. (BB)

Neurophysiology and Neuroanatomy of Smooth Pursuit in Humans

ERIC Educational Resources Information Center

Lencer, Rebekka; Trillenberg, Peter

2008-01-01

Smooth pursuit eye movements enable us to focus our eyes on moving objects by utilizing well-established mechanisms of visual motion processing, sensorimotor transformation and cognition. Novel smooth pursuit tasks and quantitative measurement techniques can help unravel the different smooth pursuit components and complex neural systems involved…

Evidence for object permanence in the smooth-pursuit eye movements of monkeys.

PubMed

Churchland, Mark M; Chou, I-Han; Lisberger, Stephen G

2003-10-01

We recorded the smooth-pursuit eye movements of monkeys in response to targets that were extinguished (blinked) for 200 ms in mid-trajectory. Eye velocity declined considerably during the target blinks, even when the blinks were completely predictable in time and space. Eye velocity declined whether blinks were presented during steady-state pursuit of a constant-velocity target, during initiation of pursuit before target velocity was reached, or during eye accelerations induced by a change in target velocity. When a physical occluder covered the trajectory of the target during blinks, creating the impression that the target moved behind it, the decline in eye velocity was reduced or abolished. If the target was occluded once the eye had reached target velocity, pursuit was only slightly poorer than normal, uninterrupted pursuit. In contrast, if the target was occluded during the initiation of pursuit, while the eye was accelerating toward target velocity, pursuit during occlusion was very different from normal pursuit. Eye velocity remained relatively stable during target occlusion, showing much less acceleration than normal pursuit and much less of a decline than was produced by a target blink. Anticipatory or predictive eye acceleration was typically observed just prior to the reappearance of the target. Computer simulations show that these results are best understood by assuming that a mechanism of eye-velocity memory remains engaged during target occlusion but is disengaged during target blinks.

MP Resulting in Autophagic Cell Death of Microglia through Zinc Changes against Spinal Cord Injury

PubMed Central

Li, Dingding; Wang, Guannan; Han, Donghe; Bi, Jing; Li, Chenyuan; Wang, Hongyu; Liu, Zhiyuan; Gao, Wei; Gao, Kai; Yao, Tianchen; Wan, Zhanghui; Li, Haihong; Mei, Xifan

2016-01-01

Methylprednisolone pulse therapy (MPPT), as a public recognized therapy of spinal cord injury (SCI), is doubted recently, and the exact mechanism of MP on SCI is unclear. This study sought to investigate the exact effect of MP on SCI. We examined the effect of MP in a model of SCI in vivo and an LPS induced model in vitro. We found that administration of MP produced an increase in the Basso, Beattie, and Bresnahan scores and motor neurons counts of injured rats. Besides the number of activated microglia was apparently reduced by MP in vivo, and Beclin-1 dependent autophagic cell death of microglia was induced by MP in LPS induced model. At the same time, MP increases cellular zinc concentration and level of ZIP8, and TPEN could revert effect of MP on autophagic cell death of microglia. Finally, we have found that MP could inhibit NF-κβ in LPS induced model. These results show that the MP could result in autophagic cell death of microglia, which mainly depends on increasing cellular labile zinc, and may be associated with inhibition of NF-κβ, and that MP can produce neuroprotective effect in SCI. PMID:27057544

Brain kinetics of methylphenidate (Ritalin) enantiomers after oral administration.

PubMed

Ding, Yu-Shin; Gatley, S John; Thanos, Panayotis K; Shea, Colleen; Garza, Victor; Xu, Youwen; Carter, Pauline; King, Payton; Warner, Don; Taintor, Nicholas B; Park, Daniel J; Pyatt, Bea; Fowler, Joanna S; Volkow, Nora D

2004-09-01

Methylphenidate (MP) (Ritalin) is widely used for the treatment of attention deficit hyperactivity disorder (ADHD). It is a chiral drug, marketed as the racemic mixture of d- and l-threo enantiomers. Our previous studies (PET and microdialysis) in humans, baboons, and rats confirm the notion that pharmacological specificity of MP resides predominantly in the d-isomer. A recent report that intraperitoneally (i.p.) administered l-threo-MP displayed potent, dose-dependent inhibition of cocaine- or apomorphine-induced locomotion in rats, raises the question of whether l-threo-MP has a similar effect when given orally. It has been speculated that l-threo-MP is poorly absorbed in humans when it is given orally because of rapid presystemic metabolism. To investigate whether l-threo-MP or its metabolites can be delivered to the brain when it is given orally, and whether l-threo-MP is pharmacologically active. PET and MicroPET studies were carried out in baboons and rats using orally delivered C-11-labeled d- and l-threo-MP ([methyl-(11)C]d-threo-MP and [methyl-(11)C]l-threo-MP). In addition, we assessed the effects of i.p. l-threo-MP on spontaneous and cocaine-stimulated locomotor activity in mice. There was a higher global uptake of carbon-11 in both baboon and rat brain for oral [(11)C]l-threo-MP than for oral [(11)C]d-threo-MP. Analysis of the chemical form of radioactivity in rat brain after [(11)C]d-threo-MP indicated mainly unchanged tracer, whereas with [(11)C]l-threo-MP, it was mainly a labeled metabolite. The possibility that this labeled metabolite might be [(11)C]methanol or [(11)C]CO(2), derived from demethylation, was excluded by ex vivo studies in rats. When l-threo-MP was given i.p. to mice at a dose of 3 mg/kg, it neither stimulated locomotor activity nor inhibited the increased locomotor activity due to cocaine administration. These results suggest that, in animal models, l-threo-MP or its metabolite(s) is (are) absorbed from the gastrointestinal tract and enters the brain after oral administration, but that l-threo-MP may not be pharmacologically active. These results are pertinent to the question of whether l-threo-MP contributes to the behavioral and side effect profile of MP during treatment of ADHD. Copyright 2004 Wiley-Liss, Inc.

Synthesis and characterization of a series of Group 4 phenoxy-thiol derivatives

DOE PAGES

Boyle, Timothy J.; Neville, Michael L.; Parkes, Marie V.

2016-02-11

In this study, a series of Group 4 phenoxy-thiols were developed from the reaction products of a series of metal tert-butoxides ([M(OBu t) 4]) with four equivalents of 4-mercaptophenol (H-4MP). The products were found by single crystal X-ray diffraction to adopt the general structure [(HOBu t)(4MP) 3M(μ-4MP)] 2 [where M = Ti (1), Zr (2), Hf (3)] from toluene and [(py) 2M(4MP)] where M = Ti (4), Zr (5) and [(py)(4MP) 3Hf(μ-4MP)] 2 (6) from pyridine (py). Varying the [Ti(OR) 4] precursors (OR = iso-propoxide (OPr i) or neo-pentoxide (ONep)) in toluene led to [(HOR)(4MP) 3Ti(μ-4MP)] 2 (OR = OPrmore » i (7), ONep (8)), which were structurally similar to 1. Lower stoichiometric reactions in toluene led to partial substitution by the 4MP ligands yielding [H][Ti(μ-4MP)(4MP)(ONep) 3] 2 (9). Independent of the stoichiometry, all of the Ti derivatives were found to be red in color, whereas the heavier congeners were colorless. Attempts to understand this phenomenon led to investigation with a series of varied –SH substituted phenols. From the reaction of H-2MP and H-3MP (2-mercaptophenol and 3-mercaptophenol, respectively), the isolated products had identical arrangements: [(ONep) 2(2MP)Ti(μ,η2-2MP)] 2 (10) and [(HOR)(3MP)M(μ-3MP)] 2 (M/OR = Ti/ONep (11); Zr/OBu t (12)) with a similar red color. Based on the simulated and observed UV–Vis spectra, it was reasoned that the color was generated due to a ligand-to-metal charge transfer for Ti that was not available for the larger congeners.« less

The feasibility study and characterization of a two-dimensional diode array in "magic phantom" for high dose rate brachytherapy quality assurance.

PubMed

Espinoza, A; Beeksma, B; Petasecca, M; Fuduli, I; Porumb, C; Cutajar, D; Corde, S; Jackson, M; Lerch, M L F; Rosenfeld, A B

2013-11-01

High dose rate (HDR) brachytherapy is a radiation treatment technique capable of delivering large dose rates to the tumor. Radiation is delivered using remote afterloaders to drive highly active sources (commonly (192)Ir with an air KERMA strength range between 20,000 and 40,000 U, where 1 U = 1 μGy m(2)/h in air) through applicators directly into the patient's prescribed region of treatment. Due to the obvious ramifications of incorrect treatment while using such an active source, it is essential that there are methods for quality assurance (QA) that can directly and accurately verify the treatment plan and the functionality of the remote afterloader. This paper describes the feasibility study of a QA system for HDR brachytherapy using a phantom based two-dimensional 11 × 11 epitaxial diode array, named "magic phantom." The HDR brachytherapy treatment plan is translated to the phantom with two rows of 10 (20 in total) HDR source flexible catheters, arranged above and below the diode array "magic plate" (MP). Four-dimensional source tracking in each catheter is based upon a developed fast iterative algorithm, utilizing the response of the diodes in close proximity to the (192)Ir source, sampled at 100 ms intervals by a fast data acquisition (DAQ) system. Using a (192)Ir source in a solid water phantom, the angular response of the developed epitaxial diodes utilized in the MP and also the variation of the MP response as a function of the source-to-detector distance (SDD) were investigated. These response data are then used by an iterative algorithm for source dwelling position determination. A measurement of the average transit speed between dwell positions was performed using the diodes and a fast DAQ. The angular response of the epitaxial diode showed a variation of 15% within 360°, with two flat regions above and below the detector face with less than 5% variation. For SDD distances of between 5 and 30 mm the relative response of the epitaxial diodes used in the MP is in good agreement (within 8%) with radial dose function measurements found within the TG-43 protocol, with SDD of up to 70 mm showing a 40% over response. A method for four-dimensional localization of the HDR source was developed, allowing the source dwell position to be derived within 0.50 mm of the expected position. An estimation of the average transit speed for varying step sizes was determined and was found to increase from (12.8 ± 0.3) up to (38.6 ± 0.4) cm/s for a step size of 2.5 and 50 mm, respectively. Our characterization of the designed QA "magic phantom" with MP in realistic HDR photon fields demonstrates the promising performance for real-time source position tracking in four dimensions and measurements of transit times. Further development of this system will allow a full suite for QA in HDR brachytherapy and analysis, and for future in vivo tracking.

High Resolution Aerospace Applications using the NASA Columbia Supercomputer

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Aftosmis, Michael J.; Berger, Marsha

2005-01-01

This paper focuses on the parallel performance of two high-performance aerodynamic simulation packages on the newly installed NASA Columbia supercomputer. These packages include both a high-fidelity, unstructured, Reynolds-averaged Navier-Stokes solver, and a fully-automated inviscid flow package for cut-cell Cartesian grids. The complementary combination of these two simulation codes enables high-fidelity characterization of aerospace vehicle design performance over the entire flight envelope through extensive parametric analysis and detailed simulation of critical regions of the flight envelope. Both packages. are industrial-level codes designed for complex geometry and incorpor.ats. CuStomized multigrid solution algorithms. The performance of these codes on Columbia is examined using both MPI and OpenMP and using both the NUMAlink and InfiniBand interconnect fabrics. Numerical results demonstrate good scalability on up to 2016 CPUs using the NUMAIink4 interconnect, with measured computational rates in the vicinity of 3 TFLOP/s, while InfiniBand showed some performance degradation at high CPU counts, particularly with multigrid. Nonetheless, the results are encouraging enough to indicate that larger test cases using combined MPI/OpenMP communication should scale well on even more processors.

A heterogeneous computing accelerated SCE-UA global optimization method using OpenMP, OpenCL, CUDA, and OpenACC.

PubMed

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Liang, Ke; Hong, Yang

2017-10-01

The shuffled complex evolution optimization developed at the University of Arizona (SCE-UA) has been successfully applied in various kinds of scientific and engineering optimization applications, such as hydrological model parameter calibration, for many years. The algorithm possesses good global optimality, convergence stability and robustness. However, benchmark and real-world applications reveal the poor computational efficiency of the SCE-UA. This research aims at the parallelization and acceleration of the SCE-UA method based on powerful heterogeneous computing technology. The parallel SCE-UA is implemented on Intel Xeon multi-core CPU (by using OpenMP and OpenCL) and NVIDIA Tesla many-core GPU (by using OpenCL, CUDA, and OpenACC). The serial and parallel SCE-UA were tested based on the Griewank benchmark function. Comparison results indicate the parallel SCE-UA significantly improves computational efficiency compared to the original serial version. The OpenCL implementation obtains the best overall acceleration results however, with the most complex source code. The parallel SCE-UA has bright prospects to be applied in real-world applications.

Real-time path planning in dynamic virtual environments using multiagent navigation graphs.

PubMed

Sud, Avneesh; Andersen, Erik; Curtis, Sean; Lin, Ming C; Manocha, Dinesh

2008-01-01

We present a novel approach for efficient path planning and navigation of multiple virtual agents in complex dynamic scenes. We introduce a new data structure, Multi-agent Navigation Graph (MaNG), which is constructed using first- and second-order Voronoi diagrams. The MaNG is used to perform route planning and proximity computations for each agent in real time. Moreover, we use the path information and proximity relationships for local dynamics computation of each agent by extending a social force model [Helbing05]. We compute the MaNG using graphics hardware and present culling techniques to accelerate the computation. We also address undersampling issues and present techniques to improve the accuracy of our algorithm. Our algorithm is used for real-time multi-agent planning in pursuit-evasion, terrain exploration and crowd simulation scenarios consisting of hundreds of moving agents, each with a distinct goal.

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

Saeed, Noha M.; El-Demerdash, Ebtehal; Abdel-Rahman, Hanaa M.

Methyl palmitate (MP) and ethyl palmitate (EP) are naturally occurring fatty acid esters reported as inflammatory cell inhibitors. In the current study, the potential anti-inflammatory activity of MP and EP was evaluated in different experimental rat models. Results showed that MP and EP caused reduction of carrageenan-induced rat paw edema in addition to diminishing prostaglandin E2 (PGE2) level in the inflammatory exudates. In lipopolysaccharide (LPS)-induced endotoxemia in rats, MP and EP reduced plasma levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). MP and EP decreased NF-κB expression in liver and lung tissues and ameliorated histopathological changes caused by LPS.more » Topical application of MP and EP reduced ear edema induced by croton oil in rats. In the same animal model, MP and EP reduced neutrophil infiltration, as indicated by decreased myeloperoxidase (MPO) activity. In conclusion, this study demonstrates the effectiveness of MP and EP in combating inflammation in several experimental models. -- Highlights: ► Efficacy of MP and EP in combating inflammation was displayed in several models. ► MP and EP reduced carrageenan-induced rat paw edema and prostaglandin E2 level. ► MP and EP decreased TNF-α and IL-6 levels in experimental endotoxemia. ► MP and EP reduced NF-κB expression and histological changes in rat liver and lung. ► MP and EP reduced croton oil-induced ear edema and neutrophil infiltration.« less

Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation.

PubMed

Bozkaya, Uğur

2018-03-15

Efficient implementations of analytic gradients for the orbital-optimized MP3 and MP2.5 and their standard versions with the density-fitting approximation, which are denoted as DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5, are presented. The DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5 methods are applied to a set of alkanes and noncovalent interaction complexes to compare the computational cost with the conventional MP3, MP2.5, OMP3, and OMP2.5. Our results demonstrate that density-fitted perturbation theory (DF-MP) methods considered substantially reduce the computational cost compared to conventional MP methods. The efficiency of our DF-MP methods arise from the reduced input/output (I/O) time and the acceleration of gradient related terms, such as computations of particle density and generalized Fock matrices (PDMs and GFM), solution of the Z-vector equation, back-transformations of PDMs and GFM, and evaluation of analytic gradients in the atomic orbital basis. Further, application results show that errors introduced by the DF approach are negligible. Mean absolute errors for bond lengths of a molecular set, with the cc-pCVQZ basis set, is 0.0001-0.0002 Å. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Methodology for the inference of gene function from phenotype data.

PubMed

Ascensao, Joao A; Dolan, Mary E; Hill, David P; Blake, Judith A

2014-12-12

Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures. We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function. We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes. We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and phenotypes that would be overlooked by a semantics-based approach. Future work will include the implementation of the described algorithms for a variety of other model organism databases, taking full advantage of the abundance of available high quality curated data.

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 8 : OR\\0x2010217 NB ML speed\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML speed-occupancy plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-21...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 7 : OR\\0x2010217 NB ML speed\\0x2010flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML speed-flow plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-217 NB,...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 9 : OR\\0x2010217 NB ML flow\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML flow occupancy plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-217...

GPU-Accelerated Hybrid Algorithm for 3D Localization of Fluorescent Emitters in Dense Clusters

NASA Astrophysics Data System (ADS)

Jung, Yoon; Barsic, Anthony; Piestun, Rafael; Fakhri, Nikta

In stochastic switching-based super-resolution imaging, a random subset of fluorescent emitters are imaged and localized for each frame to construct a single high resolution image. However, the condition of non-overlapping point spread functions (PSFs) imposes constraints on experimental parameters. Recent development in post processing methods such as dictionary-based sparse support recovery using compressive sensing has shown up to an order of magnitude higher recall rate than single emitter fitting methods. However, the computational complexity of this approach scales poorly with the grid size and requires long runtime. Here, we introduce a fast and accurate compressive sensing algorithm for localizing fluorescent emitters in high density in 3D, namely sparse support recovery using Orthogonal Matching Pursuit (OMP) and L1-Homotopy algorithm for reconstructing STORM images (SOLAR STORM). SOLAR STORM combines OMP with L1-Homotopy to reduce computational complexity, which is further accelerated by parallel implementation using GPUs. This method can be used in a variety of experimental conditions for both in vitro and live cell fluorescence imaging.

Real-time recording and classification of eye movements in an immersive virtual environment.

PubMed

Diaz, Gabriel; Cooper, Joseph; Kit, Dmitry; Hayhoe, Mary

2013-10-10

Despite the growing popularity of virtual reality environments, few laboratories are equipped to investigate eye movements within these environments. This primer is intended to reduce the time and effort required to incorporate eye-tracking equipment into a virtual reality environment. We discuss issues related to the initial startup and provide algorithms necessary for basic analysis. Algorithms are provided for the calculation of gaze angle within a virtual world using a monocular eye-tracker in a three-dimensional environment. In addition, we provide algorithms for the calculation of the angular distance between the gaze and a relevant virtual object and for the identification of fixations, saccades, and pursuit eye movements. Finally, we provide tools that temporally synchronize gaze data and the visual stimulus and enable real-time assembly of a video-based record of the experiment using the Quicktime MOV format, available at http://sourceforge.net/p/utdvrlibraries/. This record contains the visual stimulus, the gaze cursor, and associated numerical data and can be used for data exportation, visual inspection, and validation of calculated gaze movements.

Real-time recording and classification of eye movements in an immersive virtual environment

PubMed Central

Diaz, Gabriel; Cooper, Joseph; Kit, Dmitry; Hayhoe, Mary

2013-01-01

Despite the growing popularity of virtual reality environments, few laboratories are equipped to investigate eye movements within these environments. This primer is intended to reduce the time and effort required to incorporate eye-tracking equipment into a virtual reality environment. We discuss issues related to the initial startup and provide algorithms necessary for basic analysis. Algorithms are provided for the calculation of gaze angle within a virtual world using a monocular eye-tracker in a three-dimensional environment. In addition, we provide algorithms for the calculation of the angular distance between the gaze and a relevant virtual object and for the identification of fixations, saccades, and pursuit eye movements. Finally, we provide tools that temporally synchronize gaze data and the visual stimulus and enable real-time assembly of a video-based record of the experiment using the Quicktime MOV format, available at http://sourceforge.net/p/utdvrlibraries/. This record contains the visual stimulus, the gaze cursor, and associated numerical data and can be used for data exportation, visual inspection, and validation of calculated gaze movements. PMID:24113087

A prospective investigation of interpersonal influences on the pursuit of muscularity in late adolescent boys and girls.

PubMed

Shomaker, Lauren B; Furman, Wyndol

2010-04-01

This project examined whether interpersonal pressure to be muscular predicted late adolescents' pursuit of muscularity. Participants were 199 adolescents (16-19 years), mothers (n = 175), and friends (n = 159), assessed at two annual times. Pressure to be muscular was assessed with adolescents', mothers', and friends' reports of their relationships. Adolescents reported pressure from fathers and romantic partners, appearance satisfaction, disordered eating, and pursuit of muscularity. Adolescents', mothers', and friends' reports of pressure related to pursuit of muscularity at both times. Adolescents' perceptions and mothers' reports prospectively predicted pursuit of muscularity. Findings highlight the relevance of relationships to pursuit of muscularity in late adolescents.

A Prospective Investigation of Interpersonal Influences on the Pursuit of Muscularity in Late Adolescent Boys and Girls

PubMed Central

Shomaker, Lauren B.; Furman, Wyndol

2010-01-01

This project examined whether interpersonal pressure to be muscular predicted late adolescents’ pursuit of muscularity. Participants were 199 adolescents (16–19 years), mothers (n=175), and friends (n=159), assessed at two annual times. Pressure to be muscular was assessed with adolescents’, mothers’, and friends’ reports of their relationships. Adolescents reported pressure from fathers and romantic partners, appearance satisfaction, disordered eating, and pursuit of muscularity. Adolescents,’ mothers’, and friends’ reports of pressure related to pursuit of muscularity at both times. Adolescents’ perceptions and mothers’ reports prospectively predicted pursuit of muscularity. Findings highlight the relevance of relationships to pursuit of muscularity in late adolescents. PMID:20348360

Detectability of BI-RADS category 3 or higher breast lesions and reading time on mammography: comparison between 5-MP and 8-MP LCD monitors.

PubMed

Yabuuchi, Hidetake; Kawanami, Satoshi; Kamitani, Takeshi; Matsumura, Tomomi; Yamasaki, Yuzo; Morishita, Junji; Honda, Hiroshi

2017-04-01

Background Five-megapixel (MP) displays are recommended as soft copy devices for digital mammogram. An 8-MP liquid crystal display (LCD) (two 4-MP displays within one display) might offer the advantage of being able to view biplane mammography more easily than the dual planes of 5-MP LCDs. Purpose To compare detectability of Breast Imaging Reporting and Data System (BI-RADS) category 3 or higher lesions and reading time on mammography between 5- MP and 8-MP LCDs. Material and Methods The mammograms of 240 breasts of 120 patients including 60 breasts with BI-RADS category 3 or higher lesions and 180 breasts with normal or category 2 lesions were enrolled. All bilateral mammograms were displayed on bifacial 5-MP LCDs or an 8-MP LCD (two 4-MP displays within one display). Six radiologists assessed 240 breasts on each display. The observations were analyzed using receiver operating characteristic (ROC) analysis. A jack-knife method was used for statistical analysis. We employed a paired t-test to determine whether any significant differences existed in the reading time between two different displays. A P value < 0.05 was considered significant. Results The mean areas under the ROC curve obtained using 5-MP and 8-MP LCDs were 0.925 and 0.915, respectively, and there was no significant difference ( P = 0.46). There was also no significant difference in the reading time between two types of displays (57.8 min. vs. 51.5 min, P = 0.39). Conclusion The detectability of BI-RADS category 3 or higher lesions and reading time using an 8-MP LCD were comparable to those using a 5-MP LCD.

Increased endothelial microparticles and oxidative stress at extreme altitude.

PubMed

Pichler Hefti, Jacqueline; Leichtle, Alexander; Stutz, Monika; Hefti, Urs; Geiser, Thomas; Huber, Andreas R; Merz, Tobias M

2016-04-01

Hypoxia and oxidative stress affect endothelial function. Endothelial microparticles (MP) are established measures of endothelial dysfunction and influence vascular reactivity. To evaluate the effects of hypoxia and antioxidant supplementation on endothelial MP profiles, a double-blind, placebo-controlled trial, during a high altitude expedition was performed. 29 participants were randomly assigned to a treatment group (n = 14), receiving vitamin E, C, A, and N-acetylcysteine daily, and a control group (n = 15), receiving placebo. Blood samples were obtained at 490 m (baseline), 3530, 4590, and 6210 m. A sensitive tandem mass spectrometry method was used to measure 8-iso-prostaglandin F2α and hydroxyoctadecadienoic acids as markers of oxidative stress. Assessment of MP profiles including endothelial activation markers (CD62+MP and CD144+MP) and cell apoptosis markers (phosphatidylserine+MP and CD31+MP) was performed using a standardized flow cytometry-based protocol. 15 subjects reached all altitudes and were included in the final analysis. Oxidative stress increased significantly at altitude. No statistically significant changes were observed comparing baseline to altitude measurements of phosphatidylserine expressing MP (p = 0.1718) and CD31+MP (p = 0.1305). Compared to baseline measurements, a significant increase in CD62+MP (p = 0.0079) and of CD144+MP was detected (p = 0.0315) at high altitudes. No significant difference in any MP level or oxidative stress markers were found between the treatment and the control group. Hypobaric hypoxia is associated with increased oxidative stress and induces a significant increase in CD62+ and CD144+MP, whereas phosphatidylserine+MP and CD31+MP remain unchanged. This indicates that endothelial activation rather than an apoptosis is the primary factor of hypoxia induced endothelial dysfunction.

Predicting 2D target velocity cannot help 2D motion integration for smooth pursuit initiation.

PubMed

Montagnini, Anna; Spering, Miriam; Masson, Guillaume S

2006-12-01

Smooth pursuit eye movements reflect the temporal dynamics of bidimensional (2D) visual motion integration. When tracking a single, tilted line, initial pursuit direction is biased toward unidimensional (1D) edge motion signals, which are orthogonal to the line orientation. Over 200 ms, tracking direction is slowly corrected to finally match the 2D object motion during steady-state pursuit. We now show that repetition of line orientation and/or motion direction does not eliminate the transient tracking direction error nor change the time course of pursuit correction. Nonetheless, multiple successive presentations of a single orientation/direction condition elicit robust anticipatory pursuit eye movements that always go in the 2D object motion direction not the 1D edge motion direction. These results demonstrate that predictive signals about target motion cannot be used for an efficient integration of ambiguous velocity signals at pursuit initiation.

Visual motion integration for perception and pursuit

NASA Technical Reports Server (NTRS)

Stone, L. S.; Beutter, B. R.; Lorenceau, J.

2000-01-01

To examine the relationship between visual motion processing for perception and pursuit, we measured the pursuit eye-movement and perceptual responses to the same complex-motion stimuli. We show that humans can both perceive and pursue the motion of line-figure objects, even when partial occlusion makes the resulting image motion vastly different from the underlying object motion. Our results show that both perception and pursuit can perform largely accurate motion integration, i.e. the selective combination of local motion signals across the visual field to derive global object motion. Furthermore, because we manipulated perceived motion while keeping image motion identical, the observed parallel changes in perception and pursuit show that the motion signals driving steady-state pursuit and perception are linked. These findings disprove current pursuit models whose control strategy is to minimize retinal image motion, and suggest a new framework for the interplay between visual cortex and cerebellum in visuomotor control.

Visual Short-Term Memory During Smooth Pursuit Eye Movements

ERIC Educational Resources Information Center

Kerzel, Dirk; Ziegler, Nathalie E.

2005-01-01

Visual short-term memory (VSTM) was probed while observers performed smooth pursuit eye movements. Smooth pursuit keeps a moving object stabilized in the fovea. VSTM capacity for position was reduced during smooth pursuit compared with a condition with eye fixation. There was no difference between a condition in which the items were approximately…

Applying matching pursuit decomposition time-frequency processing to UGS footstep classification

NASA Astrophysics Data System (ADS)

Larsen, Brett W.; Chung, Hugh; Dominguez, Alfonso; Sciacca, Jacob; Kovvali, Narayan; Papandreou-Suppappola, Antonia; Allee, David R.

2013-06-01

The challenge of rapid footstep detection and classification in remote locations has long been an important area of study for defense technology and national security. Also, as the military seeks to create effective and disposable unattended ground sensors (UGS), computational complexity and power consumption have become essential considerations in the development of classification techniques. In response to these issues, a research project at the Flexible Display Center at Arizona State University (ASU) has experimented with footstep classification using the matching pursuit decomposition (MPD) time-frequency analysis method. The MPD provides a parsimonious signal representation by iteratively selecting matched signal components from a pre-determined dictionary. The resulting time-frequency representation of the decomposed signal provides distinctive features for different types of footsteps, including footsteps during walking or running activities. The MPD features were used in a Bayesian classification method to successfully distinguish between the different activities. The computational cost of the iterative MPD algorithm was reduced, without significant loss in performance, using a modified MPD with a dictionary consisting of signals matched to cadence temporal gait patterns obtained from real seismic measurements. The classification results were demonstrated with real data from footsteps under various conditions recorded using a low-cost seismic sensor.

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data.

PubMed

Pitonák, Michal; Neogrády, Pavel; Cerný, Jirí; Grimme, Stefan; Hobza, Pavel

2009-01-12

Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.

Directional asymmetries in human smooth pursuit eye movements.

PubMed

Ke, Sally R; Lam, Jessica; Pai, Dinesh K; Spering, Miriam

2013-06-27

Humans make smooth pursuit eye movements to bring the image of a moving object onto the fovea. Although pursuit accuracy is critical to prevent motion blur, the eye often falls behind the target. Previous studies suggest that pursuit accuracy differs between motion directions. Here, we systematically assess asymmetries in smooth pursuit. In experiment 1, binocular eye movements were recorded while observers (n = 20) tracked a small spot of light moving along one of four cardinal or diagonal axes across a featureless background. We analyzed pursuit latency, acceleration, peak velocity, gain, and catch-up saccade latency, number, and amplitude. In experiment 2 (n = 22), we examined the effects of spatial location and constrained stimulus motion within the upper or lower visual field. Pursuit was significantly faster (higher acceleration, peak velocity, and gain) and smoother (fewer and later catch-up saccades) in response to downward versus upward motion in both the upper and the lower visual fields. Pursuit was also more accurate and smoother in response to horizontal versus vertical motion. CONCLUSIONS. Our study is the first to report a consistent up-down asymmetry in human adults, regardless of visual field. Our findings suggest that pursuit asymmetries are adaptive responses to the requirements of the visual context: preferred motion directions (horizontal and downward) are more critical to our survival than nonpreferred ones.

Allocation of attention during pursuit of large objects is no different than during fixation.

PubMed

Watamaniuk, Scott N J; Heinen, Stephen J

2015-01-01

Attention allocation during pursuit of a spot is usually characterized as asymmetric with more attention placed ahead of the target than behind it. However, attention is symmetrically allocated across larger pursuit stimuli. An unresolved issue is how tightly attention is constrained on large stimuli during pursuit. Although some work shows it is tightly locked to the fovea, other work shows it is allocated flexibly. To investigate this, we had observers perform a character identification task on large pursuit stimuli composed of arrays of five, nine, or 15 characters spaced between 0.6° and 4.0° apart. Initially, the characters were identical, but at a random time, they all changed briefly, rendering one of them unique. Observers identified the unique character. Consistent with previous literature, attention appeared narrow and symmetric around the pursuit target for tightly spaced (0.6°) characters. Increasing spacing dramatically expanded the attention scope, presumably by mitigating crowding. However, when we controlled for crowding, performance was limited by set size, suffering more for eccentric targets. Interestingly, the same limitations on attention allocation were observed with stationary and pursued stimuli-evidence that attention operates similarly during fixation and pursuit of a stimulus that extends into the periphery. The results suggest that attention is flexibly allocated during pursuit, but performance is limited by crowding and set size. In addition, performing the identification task did not hurt pursuit performance, further evidence that pursuit of large stimuli is relatively inattentive.

α-Methylprednisolone conjugated cyclodextrin polymer-based nanoparticles for rheumatoid arthritis therapy

PubMed Central

Hwang, Jungyeon; Rodgers, Kathleen; Oliver, James C; Schluep, Thomas

2008-01-01

A glycinate derivative of α-methylprednisolone (MP) was prepared and conjugated to a linear cyclodextrin polymer (CDP) with a loading of 12.4% w/w. The polymer conjugate (CDP-MP) self-assembled into nanoparticles with a size of 27 nm. Release kinetics of MP from the polymer conjugate showed a half-life (t1/2) of 50 h in phosphate buffer solution (PBS) and 19 h in human plasma. In vitro, the proliferation of human lymphocytes was suppressed to a similar extent but with a delayed effect when CDP-MP was compared with free MP. In vivo, CDP-MP was administered intravenously to mice with collagen-induced arthritis and compared with free MP. CDP-MP was administered weekly for six weeks (0.07, 0.7, and 7 mg/kg/week) and MP was administered daily for six weeks (0.01, 0.1, and 1 mg/kg/day). Body weight changes were minimal in all animals. After 28 days, a significant decrease in arthritis score was observed in animals treated weekly with an intermediate or high dose of CDP-MP. Additionally, dorsoplantar swelling was reduced to baseline in animals treated with CDP-MP at the intermediate and high dose level. Histological evaluation showed a reduction in synovitis, pannus formation and disruption of architecture at the highest dose level of CDP-MP. MP administered daily at equivalent cumulative doses showed minimal efficacy in this model. This study demonstrates that conjugation of MP to a cyclodextrin-polymer may improve its efficacy, leading to lower doses and less frequent administration for a safer and more convenient management of rheumatoid arthritis. PMID:18990945

77 FR 55268 - Union Pacific Railroad Company-Acquisition and Operation Exemption-San Pedro Railroad Operating...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-07

....15 at Curtiss, Ariz., and MP 1041.32 near Curtiss (Parcel 1), and between MP 1071.16 and MP 1084 at... operating easement, in a line segment between MP 1041.32 and MP 1071.16 (Parcel 3),\\1\\ whose underlying...

Heroin - Multiple Languages

MedlinePlus

... Spanish) PDF The basics - Opioids, part 1 - English MP3 The basics - Opioids, part 1 - español (Spanish) MP3 The basics - Opioids, part 1 - English MP4 The ... Spanish) PDF Heroin - Opioid addiction, part 7 - English MP3 Heroin - Opioid addiction, part 7 - español (Spanish) MP3 ...

Mycelial development preceding basidioma formation in Moniliophthora perniciosa is associated to chitin, sugar and nutrient metabolism alterations involving autophagy.

PubMed

Gomes, Dayane Santos; Lopes, Maíza Alves; Menezes, Sara Pereira; Ribeiro, Lidiane Figueredo; Dias, Cristiano Villela; Andrade, Bruno Silva; de Jesus, Raildo Mota; Pires, Acassia Benjamin Leal; Goes-Neto, Aristóteles; Micheli, Fabienne

2016-01-01

We identified and characterized two chitinases, named MpCHIT1 and MpCHIT2, from the fungus Moniliophthora perniciosa - the etiologic agent of witches' broom disease in cacao tree (Theobroma cacao L.) - during its development, mainly in the mycelia phases preceding the basidioma formation. The expression of MpCHIT1 and MpCHIT2, together with MpCHS and MpATG8 (chitin synthase and autophagy genes, respectively), was analyzed during the M. perniciosa growth and development on bran-based solid medium as well as in liquid medium containing H2O2 or rapamycin (oxidative and nutritional related-autophagy stress agents, respectively). In order to link the expression of chitin metabolism-related genes to nutritional composition influencing fungus development, we also quantified total and reduced sugars, as well as macro- and micronutrients in the bran-based solid medium. The expression analysis showed that the MpCHS expression increased through mycelial development and then decreased in the primordium and basidioma phases, while the expression of MpCHIT1 and MpCHIT2 was higher in basidioma and primordium phases, respectively. Moreover, the expression pattern of MpCHIT1 and MpCHIT2 is distinct, the second correlated with the MpATG8 expression pattern and possibly with autophagy process, while the first may be related to the basidioma formation. The quantification of total and reduced sugars, as well as macro- and micronutrients supported the idea that the cell wall restructuration due to MpCHS, MpCHIT1 and MpCHIT2 is related to stress and fungal nutrient reallocation, allowing the formation and development of the basidioma. Experiments involving M. perniciosa growth on liquid medium containing H2O2 or rapamycin showed that MpCHIT1 and MpCHIT2 were over-expressed in response to oxidative but also to nutritional related-autophagy stresses. Interestingly, the expression level of MpCHS, MpCHIT1 and MpCHIT2 in presence of rapamycin is similar to the one observed in the primordium and basidioma from bran-based solid medium. The analysis of the overall data allowed designing a general scheme of chitin metabolism and autophagy during M. perniciosa development, focusing on the mycelium phases as crucial and environmentally influenced steps preceding the primordium and basidioma formation. These data support the idea that the nutritional environment of M. perniciosa influences its development and life cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

Responses of Purkinje cells in the oculomotor vermis of monkeys during smooth pursuit eye movements and saccades: comparison with floccular complex.

PubMed

Raghavan, Ramanujan T; Lisberger, Stephen G

2017-08-01

We recorded the responses of Purkinje cells in the oculomotor vermis during smooth pursuit and saccadic eye movements. Our goal was to characterize the responses in the vermis using approaches that would allow direct comparisons with responses of Purkinje cells in another cerebellar area for pursuit, the floccular complex. Simple-spike firing of vermis Purkinje cells is direction selective during both pursuit and saccades, but the preferred directions are sufficiently independent so that downstream circuits could decode signals to drive pursuit and saccades separately. Complex spikes also were direction selective during pursuit, and almost all Purkinje cells showed a peak in the probability of complex spikes during the initiation of pursuit in at least one direction. Unlike the floccular complex, the preferred directions for simple spikes and complex spikes were not opposite. The kinematics of smooth eye movement described the simple-spike responses of vermis Purkinje cells well. Sensitivities were similar to those in the floccular complex for eye position and considerably lower for eye velocity and acceleration. The kinematic relations were quite different for saccades vs. pursuit, supporting the idea that the contributions from the vermis to each kind of movement could contribute independently in downstream areas. Finally, neither the complex-spike nor the simple-spike responses of vermis Purkinje cells were appropriate to support direction learning in pursuit. Complex spikes were not triggered reliably by an instructive change in target direction; simple-spike responses showed very small amounts of learning. We conclude that the vermis plays a different role in pursuit eye movements compared with the floccular complex. NEW & NOTEWORTHY The midline oculomotor cerebellum plays a different role in smooth pursuit eye movements compared with the lateral, floccular complex and appears to be much less involved in direction learning in pursuit. The output from the oculomotor vermis during pursuit lies along a null-axis for saccades and vice versa. Thus the vermis can play independent roles in the two kinds of eye movement. Copyright © 2017 the American Physiological Society.

Eigensolution of finite element problems in a completely connected parallel architecture

NASA Technical Reports Server (NTRS)

Akl, Fred A.; Morel, Michael R.

1989-01-01

A parallel algorithm for the solution of the generalized eigenproblem in linear elastic finite element analysis, (K)(phi)=(M)(phi)(omega), where (K) and (M) are of order N, and (omega) is of order q is presented. The parallel algorithm is based on a completely connected parallel architecture in which each processor is allowed to communicate with all other processors. The algorithm has been successfully implemented on a tightly coupled multiple-instruction-multiple-data (MIMD) parallel processing computer, Cray X-MP. A finite element model is divided into m domains each of which is assumed to process n elements. Each domain is then assigned to a processor, or to a logical processor (task) if the number of domains exceeds the number of physical processors. The macro-tasking library routines are used in mapping each domain to a user task. Computational speed-up and efficiency are used to determine the effectiveness of the algorithm. The effect of the number of domains, the number of degrees-of-freedom located along the global fronts and the dimension of the subspace on the performance of the algorithm are investigated. For a 64-element rectangular plate, speed-ups of 1.86, 3.13, 3.18 and 3.61 are achieved on two, four, six and eight processors, respectively.

Prescription Drug Abuse - Multiple Languages

MedlinePlus

... Spanish) PDF The basics - Opioids, part 1 - English MP3 The basics - Opioids, part 1 - español (Spanish) MP3 The basics - Opioids, part 1 - English MP4 The ... español (Spanish) PDF Pain - Opioids, part 2 - English MP3 Pain - Opioids, part 2 - español (Spanish) MP3 Pain - ...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 2 : I\\0x2010 205 NB speed flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various speed flow plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2; I-2...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 4 : I\\0x2010205 NB flow\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various flow-occupancy plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2;...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 3 : I\\0x2010205 NB speed\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various speed-occupancy plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2...

An integrated model of water resources optimization allocation based on projection pursuit model - Grey wolf optimization method in a transboundary river basin

NASA Astrophysics Data System (ADS)

Yu, Sen; Lu, Hongwei

2018-04-01

Under the effects of global change, water crisis ranks as the top global risk in the future decade, and water conflict in transboundary river basins as well as the geostrategic competition led by it is most concerned. This study presents an innovative integrated PPMGWO model of water resources optimization allocation in a transboundary river basin, which is integrated through the projection pursuit model (PPM) and Grey wolf optimization (GWO) method. This study uses the Songhua River basin and 25 control units as examples, adopting the PPMGWO model proposed in this study to allocate the water quantity. Using water consumption in all control units in the Songhua River basin in 2015 as reference to compare with optimization allocation results of firefly algorithm (FA) and Particle Swarm Optimization (PSO) algorithms as well as the PPMGWO model, results indicate that the average difference between corresponding allocation results and reference values are 0.195 bil m3, 0.151 bil m3, and 0.085 bil m3, respectively. Obviously, the average difference of the PPMGWO model is the lowest and its optimization allocation result is closer to reality, which further confirms the reasonability, feasibility, and accuracy of the PPMGWO model. And then the PPMGWO model is adopted to simulate allocation of available water quantity in Songhua River basin in 2018, 2020, and 2030. The simulation results show water quantity which could be allocated in all controls demonstrates an overall increasing trend with reasonable and equal exploitation and utilization of water resources in the Songhua River basin in future. In addition, this study has a certain reference value and application meaning to comprehensive management and water resources allocation in other transboundary river basins.

A Review of Challenges in the Use of fMRI for Disease Classification / Characterization and A Projection Pursuit Application from Multi-site fMRI Schizophrenia Study.

PubMed

Demirci, Oguz; Clark, Vincent P; Magnotta, Vincent A; Andreasen, Nancy C; Lauriello, John; Kiehl, Kent A; Pearlson, Godfrey D; Calhoun, Vince D

2008-09-01

Functional magnetic resonance imaging (fMRI) is a fairly new technique that has the potential to characterize and classify brain disorders such as schizophrenia. It has the possibility of playing a crucial role in designing objective prognostic/diagnostic tools, but also presents numerous challenges to analysis and interpretation. Classification provides results for individual subjects, rather than results related to group differences. This is a more complicated endeavor that must be approached more carefully and efficient methods should be developed to draw generalized and valid conclusions out of high dimensional data with a limited number of subjects, especially for heterogeneous disorders whose pathophysiology is unknown. Numerous research efforts have been reported in the field using fMRI activation of schizophrenia patients and healthy controls. However, the results are usually not generalizable to larger data sets and require careful definition of the techniques used both in designing algorithms and reporting prediction accuracies. In this review paper, we survey a number of previous reports and also identify possible biases (cross-validation, class size, e.g.) in class comparison/prediction problems. Some suggestions to improve the effectiveness of the presentation of the prediction accuracy results are provided. We also present our own results using a projection pursuit algorithm followed by an application of independent component analysis proposed in an earlier study. We classify schizophrenia versus healthy controls using fMRI data of 155 subjects from two sites obtained during three different tasks. The results are compared in order to investigate the effectiveness of each task and differences between patients with schizophrenia and healthy controls were investigated.

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

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes

PubMed Central

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation. PMID:28582389

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes.

PubMed

Einkemmer, Lukas

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation.

Taking movement data to new depths: Inferring prey availability and patch profitability from seabird foraging behavior.

PubMed

Chimienti, Marianna; Cornulier, Thomas; Owen, Ellie; Bolton, Mark; Davies, Ian M; Travis, Justin M J; Scott, Beth E

2017-12-01

Detailed information acquired using tracking technology has the potential to provide accurate pictures of the types of movements and behaviors performed by animals. To date, such data have not been widely exploited to provide inferred information about the foraging habitat. We collected data using multiple sensors (GPS, time depth recorders, and accelerometers) from two species of diving seabirds, razorbills ( Alca torda , N  = 5, from Fair Isle, UK) and common guillemots ( Uria aalge , N  = 2 from Fair Isle and N  = 2 from Colonsay, UK). We used a clustering algorithm to identify pursuit and catching events and the time spent pursuing and catching underwater, which we then used as indicators for inferring prey encounters throughout the water column and responses to changes in prey availability of the areas visited at two levels: individual dives and groups of dives. For each individual dive ( N  = 661 for guillemots, 6214 for razorbills), we modeled the number of pursuit and catching events, in relation to dive depth, duration, and type of dive performed (benthic vs. pelagic). For groups of dives ( N  = 58 for guillemots, 156 for razorbills), we modeled the total time spent pursuing and catching in relation to time spent underwater. Razorbills performed only pelagic dives, most likely exploiting prey available at shallow depths as indicated by the vertical distribution of pursuit and catching events. In contrast, guillemots were more flexible in their behavior, switching between benthic and pelagic dives. Capture attempt rates indicated that they were exploiting deep prey aggregations. The study highlights how novel analysis of movement data can give new insights into how animals exploit food patches, offering a unique opportunity to comprehend the behavioral ecology behind different movement patterns and understand how animals might respond to changes in prey distributions.

Sex Differences in the Physiological and Behavioral Effects of Chronic Oral Methylphenidate Treatment in Rats

PubMed Central

Robison, Lisa S.; Michaelos, Michalis; Gandhi, Jason; Fricke, Dennis; Miao, Erick; Lam, Chiu-Yim; Mauceri, Anthony; Vitale, Melissa; Lee, Junho; Paeng, Soyeh; Komatsu, David E.; Hadjiargyrou, Michael; Thanos, Panayotis K.

2017-01-01

Methylphenidate (MP) is a psychostimulant prescribed for Attention Deficit Hyperactivity Disorder. Previously, we developed a dual bottle 8-h-limited-access-drinking-paradigm for oral MP treatment of rats that mimics the pharmacokinetic profile of treated patients. This study assessed sex differences in response to this treatment. Male and female Sprague Dawley rats were assigned to one of three treatment groups at 4 weeks of age (n = 12/group): Control (water), low dose (LD) MP, and high dose (HD) MP. Rats drank 4 mg/kg MP (LD) or 30 mg/kg MP (HD) during the first hour, and 10 mg/kg (LD) or 60 mg/kg MP (HD) for the remaining 7 h each day. Throughout 3 months of treatment, rats were monitored for body weight, food intake, and fluid intake; as well as tested for open field behavior, circadian activity, novel object recognition, and social interaction. Chronic MP treated rats exhibited reduced fluid intake during distinct treatment weeks to a greater extent in males, and reduced total fluid intake in males only. HD MP treatment decreased body weight in both sexes, while HD MP increased total food intake in females only, likely to offset energy deficits resulting from MP-induced hyperactivity. LD and HD MP increased locomotor activity in the open field, particularly in females and during later treatment weeks. MP dose-dependently increased activity during the dark cycle of circadian testing in females, while in males hyperactivity was only exhibited by HD rats. HD MP increased center activity to a greater extent in males, while MP increased rearing behavior in females only. MP had no effect on social behavior or novel object recognition in either sex. This study concludes that chronic oral MP treatment at clinically-relevant dosages has significant effects on food intake, body weight, open field behavior, and wake cycle activity. Particularly marked sex differences were apparent for locomotor activity, with females being significantly more sensitive to the hyperactivating effects of the drug. These findings suggest that chronic MP exposure beginning in adolescence can have significant behavioral effects that are both dose- and sex-dependent, and raise concerns regarding the reversibility of these effects post-discontinuation of treatment. PMID:28400722

Distinct Subtypes of Microparticle-containing Immune Complexes Are Associated with Disease Activity, Damage, and Carotid Intima-media Thickness in Systemic Lupus Erythematosus.

PubMed

Fortin, Paul R; Cloutier, Nathalie; Bissonnette, Vincent; Aghdassi, Ellie; Eder, Lihi; Simonyan, David; Laflamme, Nathalie; Boilard, Eric

2016-11-01

Microparticles (MP) are small extracellular vesicles present in body fluids. MP originate from different cellular lineages, principally from platelets in blood, and may expose phosphatidylserine (PS). In systemic lupus erythematosus (SLE), MP harbor immunoglobulin G (IgG), thereby forming MP-containing immune complexes (mpIC). We aimed to verify an association between SLE disease activity, damage, and surrogate markers of atherosclerosis and MP harboring IgG, taking into account the platelet origin and PS exposure of MP. MP expressing surface IgG, platelet antigen (CD41+), and PS were quantified using flow cytometry in plasma of 191 women with SLE. Carotid ultrasounds (US) were available in 113 patients. Spearman correlation analysis was used to analyze whether levels of MP were associated with the following outcomes: SLE Disease Activity Index 2000 (SLEDAI-2K), Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI), and carotid US plaques and intima-media thickness (CIMT) as surrogates for vascular damage. We found CD41+ MP harboring IgG present in SLE. A positive correlation was found between SLEDAI-2K and levels of CD41+ MP harboring IgG and exposing (p = 0.027) and non-exposing PS (p = 0.001). Conversely, SDI (p = 0.024) and CIMT (p = 0.016) correlated with concentrations of CD41- MP harboring IgG and exposing PS. Associations were independent of low-density lipoprotein cholesterol level, body mass index, and antimalarial drug use. Different subtypes of mpIC are produced in SLE and are associated with distinct clinical characteristics such as disease activity and vascular damage. The assessment of MP subtypes might serve for the design of predictive markers of disease activity and vascular damage in patients.

Sequence variations in RepMP2/3 and RepMP4 elements reveal intragenomic homologous DNA recombination events in Mycoplasma pneumoniae.

PubMed

Spuesens, Emiel B M; Oduber, Minoushka; Hoogenboezem, Theo; Sluijter, Marcel; Hartwig, Nico G; van Rossum, Annemarie M C; Vink, Cornelis

2009-07-01

The gene encoding major adhesin protein P1 of Mycoplasma pneumoniae, MPN141, contains two DNA sequence stretches, designated RepMP2/3 and RepMP4, which display variation among strains. This variation allows strains to be differentiated into two major P1 genotypes (1 and 2) and several variants. Interestingly, multiple versions of the RepMP2/3 and RepMP4 elements exist at other sites within the bacterial genome. Because these versions are closely related in sequence, but not identical, it has been hypothesized that they have the capacity to recombine with their counterparts within MPN141, and thereby serve as a source of sequence variation of the P1 protein. In order to determine the variation within the RepMP2/3 and RepMP4 elements, both within the bacterial genome and among strains, we analysed the DNA sequences of all RepMP2/3 and RepMP4 elements within the genomes of 23 M. pneumoniae strains. Our data demonstrate that: (i) recombination is likely to have occurred between two RepMP2/3 elements in four of the strains, and (ii) all previously described P1 genotypes can be explained by inter-RepMP recombination events. Moreover, the difference between the two major P1 genotypes was reflected in all RepMP elements, such that subtype 1 and 2 strains can be differentiated on the basis of sequence variation in each RepMP element. This implies that subtype 1 and subtype 2 strains represent evolutionarily diverged strain lineages. Finally, a classification scheme is proposed in which the P1 genotype of M. pneumoniae isolates can be described in a sequence-based, universal fashion.

Modifying mesoporous silica nanoparticles to avoid the metabolic deactivation of 6-mercaptopurine and methotrexate in combinatorial chemotherapy.

PubMed

Wang, Wenjing; Fang, Chenjie; Wang, Xiaozhu; Chen, Yuxi; Wang, Yaonan; Feng, Wei; Yan, Chunhua; Zhao, Ming; Peng, Shiqi

2013-07-21

Mesoporous silica nanoparticles with amino and thiol groups (MSNSN) were prepared and covalently modified with methotrexate and 6-mercaptopurine to form 6-MP-MSNSN-MTX. In the presence of DTT, 6-MP-MSNSN-MTX gradually releases 6-MP. In rat plasma, 6-MP-MSNSN-MTX effectively inhibits the metabolic deactivation of 6-MP and MTX. 6-MP-MSNSN-MTX could be an agent for long-acting chemotherapy.

A ROSE-based OpenMP 3.0 Research Compiler Supporting Multiple Runtime Libraries

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

Liao, C; Quinlan, D; Panas, T

2010-01-25

OpenMP is a popular and evolving programming model for shared-memory platforms. It relies on compilers for optimal performance and to target modern hardware architectures. A variety of extensible and robust research compilers are key to OpenMP's sustainable success in the future. In this paper, we present our efforts to build an OpenMP 3.0 research compiler for C, C++, and Fortran; using the ROSE source-to-source compiler framework. Our goal is to support OpenMP research for ourselves and others. We have extended ROSE's internal representation to handle all of the OpenMP 3.0 constructs and facilitate their manipulation. Since OpenMP research is oftenmore » complicated by the tight coupling of the compiler translations and the runtime system, we present a set of rules to define a common OpenMP runtime library (XOMP) on top of multiple runtime libraries. These rules additionally define how to build a set of translations targeting XOMP. Our work demonstrates how to reuse OpenMP translations across different runtime libraries. This work simplifies OpenMP research by decoupling the problematic dependence between the compiler translations and the runtime libraries. We present an evaluation of our work by demonstrating an analysis tool for OpenMP correctness. We also show how XOMP can be defined using both GOMP and Omni and present comparative performance results against other OpenMP compilers.« less

Misc Tandem Pix

Science.gov Websites

looking east.jpg 183 KB UNIS Ion Source 111 KB MP-7 Low Energy.jpg 138 KB MP-7 Object West.jpg 117 KB MP-7 Object Middle.jpg 120 KB MP-7 Object East.jpg 142 KB MP-7 Image.jpg 151 KB SEU area in TR-4 looking

Attention is allocated closely ahead of the target during smooth pursuit eye movements: Evidence from EEG frequency tagging.

PubMed

Chen, Jing; Valsecchi, Matteo; Gegenfurtner, Karl R

2017-07-28

It is under debate whether attention during smooth pursuit is centered right on the pursuit target or allocated preferentially ahead of it. Attentional deployment was previously probed using a secondary task, which might have altered attention allocation and led to inconsistent findings. We measured frequency-tagged steady-state visual evoked potentials (SSVEP) to measure attention allocation in the absence of any secondary probing task. The observers pursued a moving dot while stimuli flickering at different frequencies were presented at various locations ahead or behind the pursuit target. We observed a significant increase in EEG power at the flicker frequency of the stimulus in front of the pursuit target, compared to the frequency of the stimulus behind. When testing many different locations, we found that the enhancement was detectable up to about 1.5° ahead during pursuit, but vanished by 3.5°. In a control condition using attentional cueing during fixation, we did observe an enhanced EEG response to stimuli at this eccentricity, indicating that the focus of attention during pursuit is narrower than allowed for by the resolution of the attentional system. In a third experiment, we ruled out the possibility that the SSVEP enhancement was a byproduct of the catch-up saccades occurring during pursuit. Overall, we showed that attention is on average allocated ahead of the pursuit target during smooth pursuit. EEG frequency tagging seems to be a powerful technique that allows for the investigation of attention/perception implicitly when an overt task would be confounding. Copyright © 2017 Elsevier Ltd. All rights reserved.

Smooth Pursuit Eye Movement of Monkeys Naive to Laboratory Setups With Pictures and Artificial Stimuli.

PubMed

Botschko, Yehudit; Yarkoni, Merav; Joshua, Mati

2018-01-01

When animal behavior is studied in a laboratory environment, the animals are often extensively trained to shape their behavior. A crucial question is whether the behavior observed after training is part of the natural repertoire of the animal or represents an outlier in the animal's natural capabilities. This can be investigated by assessing the extent to which the target behavior is manifested during the initial stages of training and the time course of learning. We explored this issue by examining smooth pursuit eye movements in monkeys naïve to smooth pursuit tasks. We recorded the eye movements of monkeys from the 1st days of training on a step-ramp paradigm. We used bright spots, monkey pictures and scrambled versions of the pictures as moving targets. We found that during the initial stages of training, the pursuit initiation was largest for the monkey pictures and in some direction conditions close to target velocity. When the pursuit initiation was large, the monkeys mostly continued to track the target with smooth pursuit movements while correcting for displacement errors with small saccades. Two weeks of training increased the pursuit eye velocity in all stimulus conditions, whereas further extensive training enhanced pursuit slightly more. The training decreased the coefficient of variation of the eye velocity. Anisotropies that grade pursuit across directions were observed from the 1st day of training and mostly persisted across training. Thus, smooth pursuit in the step-ramp paradigm appears to be part of the natural repertoire of monkeys' behavior and training adjusts monkeys' natural predisposed behavior.

Methylphenidate and the response to growth hormone treatment in short children born small for gestational age.

PubMed

Renes, Judith S; de Ridder, Maria A J; Breukhoven, Petra E; Lem, Annemieke J; Hokken-Koelega, Anita C S

2012-01-01

Growth hormone (GH) treatment has become a frequently applied growth promoting therapy in short children born small for gestational age (SGA). Children born SGA have a higher risk of developing attention deficit hyperactivity disorder (ADHD). Treatment of ADHD with methylphenidate (MP) has greatly increased in recent years, therefore more children are being treated with GH and MP simultaneously. Some studies have found an association between MP treatment and growth deceleration, but data are contradictory. To explore the effects of MP treatment on growth in GH-treated short SGA children Anthropometric measurements were performed in 78 GH-treated short SGA children (mean age 10.6 yr), 39 of whom were also treated with MP (SGA-GH/MP). The SGA-GH/MP group was compared to 39 SGA-GH treated subjects. They were matched for sex, age and height at start of GH, height SDS at start of MP treatment and target height SDS. Serum insulin-like growth factor-I (IGF-I) and IGF binding protein-3 (IGFBP-3) levels were yearly determined. Growth, serum IGF-I and IGFBP-3 levels during the first three years of treatment were analyzed using repeated measures regression analysis. The SGA-GH/MP group had a lower height gain during the first 3 years than the SGA-GH subjects, only significant between 6 and 12 months of MP treatment. After 3 years of MP treatment, the height gain was 0.2 SDS (± 0.1 SD) lower in the SGA-GH/MP group (P = 0.17). Adult height was not significantly different between the SGA-GH/MP and SGA-GH group (-1.9 SDS and -1.9 SDS respectively, P = 0.46). Moreover, during the first 3 years of MP treatment IGF-I and IGFBP-3 measurements were similar in both groups. MP has some negative effect on growth during the first years in short SGA children treated with GH, but adult height is not affected.

High glucose increases the formation and pro-oxidative activity of endothelial microparticles.

PubMed

Burger, Dylan; Turner, Maddison; Xiao, Fengxia; Munkonda, Mercedes N; Akbari, Shareef; Burns, Kevin D

2017-09-01

Individuals with diabetes exhibit increases in circulating endothelial microparticles (eMPs, also referred to as endothelial microvesicles), which are associated with endothelial dysfunction and a heightened risk of cardiovascular complications. We have shown that eMPs are markers and mediators of vascular injury although their role in diabetes is unclear. We hypothesised that the composition and biological activity of eMPs are altered in response to high glucose exposure. We assessed the effects of high glucose on eMP formation, composition and signalling in cultured HUVECs. eMPs were isolated from the media of HUVECs cultured under conditions of normal glucose (eMP NG ), high glucose (eMP HG ) or osmotic control of L-glucose (eMP LG ). eMP size, concentration and surface charge were assessed by nanoparticle tracking analysis and flow cytometry. eMP protein composition was assessed by liquid chromatography-tandem mass spectrometry, and eMP-mediated effects on coagulation, reactive oxygen species (ROS) production and vessel function were assessed. Exposure of HUVECs to high glucose for 24 h caused a threefold increase in eMP formation, increased mean particle size (269 ± 18 nm vs 226 ± 11 nm) and decreased surface charge. Compared with eMP NG or eMP LG , eMP HG possessed approximately threefold greater pro-coagulant activity, stimulated HUVEC ROS production to a greater extent (~250% of eMP NG ) and were more potent inhibitors of endothelial-dependent relaxation. Proteomic analysis of eMPs identified 1212 independent proteins of which 68 were exclusively found in eMP HG . Gene ontology analysis revealed that eMP HG -exclusive proteins were associated with signalling pathways related to blood coagulation, cell signalling and immune cell activation. Our results indicate that elevated glucose is a potent stimulus for eMP formation that also alters their molecular composition leading to increased bioactivity. Such effects may contribute to progressive endothelial injury and subsequent cardiovascular complications in diabetes.

The Neural Basis of Smooth Pursuit Eye Movements in the Rhesus Monkey Brain

ERIC Educational Resources Information Center

Ilg, Uwe J.; Thier, Peter

2008-01-01

Smooth pursuit eye movements are performed in order to prevent retinal image blur of a moving object. Rhesus monkeys are able to perform smooth pursuit eye movements quite similar as humans, even if the pursuit target does not consist in a simple moving dot. Therefore, the study of the neuronal responses as well as the consequences of…

6-Mercaptopurine transport by equilibrative nucleoside transporters in conditionally immortalized rat syncytiotrophoblast cell lines TR-TBTs.

PubMed

Lee, Na-young; Sai, Yoshimichi; Nakashima, Emi; Ohtsuki, Sumio; Kang, Young-sook

2011-09-01

Recently, more women were provided with 6-mercaptopurine (6-MP) during pregnancy. Therefore, we attempted to clarify the transport mechanisms of 6-MP through blood-placenta barrier using rat conditionally immortalized syncytiotrophoblast cell lines (TR-TBTs). The uptake of 6-MP was time- and ATP dependent, but sodium independent in TR-TBTs. 6-MP was eliminated over 50% from the cells within 30 min. The uptake of 6-MP was saturable with Michaelis-Menten constant values of 198 μM and 250 μM in TR-TBT 18d-1 and TR-TBT 18d-2, respectively. 6-Thioguanine, azathioprine, and hypoxantine, structural analogues of 6-MP, strongly inhibited [(14) C]6-MP uptake. Equilibrative nucleoside transporter (ENT) inhibitors, adenosine and uridine, significantly inhibited [(14) C]6-MP uptake. However, several organic anions and cations had no effect on [(14) C]6-MP uptake in TR-TBTs. These results suggest that sodium-independent transporters, ENTs, may be involved in 6-MP uptake at the placenta. In addition, multidrug resistance protein (MRP) inhibitors, methotrexate, probenecid, cefmetazole, and sulfinpyrazone, significantly increased the accumulation of [(14) C]6-MP in the cells. It is indicated that 6-MP may be eliminated across the blood-placental barrier via MRPs. TR-TBTs expressed mRNA of ENT1, ENT2, MRP4, and MRP5. These findings are important for the therapy of acute lymphoblastic leukemia and autoimmune diseases of pregnant women, and should be useful data in elucidating teratogenicity of 6-MP during pregnancy. Copyright © 2011 Wiley-Liss, Inc.

Mental practice for upper limb rehabilitation after stroke: a systematic review and meta-analysis.

PubMed

Park, Si-Woon; Kim, Jae-Hyung; Yang, Yun-Jung

2018-06-14

Mental practice (MP) is usually provided in combination with other therapies, and new developments for neurofeedback to support MP have been made recently. The objectives of this study were to evaluate the effectiveness of MP and to investigate the intervention characteristics including neurofeedback that may affect treatment outcome. The Cochrane Central Register of Controlled Trials, PubMed, Embase, KoreaMed, Scopus, Web of Science, PEDro, and CIRRIE were searched from inception to March 2017 for randomized controlled trials to assess the effect of MP for upper limb rehabilitation after stroke. Fugl-Meyer Assessment (FMA) was used as the outcome measure for meta-analysis. Twenty-five trials met the inclusion criteria, and 15 trials were eligible for meta-analysis. Among the trials selected for meta-analysis, MP was added to conventional therapy in eight trials or to modified constraint-induced movement therapy in one trial. The other trials provided neurofeedback to support MP: MP-guided neuromuscular electrical stimulation (NMES) in four trials and MP-guided robot-assisted therapy (RAT) in two trials. MP added to conventional therapy resulted in significantly higher FMA gain than conventional therapy alone. MP-guided NMES showed superior result than conventional NMES as well. However, the FMA gain of MP-guided RAT was not significantly higher than RAT alone. We suggest that MP is an effective complementary therapy either given with neurofeedback or not. Neurofeedback applied to MP showed different results depending on the therapy provided. This study has limitations because of heterogeneity and inadequate quality of trials. Further research is requested.

Mental practice with interactive 3D visual aids enhances surgical performance.

PubMed

Yiasemidou, Marina; Glassman, Daniel; Mushtaq, Faisal; Athanasiou, Christos; Williams, Mark-Mon; Jayne, David; Miskovic, Danilo

2017-10-01

Evidence suggests that Mental Practice (MP) could be used to finesse surgical skills. However, MP is cognitively demanding and may be dependent on the ability of individuals to produce mental images. In this study, we hypothesised that the provision of interactive 3D visual aids during MP could facilitate surgical skill performance. 20 surgical trainees were case-matched to one of three different preparation methods prior to performing a simulated Laparoscopic Cholecystectomy (LC). Two intervention groups underwent a 25-minute MP session; one with interactive 3D visual aids depicting the relevant surgical anatomy (3D-MP group, n = 5) and one without (MP-Only, n = 5). A control group (n = 10) watched a didactic video of a real LC. Scores relating to technical performance and safety were recorded by a surgical simulator. The Control group took longer to complete the procedure relative to the 3D&MP condition (p = .002). The number of movements was also statistically different across groups (p = .001), with the 3D&MP group making fewer movements relative to controls (p = .001). Likewise, the control group moved further in comparison to the 3D&MP condition and the MP-Only condition (p = .004). No reliable differences were observed for safety metrics. These data provide evidence for the potential value of MP in improving performance. Furthermore, they suggest that 3D interactive visual aids during MP could potentially enhance performance, beyond the benefits of MP alone. These findings pave the way for future RCTs on surgical preparation and performance.

EMDR Effects on Pursuit Eye Movements

PubMed Central

Kapoula, Zoi; Yang, Qing; Bonnet, Audrey; Bourtoire, Pauline; Sandretto, Jean

2010-01-01

This study aimed to objectivize the quality of smooth pursuit eye movements in a standard laboratory task before and after an Eye Movement Desensitization and Reprocessing (EMDR) session run on seven healthy volunteers. EMDR was applied on autobiographic worries causing moderate distress. The EMDR session was complete in 5 out of the 7 cases; distress measured by SUDS (Subjective Units of Discomfort Scale) decreased to a near zero value. Smooth pursuit eye movements were recorded by an Eyelink II video system before and after EMDR. For the five complete sessions, pursuit eye movement improved after their EMDR session. Notably, the number of saccade intrusions—catch-up saccades (CUS)—decreased and, reciprocally, there was an increase in the smooth components of the pursuit. Such an increase in the smoothness of the pursuit presumably reflects an improvement in the use of visual attention needed to follow the target accurately. Perhaps EMDR reduces distress thereby activating a cholinergic effect known to improve ocular pursuit. PMID:20505828

Ab initio investigation of structure, stability, thermal behavior, bonding, and infrared spectra of ionized water cluster (H2O)6+

NASA Astrophysics Data System (ADS)

Liu, Lei; Hu, Cui-E.; Tang, Mei; Chen, Xiang-Rong; Cai, Ling-Cang

2016-10-01

The low-lying isomers of cationic water cluster (H2O)6+ have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6+ and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level. The interaction energies using the complete basis set limits at MP2 level are also reported. The relationships between their structure arrangement and their energies are discussed. Based on the results of thermal simulation, structural change from a four-numbered ring to a tree-like structure occurs at T ≈ 45 K, and the relative population of six lowest-free-energy isomers is found to exceed 4% at some point within the studied temperature range. Studies reveal that, among these six isomers, two new-found isomers constitute 10% of isomer population at 180 K, and the experimental spectra can be better explained with inclusions of the two isomers. The molecular orbitals for six representative cationic water clusters are also studied. Through topological and reduced density gradient analysis, we investigated the structural characteristics and the bonding strengths of these water cluster radical cations.

Aerosol Measurements by the Globally Distributed Micro Pulse Lidar Network

NASA Technical Reports Server (NTRS)

Spinhirne, James; Welton, Judd; Campbell, James; Berkoff, Tim; Starr, David (Technical Monitor)

2001-01-01

Full time measurements of the vertical distribution of aerosol are now being acquired at a number of globally distributed MP (micro pulse) lidar sites. The MP lidar systems provide full time profiling of all significant cloud and aerosol to the limit of signal attenuation from compact, eye safe instruments. There are currently eight sites in operation and over a dozen planned. At all sited there are also passive aerosol and radiation measurements supporting the lidar data. Four of the installations are at Atmospheric Radiation Measurement program sites. The network operation includes instrument operation and calibration and the processing of aerosol measurements with standard retrievals and data products from the network sites. Data products include optical thickness and extinction cross section profiles. Application of data is to supplement satellite aerosol measurements and to provide a climatology of the height distribution of aerosol. The height distribution of aerosol is important for aerosol transport and the direct scattering and absorption of shortwave radiation in the atmosphere. Current satellite and other data already provide a great amount of information on aerosol distribution, but no passive technique can adequately resolve the height profile of aerosol. The Geoscience Laser Altimeter System (GLAS) is an orbital lidar to be launched in early 2002. GLAS will provide global measurements of the height distribution of aerosol. The MP lidar network will provide ground truth and analysis support for GLAS and other NASA Earth Observing System data. The instruments, sites, calibration procedures and standard data product algorithms for the MPL network will be described.

Hybrid MPI-OpenMP Parallelism in the ONETEP Linear-Scaling Electronic Structure Code: Application to the Delamination of Cellulose Nanofibrils.

PubMed

Wilkinson, Karl A; Hine, Nicholas D M; Skylaris, Chris-Kriton

2014-11-11

We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. We illustrate its performance on a range of high performance computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused on applying OpenMP parallelism to the routines which dominate the computational load, attempting where possible to parallelize different loops from those already parallelized within MPI. This includes 3D FFT box operations, sparse matrix algebra operations, calculation of integrals, and Ewald summation. While the underlying numerical methods are unchanged, these developments represent significant changes to the algorithms used within ONETEP to distribute the workload across CPU cores. The new hybrid code exhibits much-improved strong scaling relative to the MPI-only code and permits calculations with a much higher ratio of cores to atoms. These developments result in a significantly shorter time to solution than was possible using MPI alone and facilitate the application of the ONETEP code to systems larger than previously feasible. We illustrate this with benchmark calculations from an amyloid fibril trimer containing 41,907 atoms. We use the code to study the mechanism of delamination of cellulose nanofibrils when undergoing sonification, a process which is controlled by a large number of interactions that collectively determine the structural properties of the fibrils. Many energy evaluations were needed for these simulations, and as these systems comprise up to 21,276 atoms this would not have been feasible without the developments described here.

Monitoring of the data processing and simulated production at CMS with a web-based service: the Production Monitoring Platform (pMp)

NASA Astrophysics Data System (ADS)

Franzoni, G.; Norkus, A.; Pol, A. A.; Srimanobhas, N.; Walker, J.

2017-10-01

Physics analysis at the Compact Muon Solenoid requires both the production of simulated events and processing of the data collected by the experiment. Since the end of the LHC Run-I in 2012, CMS has produced over 20 billion simulated events, from 75 thousand processing requests organised in one hundred different campaigns. These campaigns emulate different configurations of collision events, the detector, and LHC running conditions. In the same time span, sixteen data processing campaigns have taken place to reconstruct different portions of the Run-I and Run-II data with ever improving algorithms and calibrations. The scale and complexity of the events simulation and processing, and the requirement that multiple campaigns must proceed in parallel, demand that a comprehensive, frequently updated and easily accessible monitoring be made available. The monitoring must serve both the analysts, who want to know which and when datasets will become available, and the central production teams in charge of submitting, prioritizing, and running the requests across the distributed computing infrastructure. The Production Monitoring Platform (pMp) web-based service, has been developed in 2015 to address those needs. It aggregates information from multiple services used to define, organize, and run the processing requests. Information is updated hourly using a dedicated elastic database and the monitoring provides multiple configurable views to assess the status of single datasets as well as entire production campaigns. This contribution will describe the pMp development, the evolution of its functionalities, and one and half year of operational experience.

The investigation of the binding of 6-mercaptopurine to site I on human serum albumin.

PubMed

Sochacka, Jolanta; Baran, Wojciech

2012-12-01

6-Mercaptopurine (6-MP) is one of a large series of purine analogues which has been found active against human leukemias. The equilibrium dialysis, circular dichroism (CD) and molecular docking were employed to study the binding of 6-MP to human serum albumin (HSA). The binding of 6-MP to HSA in the equilibrium dialysis experiment was detected by measuring the displacement of 6-MP by specific markers for site I on HSA, warfarin (RWF), phenylbutazone (PhB) and n-butyl p-aminobenzoate (ABE). It was shown, according to CD data, that binding of 6-MP to HSA leads to alteration of HSA secondary structure. Based on the findings from displacement experiment and molecular docking simulation it was found that 6-MP was located within binding cavity of subdomain IIA and the space occupied by site markers overlapped with that of 6-MP. Displacement of 6-MP by the RWF or PhB was not up the level expected for a competitive mechanism, therefore displacement of 6-MP was rather by non-cooperative than that the direct competition. Instead, in case of the interaction between ABE and 6-MP, when the little enhancement of the binding of ABE by 6-MP was found, the interaction could be via a positively cooperative mechanism.

Nature and position of functional group on thiopurine substrates influence activity of xanthine oxidase--enzymatic reaction pathways of 6-mercaptopurine and 2-mercaptopurine are different.

PubMed

Tamta, Hemlata; Kalra, Sukirti; Thilagavathi, Ramasamy; Chakraborti, Asit K; Mukhopadhyay, Anup K

2007-02-01

Xanthine oxidase-catalyzed hydroxylation reactions of the anticancer drug 6-mercaptopurine (6-MP) and its analog 2-mercaptopurine (2-MP) as well as 6-thioxanthine (6-TX) and 2-thioxanthine (2-TX) have been studied using UV-spectroscopy, high pressure liquid chromatography, photodiode array, and liquid chromatography-based mass spectral analysis. It is shown that 6-MP and 2-MP are oxidatively hydroxylated through different pathways. Enzymatic hydroxylation of 6-MP forms 6-thiouric acid in two steps involving 6-TX as the intermediate, whereas 2-MP is converted to 8-hydroxy-2-mercaptopurine as the expected end product in one step. Surprisingly, in contrast to the other thiopurines, enzymatic hydroxylation of 2-MP showed a unique hyperchromic effect at 264 nm as the reaction proceeded. However, when 2-TX is used as the substrate, it is hydroxylated to 2-thiouric acid. The enzymatic hydroxylation of 2-MP is considerably faster than that of 6-MP, while 6-TX and 2-TX show similar rates under identical reaction conditions. The reason why 2-MP is a better substrate than 6-MP and how the chemical nature and position of the functional groups present on the thiopurine substrates influence xanthine oxidase activity are discussed.

Improved human islet preparations using Glucocorticoid and Exendin-4

PubMed Central

Miki, Atsushi.; Ricordi, Camillo.; Yamamoto, Toshiyuki.; Sakuma, Yasunaru.; Misawa, Ryosuke.; Mita, Atsuyoshi.; Inverardi, Luca.; Alejandro, Rodolfo; Ichii, Hirohito.

2014-01-01

Objectives The effects of Glucocorticoid during culture on human islet cells have been controversial. Exendin-4 (EX) enhances the insulin secretion and significantly improves clinical outcomes in islet cell transplantation. In this study, we examined the effects of Glucocorticoids and exendin-4 on human islet cells during pre-transplant culture. Methods Methylprednisolone (MP) and/or EX were added to the standard culture medium for clinical islet cell transplantation. Islets were cultured for 24 hours with three different conditions (Control: no additives, MP alone, MP+EX). Beta cell fractional viability, cellular composition, multiple cytokine/chemokine production, multiple phosphorylation proteins and glucose induced insulin secretion were evaluated. Results Viable beta cell survival in MP and MP+EX group was significantly higher than in the control group. EX prevented MP induced reduction of insulin secretion. MP supplementation to the culture medium decreased cytokine and chemokine production. Moreover, Erk1/2 phosphorylation was significantly increased by MP and MP+EX. Conclusions Glucocorticoid supplementation into culture media significantly decreased the cytokine/chemokine production and increased the Erk1/2 phosphorylation, resulting in the improvement of human beta cell survival. In addition, EX maintained the insulin secretion suppressed by MP. The supplementation of MP and EX together could be a useful strategy to create suitable human islets for transplantation. PMID:25036907

Cell-derived microparticles and vascular pregnancy complications: a systematic and comprehensive review.

PubMed

Alijotas-Reig, Jaume; Palacio-Garcia, Carles; Llurba, Elisa; Vilardell-Tarres, Miquel

2013-02-01

To assess current studies on the relationship between cell-derived microparticles (cMP) and recurrent miscarriages (RM) and pre-eclampsia (PE), and review the relationships between cMP and inflammatory and clot pathways, antiphospholipid antibodies (aPL), cytokines, and pregnancy complications. Systematic and comprehensive review of the literature from January 2000 to January 2012. Vall d'Hebron University Hospital. Women with recurrent miscarriages or PE, healthy nonpregnant women, and healthy pregnant women. None. Comparison of cMP numbers and types among groups. Platelet and endothelial cMP are increased in women with normal pregnancies compared with nonpregnant healthy women. Only five case-control studies regarding cMP and RM and 16 on cMP and PE were found to match our objective. Three of five articles referring to RM showed differences in cMP numbering, and 13 of 16 on cMP and PE showed differences in some type of cMP compared with controls. Cell-derived microparticles were raised in normal pregnancy. Recurrent miscarriage seems to be related to endothelial and platelet cell activation and/or consumption. An increase in almost all cMP types was observed in PE. A relationship between cMP and endothelial activation and proinflammatory status seems to exist. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Cell-to-cell movement of Alfalfa mosaic virus can be mediated by the movement proteins of Ilar-, bromo-, cucumo-, tobamo- and comoviruses and does not require virion formation.

PubMed

Sánchez-Navarro, Jesús A; Carmen Herranz, María; Pallás, Vicente

2006-03-01

RNA 3 of Alfalfa mosaic virus (AMV) encodes the movement protein (MP) and coat protein (CP). Chimeric RNA 3 with the AMV MP gene replaced by the corresponding MP gene of Prunus necrotic ringspot virus, Brome mosaic virus, Cucumber mosaic virus or Cowpea mosaic virus efficiently moved from cell-to-cell only when the expressed MP was extended at its C-terminus with the C-terminal 44 amino acids of AMV MP. MP of Tobacco mosaic virus supported the movement of the chimeric RNA 3 whether or not the MP was extended with the C-terminal AMV MP sequence. The replacement of the CP gene in RNA 3 by a mutant gene encoding a CP defective in virion formation did not affect cell-to-cell transport of the chimera's with a functional MP. A GST pull-down technique was used to demonstrate for the first time that the C-terminal 44 amino acids of the MP of a virus belonging to the family Bromoviridae interact specifically with AMV virus particles. Together, these results demonstrate that AMV RNA 3 can be transported from cell-to-cell by both tubule-forming and non-tubule-forming MPs if a specific MP-CP interaction occurs.

First on the List: Effectiveness at Self-Regulation and Prioritizing Difficult Exercise Goal Pursuit

PubMed Central

Delose, Julie E.; vanDellen, Michelle R.; Hoyle, Rick H.

2015-01-01

Identifying and understanding the goal pursuit strategies that distinguish effective self-regulators from less effective self-regulators is important for elucidating how individuals achieve their goals. We suggest that the timing of plans for difficult goal pursuits is one differentiation. A pilot study shows that effective self-regulators tend to believe they are best suited to pursue difficult goals earlier in the day, and two studies provide evidence that effective and less effective self-regulators differ in the timing of their plans for difficult goal pursuits. Results indicate that when exercising is perceived as difficult goal pursuit, effective self-regulators prioritize that difficult goal pursuit by planning to exercise earlier in the day whereas less effective self-regulators plan exercise for later in the day. PMID:26957951

Orbital-optimized third-order Møller-Plesset perturbation theory and its spin-component and spin-opposite scaled variants: Application to symmetry breaking problems

NASA Astrophysics Data System (ADS)

Bozkaya, Uǧur

2011-12-01

In this research, orbital-optimized third-order Møller-Plesset perturbation theory (OMP3) and its spin-component and spin-opposite scaled variants (SCS-OMP3 and SOS-OMP3) are introduced. Using a Lagrangian-based approach, an efficient, quadratically convergent algorithm for variational optimization of the molecular orbitals (MOs) for third-order Møller-Plesset perturbation theory (MP3) is presented. Explicit equations for response density matrices, the MO gradient, and Hessian are reported in spin-orbital form. The OMP3, SCS-OMP3, and SOS-OMP3 approaches are compared with the second-order Møller-Plesset perturbation theory (MP2), MP3, coupled-cluster doubles (CCD), optimized-doubles (OD), and coupled-cluster singles and doubles (CCSD) methods. All these methods are applied to the O4 +, O3, and seven diatomic molecules. Results demonstrate that the OMP3 and its variants provide significantly better vibrational frequencies than MP3, CCSD, and OD for the molecules where the symmetry-breaking problems are observed. For O4 +, the OMP3 prediction, 1343 cm-1, for ω6 (b3u) mode, where symmetry-breaking appears, is even better than presumably more reliable methods such as Brueckner doubles (BD), 1194 cm-1, and OD, 1193 cm-1, methods (the experimental value is 1320 cm-1). For O3, the predictions of SCS-OMP3 (1143 cm-1) and SOS-OMP3 (1165 cm-1) are remarkably better than the more robust OD method (1282 cm-1); the experimental value is 1089 cm-1. For the seven diatomics, again the SCS-OMP3 and SOS-OMP3 methods provide the lowest average errors, |Δωe| = 44 and |Δωe| = 35 cm-1, respectively, while for OD, |Δωe| = 161 cm-1and CCSD |Δωe| = 106 cm-1. Hence, the OMP3 and especially its spin-scaled variants perform much better than the MP3, CCSD, and more robust OD approaches for considered test cases. Therefore, considering both the computational cost and the reliability, SCS-OMP3 and SOS-OMP3 appear to be the best methods for the symmetry-breaking cases, based on present application results. The OMP3 method offers certain advantages: it provides reliable vibrational frequencies in case of symmetry-breaking problems, especially with spin-scaling tricks, its analytic gradients are easier to compute since there is no need to solve the coupled-perturbed equations for the orbital response, and the computation of one-electron properties are easier because there is no response contribution to the particle density matrices. The OMP3 has further advantages over standard MP3, making it promising for excited state properties via linear response theory.

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units

DOE PAGES

Song, Chenchen; Martinez, Todd J.

2017-08-29

Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. Furthermore, the resulting energy conservation in micro-canonical AIMD demonstrates that the implementationmore » provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.« less

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2017-10-01

Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. The resulting energy conservation in micro-canonical AIMD demonstrates that the implementation provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units

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

Song, Chenchen; Martinez, Todd J.

Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. Furthermore, the resulting energy conservation in micro-canonical AIMD demonstrates that the implementationmore » provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.« less

Protective effect of polysaccharide from maca (Lepidium meyenii) on Hep-G2 cells and alcoholic liver oxidative injury in mice.

PubMed

Zhang, Lijun; Zhao, Qingsheng; Wang, Liwei; Zhao, Mingxia; Zhao, Bing

2017-06-01

To study the characterization and hepatoprotective activity of polysaccharide from maca (Lepidium meyenii), the main polysaccharide from maca (MP-1) was obtained by DEAE-52 cellulose column. The average molecular weight of MP-1 was 1067.3kDa and the polysaccharide purity was 91.63%. In order to assess the antioxidant activities of MP-1, four kinds of methods were used, including scavenging hydroxyl radical, DPPH, superoxide anion radical, and FRAP, and the results indicated high antioxidant activities. Furthermore, hepatoprotective activity of MP-1 was studied both in vitro and vivo. In vitro, the alcohol induced Hep-G2 cells model was established to evaluate the protective effect of MP-1, which demonstrated MP-1 can alleviate alcohol damage in Hep-G2 cells. In vivo, the Institute　of　Cancer　Researcch (ICR) mice were used to evaluate hepatoprotecive effects of MP-1 on alcoholic liver disease (ALD). Supplement with MP-1 supressed the triglyceride level both in serum and in hepatic tissue. In addition, MP-1 ameliorated serous transaminases increase induced by alcohol, including aspartate transaminase, alanine aminotransferase, and γ-glutamyl transpeptidase. Moreover, MP-1 also dramatically increased the superoxide dismutase, glutathione peroxidase, and glutathione s-transferase levels in alcoholic mice. Meantime, histopathologic results MP-1 lighten inflammation induced by alcohol. These results indicate that MP-1 possesses hepatoprotective activity against hepatic injury induced by alcohol. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrated Navigation System Design for Micro Planetary Rovers: Comparison of Absolute Heading Estimation Algorithms and Nonlinear Filtering

PubMed Central

Ilyas, Muhammad; Hong, Beomjin; Cho, Kuk; Baeg, Seung-Ho; Park, Sangdeok

2016-01-01

This paper provides algorithms to fuse relative and absolute microelectromechanical systems (MEMS) navigation sensors, suitable for micro planetary rovers, to provide a more accurate estimation of navigation information, specifically, attitude and position. Planetary rovers have extremely slow speed (~1 cm/s) and lack conventional navigation sensors/systems, hence the general methods of terrestrial navigation may not be applicable to these applications. While relative attitude and position can be tracked in a way similar to those for ground robots, absolute navigation information is hard to achieve on a remote celestial body, like Moon or Mars, in contrast to terrestrial applications. In this study, two absolute attitude estimation algorithms were developed and compared for accuracy and robustness. The estimated absolute attitude was fused with the relative attitude sensors in a framework of nonlinear filters. The nonlinear Extended Kalman filter (EKF) and Unscented Kalman filter (UKF) were compared in pursuit of better accuracy and reliability in this nonlinear estimation problem, using only on-board low cost MEMS sensors. Experimental results confirmed the viability of the proposed algorithms and the sensor suite, for low cost and low weight micro planetary rovers. It is demonstrated that integrating the relative and absolute navigation MEMS sensors reduces the navigation errors to the desired level. PMID:27223293

Integrated Navigation System Design for Micro Planetary Rovers: Comparison of Absolute Heading Estimation Algorithms and Nonlinear Filtering.

PubMed

Ilyas, Muhammad; Hong, Beomjin; Cho, Kuk; Baeg, Seung-Ho; Park, Sangdeok

2016-05-23

This paper provides algorithms to fuse relative and absolute microelectromechanical systems (MEMS) navigation sensors, suitable for micro planetary rovers, to provide a more accurate estimation of navigation information, specifically, attitude and position. Planetary rovers have extremely slow speed (~1 cm/s) and lack conventional navigation sensors/systems, hence the general methods of terrestrial navigation may not be applicable to these applications. While relative attitude and position can be tracked in a way similar to those for ground robots, absolute navigation information is hard to achieve on a remote celestial body, like Moon or Mars, in contrast to terrestrial applications. In this study, two absolute attitude estimation algorithms were developed and compared for accuracy and robustness. The estimated absolute attitude was fused with the relative attitude sensors in a framework of nonlinear filters. The nonlinear Extended Kalman filter (EKF) and Unscented Kalman filter (UKF) were compared in pursuit of better accuracy and reliability in this nonlinear estimation problem, using only on-board low cost MEMS sensors. Experimental results confirmed the viability of the proposed algorithms and the sensor suite, for low cost and low weight micro planetary rovers. It is demonstrated that integrating the relative and absolute navigation MEMS sensors reduces the navigation errors to the desired level.

The Performance of Short-Term Heart Rate Variability in the Detection of Congestive Heart Failure

PubMed Central

Barros, Allan Kardec; Ohnishi, Noboru

2016-01-01

Congestive heart failure (CHF) is a cardiac disease associated with the decreasing capacity of the cardiac output. It has been shown that the CHF is the main cause of the cardiac death around the world. Some works proposed to discriminate CHF subjects from healthy subjects using either electrocardiogram (ECG) or heart rate variability (HRV) from long-term recordings. In this work, we propose an alternative framework to discriminate CHF from healthy subjects by using HRV short-term intervals based on 256 RR continuous samples. Our framework uses a matching pursuit algorithm based on Gabor functions. From the selected Gabor functions, we derived a set of features that are inputted into a hybrid framework which uses a genetic algorithm and k-nearest neighbour classifier to select a subset of features that has the best classification performance. The performance of the framework is analyzed using both Fantasia and CHF database from Physionet archives which are, respectively, composed of 40 healthy volunteers and 29 subjects. From a set of nonstandard 16 features, the proposed framework reaches an overall accuracy of 100% with five features. Our results suggest that the application of hybrid frameworks whose classifier algorithms are based on genetic algorithms has outperformed well-known classifier methods. PMID:27891509

On the parallel solution of parabolic equations

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Youcef

1989-01-01

Parallel algorithms for the solution of linear parabolic problems are proposed. The first of these methods is based on using polynomial approximation to the exponential. It does not require solving any linear systems and is highly parallelizable. The two other methods proposed are based on Pade and Chebyshev approximations to the matrix exponential. The parallelization of these methods is achieved by using partial fraction decomposition techniques to solve the resulting systems and thus offers the potential for increased time parallelism in time dependent problems. Experimental results from the Alliant FX/8 and the Cray Y-MP/832 vector multiprocessors are also presented.

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

D'Azevedo, Eduardo; Abbott, Stephen; Koskela, Tuomas

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning.

General Electromagnetic Model for the Analysis of Complex Systems (GEMACS) Computer Code Documentation (Version 3). Volume 3. Part 2.

DTIC Science & Technology

1983-09-01

F.P. PX /AMPZIJ/ REFH /AMPZIJ/ REFV /AI4PZIJ/ * RHOX /AI4PZIJ/ RHOY /At4PZIJ/ RHOZ /AI4PZIJ/ S A-ZJ SA /AMPZIJ/ SALP /AMPZIJ/ 6. CALLING ROUTINE: FLDDRV...US3NG ALGORITHM 72 COMPUTE P- YES .~:*:.~~ USING* *. 1. NAME: PLAINT (GTD) ] 2. PURPOSE: To determine if a ray traveling from a given source loca...determine if a source ray reflection from plate MP occurs. If a ray traveling from the source image location in the reflected ray direction passes through

Bone repair of critical size defects treated with mussel powder associated or not with bovine bone graft: histologic and histomorphometric study in rat calvaria.

PubMed

Trotta, Daniel Rizzo; Gorny, Clayton; Zielak, João César; Gonzaga, Carla Castiglia; Giovanini, Allan Fernando; Deliberador, Tatiana Miranda

2014-09-01

The objective of this study was to evaluate the bone repair of critical size defects treated with mussel powder with or without additional bovine bone. Critical size defects of 5 mm were realized in the calvaria of 70 rats, which were randomly divided in 5 groups - Control (C), Autogenous Bone (AB), Mussel Powder (MP), Mussel Powder and Bovine Bone (MP-BB) and Bovine Bone (BB). Histological and histomorphometric analysis were performed 30 and 90 days after the surgical procedures (ANOVA e Tukey p < 0.05). After 30 days, the measures of remaining particles were: 28.36% (MP-BB), 26.63% (BB) and 8.64% (MP) with a statistically significant difference between BB and MP. The percentage of osseous matrix after 30 days was, AB (55.17%), 23.31% (BB), 11.66% (MP) and 10.71% (MP-BB) with statistically significant differences among all groups. After 90 days the figures were 25.05% (BB), 21.53% (MP-BB) and 1.97% (MP) with statistically significant differences between MP-BB and MP. Percentages of new bone formation after 90 days were 89.47% (AB), 35.70% (BB), 26.48% (MP-BB) and 7.37% (MP) with statistically significant differences between AB and the other groups. Within the limits of this study, we conclude that mussel powder, with or without additional bovine bone, did not induce new bone formation and did not repair critical size defects in rat calvaria. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Mucuna pruriens in Parkinson disease

PubMed Central

Laguna, Janeth; Cassani, Erica; Cereda, Emanuele; Pozzi, Nicolò G.; Isaias, Ioannis U.; Contin, Manuela; Barichella, Michela; Pezzoli, Gianni

2017-01-01

Objective: To investigate whether Mucuna pruriens (MP), a levodopa-containing leguminous plant growing in all tropical areas worldwide, may be used as alternative source of levodopa for indigent individuals with Parkinson disease (PD) who cannot afford long-term therapy with marketed levodopa preparations. Methods: We investigated efficacy and safety of single-dose intake of MP powder from roasted seeds obtained without any pharmacologic processing. Eighteen patients with advanced PD received the following treatments, whose sequence was randomized: (1) dispersible levodopa at 3.5 mg/kg combined with the dopa-decarboxylase inhibitor benserazide (LD+DDCI; the reference treatment); (2) high-dose MP (MP-Hd; 17.5 mg/kg); (3) low-dose MP (MP-Ld; 12.5 mg/kg); (4) pharmaceutical preparation of LD without DDCI (LD−DDCI; 17.5 mg/kg); (5) MP plus benserazide (MP+DDCI; 3.5 mg/kg); (6) placebo. Efficacy outcomes were the change in motor response at 90 and 180 minutes and the duration of on state. Safety measures included any adverse event (AE), changes in blood pressure and heart rate, and the severity of dyskinesias. Results: When compared to LD+DDCI, MP-Ld showed similar motor response with fewer dyskinesias and AEs, while MP-Hd induced greater motor improvement at 90 and 180 minutes, longer ON duration, and fewer dyskinesias. MP-Hd induced less AEs than LD+DDCI and LD−DDCI. No differences in cardiovascular response were recorded. Conclusion: Single-dose MP intake met all noninferiority efficacy and safety outcome measures in comparison to dispersible levodopa/benserazide. Clinical effects of high-dose MP were similar to levodopa alone at the same dose, with a more favorable tolerability profile. ClinicalTrials.gov identifier: NCT02680977. PMID:28679598

Mucuna pruriens in Parkinson disease: A double-blind, randomized, controlled, crossover study.

PubMed

Cilia, Roberto; Laguna, Janeth; Cassani, Erica; Cereda, Emanuele; Pozzi, Nicolò G; Isaias, Ioannis U; Contin, Manuela; Barichella, Michela; Pezzoli, Gianni

2017-08-01

To investigate whether Mucuna pruriens (MP), a levodopa-containing leguminous plant growing in all tropical areas worldwide, may be used as alternative source of levodopa for indigent individuals with Parkinson disease (PD) who cannot afford long-term therapy with marketed levodopa preparations. We investigated efficacy and safety of single-dose intake of MP powder from roasted seeds obtained without any pharmacologic processing. Eighteen patients with advanced PD received the following treatments, whose sequence was randomized: (1) dispersible levodopa at 3.5 mg/kg combined with the dopa-decarboxylase inhibitor benserazide (LD+DDCI; the reference treatment); (2) high-dose MP (MP-Hd; 17.5 mg/kg); (3) low-dose MP (MP-Ld; 12.5 mg/kg); (4) pharmaceutical preparation of LD without DDCI (LD-DDCI; 17.5 mg/kg); (5) MP plus benserazide (MP+DDCI; 3.5 mg/kg); (6) placebo. Efficacy outcomes were the change in motor response at 90 and 180 minutes and the duration of on state. Safety measures included any adverse event (AE), changes in blood pressure and heart rate, and the severity of dyskinesias. When compared to LD+DDCI, MP-Ld showed similar motor response with fewer dyskinesias and AEs, while MP-Hd induced greater motor improvement at 90 and 180 minutes, longer ON duration, and fewer dyskinesias. MP-Hd induced less AEs than LD+DDCI and LD-DDCI. No differences in cardiovascular response were recorded. Single-dose MP intake met all noninferiority efficacy and safety outcome measures in comparison to dispersible levodopa/benserazide. Clinical effects of high-dose MP were similar to levodopa alone at the same dose, with a more favorable tolerability profile. NCT02680977. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Cell-derived microparticles promote coagulation after moderate exercise.

PubMed

Sossdorf, Maik; Otto, Gordon P; Claus, Ralf A; Gabriel, Holger H W; Lösche, Wolfgang

2011-07-01

Cell-derived procoagulant microparticles (MP) might be able to contribute to exercise-induced changes in blood hemostasis. This study aimed to examine (i) the concentration and procoagulant activity of cell-derived MP after a moderate endurance exercise and (ii) the differences in the release, clearance, and activity of MP before and after exercise between trained and untrained individuals. All subjects performed a single bout of physical exercise on a bicycle ergometer for 90 min at 80% of their individual anaerobic threshold. MP were identified and quantified by flow cytometry measurements. Procoagulant activity of MP was measured by a prothrombinase activity assay as well as tissue factor-induced fibrin formation in MP-containing plasma. At baseline, no differences were observed for the absolute number and procoagulant activities of MP between trained and untrained subjects. However, trained individuals had a lower number of tissue factor-positive monocyte-derived MP compared with untrained individuals. In trained subjects, exercise induced a significant increase in the number of MP derived from platelets, monocytes, and endothelial cells, with maximum values at 45 min after exercise and returned to basal levels at 2 h after exercise. Untrained subjects revealed a similar increase in platelet-derived MP, but their level was still increased at 2 h after exercise, indicating a reduced clearance compared with trained individuals. Procoagulant activities of MP were increased immediately after exercise and remained elevated up to 2 h after exercise. We conclude that increased levels of MP were found in healthy individuals after an acute bout of exercise, that the amount of circulating MP contributes to an exercise-induced increase of hemostatic potential, and that there were differences in kinetic and dynamic characteristics between trained and untrained individuals.

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. II. Relationships between chemical model and partition function algorithm.

PubMed

Fisicaro, E; Braibanti, A; Lamb, J D; Oscarson, J L

1990-05-01

The relationships between the chemical properties of a system and the partition function algorithm as applied to the description of multiple equilibria in solution are explained. The partition functions ZM, ZA, and ZH are obtained from powers of the binary generating functions Jj = (1 + kappa j gamma j,i[Y])i tau j, where i tau j = p tau j, q tau j, or r tau j represent the maximum number of sites in sites in class j, for Y = M, A, or H, respectively. Each term of the generating function can be considered an element (ij) of a vector Jj and each power of the cooperativity factor gamma ij,i can be considered an element of a diagonal cooperativity matrix gamma j. The vectors Jj are combined in tensor product matrices L tau = (J1) [J2]...[Jj]..., thus representing different receptor-ligand combinations. The partition functions are obtained by summing elements of the tensor matrices. The relationship of the partition functions with the total chemical amounts TM, TA, and TH has been found. The aim is to describe the total chemical amounts TM, TA, and TH as functions of the site affinity constants kappa j and cooperativity coefficients bj. The total amounts are calculated from the sum of elements of tensor matrices Ll. Each set of indices (pj..., qj..., rj...) represents one element of a tensor matrix L tau and defines each term of the summation. Each term corresponds to the concentration of a chemical microspecies. The distinction between microspecies MpjAqjHrj with ligands bound on specific sites and macrospecies MpAqHR corresponding to a chemical stoichiometric composition is shown. The translation of the properties of chemical model schemes into the algorithms for the generation of partition functions is illustrated with reference to a series of examples of gradually increasing complexity. The equilibria examined concern: (1) a unique class of sites; (2) the protonation of a base with two classes of sites; (3) the simultaneous binding of ligand A and proton H to a macromolecule or receptor M with four classes of sites; and (4) the binding to a macromolecule M of ligand A which is in turn a receptor for proton H. With reference to a specific example, it is shown how a computer program for least-squares refinement of variables kappa j and bj can be organized. The chemical model from the free components M, A, and H to the saturated macrospecies MpAQHR, with possible complex macrospecies MpAq and AHR, is defined first.(ABSTRACT TRUNCATED AT 250 WORDS)

Moving target detection for frequency agility radar by sparse reconstruction

NASA Astrophysics Data System (ADS)

Quan, Yinghui; Li, YaChao; Wu, Yaojun; Ran, Lei; Xing, Mengdao; Liu, Mengqi

2016-09-01

Frequency agility radar, with randomly varied carrier frequency from pulse to pulse, exhibits superior performance compared to the conventional fixed carrier frequency pulse-Doppler radar against the electromagnetic interference. A novel moving target detection (MTD) method is proposed for the estimation of the target's velocity of frequency agility radar based on pulses within a coherent processing interval by using sparse reconstruction. Hardware implementation of orthogonal matching pursuit algorithm is executed on Xilinx Virtex-7 Field Programmable Gata Array (FPGA) to perform sparse optimization. Finally, a series of experiments are performed to evaluate the performance of proposed MTD method for frequency agility radar systems.

Mismatch and resolution in compressive imaging

NASA Astrophysics Data System (ADS)

Fannjiang, Albert; Liao, Wenjing

2011-09-01

Highly coherent sensing matrices arise in discretization of continuum problems such as radar and medical imaging when the grid spacing is below the Rayleigh threshold as well as in using highly coherent, redundant dictionaries as sparsifying operators. Algorithms (BOMP, BLOOMP) based on techniques of band exclusion and local optimization are proposed to enhance Orthogonal Matching Pursuit (OMP) and deal with such coherent sensing matrices. BOMP and BLOOMP have provably performance guarantee of reconstructing sparse, widely separated objects independent of the redundancy and have a sparsity constraint and computational cost similar to OMP's. Numerical study demonstrates the effectiveness of BLOOMP for compressed sensing with highly coherent, redundant sensing matrices.

Sparsity-aware multiple relay selection in large multi-hop decode-and-forward relay networks

NASA Astrophysics Data System (ADS)

Gouissem, A.; Hamila, R.; Al-Dhahir, N.; Foufou, S.

2016-12-01

In this paper, we propose and investigate two novel techniques to perform multiple relay selection in large multi-hop decode-and-forward relay networks. The two proposed techniques exploit sparse signal recovery theory to select multiple relays using the orthogonal matching pursuit algorithm and outperform state-of-the-art techniques in terms of outage probability and computation complexity. To reduce the amount of collected channel state information (CSI), we propose a limited-feedback scheme where only a limited number of relays feedback their CSI. Furthermore, a detailed performance-complexity tradeoff investigation is conducted for the different studied techniques and verified by Monte Carlo simulations.

Moving target detection for frequency agility radar by sparse reconstruction.

PubMed

Quan, Yinghui; Li, YaChao; Wu, Yaojun; Ran, Lei; Xing, Mengdao; Liu, Mengqi

2016-09-01

Frequency agility radar, with randomly varied carrier frequency from pulse to pulse, exhibits superior performance compared to the conventional fixed carrier frequency pulse-Doppler radar against the electromagnetic interference. A novel moving target detection (MTD) method is proposed for the estimation of the target's velocity of frequency agility radar based on pulses within a coherent processing interval by using sparse reconstruction. Hardware implementation of orthogonal matching pursuit algorithm is executed on Xilinx Virtex-7 Field Programmable Gata Array (FPGA) to perform sparse optimization. Finally, a series of experiments are performed to evaluate the performance of proposed MTD method for frequency agility radar systems.

AutoAssemblyD: a graphical user interface system for several genome assemblers.

PubMed

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

Coordinated Control of Three-Dimensional Components of Smooth Pursuit to Rotating and Translating Textures.

PubMed

Edinger, Janick; Pai, Dinesh K; Spering, Miriam

2017-01-01

The neural control of pursuit eye movements to visual textures that simultaneously translate and rotate has largely been neglected. Here we propose that pursuit of such targets-texture pursuit-is a fully three-dimensional task that utilizes all three degrees of freedom of the eye, including torsion. Head-fixed healthy human adults (n = 8) tracked a translating and rotating random dot pattern, shown on a computer monitor, with their eyes. Horizontal, vertical, and torsional eye positions were recorded with a head-mounted eye tracker. The torsional component of pursuit is a function of the rotation of the texture, aligned with its visual properties. We observed distinct behaviors between those trials in which stimulus rotation was in the same direction as that of a rolling ball ("natural") in comparison to those with the opposite rotation ("unnatural"): Natural rotation enhanced and unnatural rotation reversed torsional velocity during pursuit, as compared to torsion triggered by a nonrotating random dot pattern. Natural rotation also triggered pursuit with a higher horizontal velocity gain and fewer and smaller corrective saccades. Furthermore, we show that horizontal corrective saccades are synchronized with torsional corrective saccades, indicating temporal coupling of horizontal and torsional saccade control. Pursuit eye movements have a torsional component that depends on the visual stimulus. Horizontal and torsional eye movements are separated in the motor periphery. Our findings suggest that translational and rotational motion signals might be coordinated in descending pursuit pathways.

A Battery-Aware Algorithm for Supporting Collaborative Applications

NASA Astrophysics Data System (ADS)

Rollins, Sami; Chang-Yit, Cheryl

Battery-powered devices such as laptops, cell phones, and MP3 players are becoming ubiquitous. There are several significant ways in which the ubiquity of battery-powered technology impacts the field of collaborative computing. First, applications such as collaborative data gathering, become possible. Also, existing applications that depend on collaborating devices to maintain the system infrastructure must be reconsidered. Fundamentally, the problem lies in the fact that collaborative applications often require end-user computing devices to perform tasks that happen in the background and are not directly advantageous to the user. In this work, we seek to better understand how laptop users use the batteries attached to their devices and analyze a battery-aware alternative to Gnutella’s ultrapeer selection algorithm. Our algorithm provides insight into how system maintenance tasks can be allocated to battery-powered nodes. The most significant result of our study indicates that a large portion of laptop users can participate in system maintenance without sacrificing any of their battery. These results show great promise for existing collaborative applications as well as new applications, such as collaborative data gathering, that rely upon battery-powered devices.

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

Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl; Rudnicki, Witold R.; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw

The second generation Reactive Bond Order (REBO) empirical potential is commonly used to accurately model a wide range hydrocarbon materials. It is also extensible to other atom types and interactions. REBO potential assumes complex multi-body interaction model, that is difficult to represent efficiently in the SIMD or SIMT programming model. Hence, despite its importance, no efficient GPGPU implementation has been developed for this potential. Here we present a detailed description of a highly efficient GPGPU implementation of molecular dynamics algorithm using REBO potential. The presented algorithm takes advantage of rarely used properties of the SIMT architecture of a modern GPUmore » to solve difficult synchronizations issues that arise in computations of multi-body potential. Techniques developed for this problem may be also used to achieve efficient solutions of different problems. The performance of proposed algorithm is assessed using a range of model systems. It is compared to highly optimized CPU implementation (both single core and OpenMP) available in LAMMPS package. These experiments show up to 6x improvement in forces computation time using single processor of the NVIDIA Tesla K80 compared to high end 16-core Intel Xeon processor.« less

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales

PubMed Central

Huebsch, Nathaniel; Loskill, Peter; Mandegar, Mohammad A.; Marks, Natalie C.; Sheehan, Alice S.; Ma, Zhen; Mathur, Anurag; Nguyen, Trieu N.; Yoo, Jennie C.; Judge, Luke M.; Spencer, C. Ian; Chukka, Anand C.; Russell, Caitlin R.; So, Po-Lin

2015-01-01

Contractile motion is the simplest metric of cardiomyocyte health in vitro, but unbiased quantification is challenging. We describe a rapid automated method, requiring only standard video microscopy, to analyze the contractility of human-induced pluripotent stem cell-derived cardiomyocytes (iPS-CM). New algorithms for generating and filtering motion vectors combined with a newly developed isogenic iPSC line harboring genetically encoded calcium indicator, GCaMP6f, allow simultaneous user-independent measurement and analysis of the coupling between calcium flux and contractility. The relative performance of these algorithms, in terms of improving signal to noise, was tested. Applying these algorithms allowed analysis of contractility in iPS-CM cultured over multiple spatial scales from single cells to three-dimensional constructs. This open source software was validated with analysis of isoproterenol response in these cells, and can be applied in future studies comparing the drug responsiveness of iPS-CM cultured in different microenvironments in the context of tissue engineering. PMID:25333967

VizieR Online Data Catalog: ChaMP X-ray point source catalog (Kim+, 2007)

NASA Astrophysics Data System (ADS)

Kim, M.; Kim, D.-W.; Wilkes, B. J.; Green, P. J.; Kim, E.; Anderson, C. S.; Barkhouse, W. A.; Evans, N. R.; Ivezic, Z.; Karovska, M.; Kashyap, V. L.; Lee, M. G.; Maksym, P.; Mossman, A. E.; Silverman, J. D.; Tananbaum, H. D.

2009-01-01

We present the Chandra Multiwavelength Project (ChaMP) X-ray point source catalog with ~6800 X-ray sources detected in 149 Chandra observations covering ~10deg2. The full ChaMP catalog sample is 7 times larger than the initial published ChaMP catalog. The exposure time of the fields in our sample ranges from 0.9 to 124ks, corresponding to a deepest X-ray flux limit of f0.5-8.0=9x10-16ergs/cm2/s. The ChaMP X-ray data have been uniformly reduced and analyzed with ChaMP-specific pipelines and then carefully validated by visual inspection. The ChaMP catalog includes X-ray photometric data in eight different energy bands as well as X-ray spectral hardness ratios and colors. To best utilize the ChaMP catalog, we also present the source reliability, detection probability, and positional uncertainty. (10 data files).

Arctic sea ice is an important temporal sink and means of transport for microplastic.

PubMed

Peeken, Ilka; Primpke, Sebastian; Beyer, Birte; Gütermann, Julia; Katlein, Christian; Krumpen, Thomas; Bergmann, Melanie; Hehemann, Laura; Gerdts, Gunnar

2018-04-24

Microplastics (MP) are recognized as a growing environmental hazard and have been identified as far as the remote Polar Regions, with particularly high concentrations of microplastics in sea ice. Little is known regarding the horizontal variability of MP within sea ice and how the underlying water body affects MP composition during sea ice growth. Here we show that sea ice MP has no uniform polymer composition and that, depending on the growth region and drift paths of the sea ice, unique MP patterns can be observed in different sea ice horizons. Thus even in remote regions such as the Arctic Ocean, certain MP indicate the presence of localized sources. Increasing exploitation of Arctic resources will likely lead to a higher MP load in the Arctic sea ice and will enhance the release of MP in the areas of strong seasonal sea ice melt and the outflow gateways.

Does the noise matter? Effects of different kinematogram types on smooth pursuit eye movements and perception

PubMed Central

Schütz, Alexander C.; Braun, Doris I.; Movshon, J. Anthony; Gegenfurtner, Karl R.

2011-01-01

We investigated how the human visual system and the pursuit system react to visual motion noise. We presented three different types of random-dot kinematograms at five different coherence levels. For transparent motion, the signal and noise labels on each dot were preserved throughout each trial, and noise dots moved with the same speed as the signal dots but in fixed random directions. For white noise motion, every 20 ms the signal and noise labels were randomly assigned to each dot and noise dots appeared at random positions. For Brownian motion, signal and noise labels were also randomly assigned, but the noise dots moved at the signal speed in a direction that varied randomly from moment to moment. Neither pursuit latency nor early eye acceleration differed among the different types of kinematograms. Late acceleration, pursuit gain, and perceived speed all depended on kinematogram type, with good agreement between pursuit gain and perceived speed. For transparent motion, pursuit gain and perceived speed were independent of coherence level. For white and Brownian motions, pursuit gain and perceived speed increased with coherence but were higher for white than for Brownian motion. This suggests that under our conditions, the pursuit system integrates across all directions of motion but not across all speeds. PMID:21149307

Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions.

PubMed

Soydaş, Emine; Bozkaya, Uğur

2015-04-14

An assessment of orbital-optimized MP2.5 (OMP2.5) [ Bozkaya, U.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 204105 ] for thermochemistry and kinetics is presented. The OMP2.5 method is applied to closed- and open-shell reaction energies, barrier heights, and aromatic bond dissociation energies. The performance of OMP2.5 is compared with that of the MP2, OMP2, MP2.5, MP3, OMP3, CCSD, and CCSD(T) methods. For most of the test sets, the OMP2.5 method performs better than MP2.5 and CCSD, and provides accurate results. For barrier heights of radical reactions and aromatic bond dissociation energies OMP2.5-MP2.5, OMP2-MP2, and OMP3-MP3 differences become obvious. Especially, for aromatic bond dissociation energies, standard perturbation theory (MP) approaches dramatically fail, providing mean absolute errors (MAEs) of 22.5 (MP2), 17.7 (MP2.5), and 12.8 (MP3) kcal mol(-1), while the MAE values of the orbital-optimized counterparts are 2.7, 2.4, and 2.4 kcal mol(-1), respectively. Hence, there are 5-8-folds reductions in errors when optimized orbitals are employed. Our results demonstrate that standard MP approaches dramatically fail when the reference wave function suffers from the spin-contamination problem. On the other hand, the OMP2.5 method can reduce spin-contamination in the unrestricted Hartree-Fock (UHF) initial guess orbitals. For overall evaluation, we conclude that the OMP2.5 method is very helpful not only for challenging open-shell systems and transition-states but also for closed-shell molecules. Hence, one may prefer OMP2.5 over MP2.5 and CCSD as an O(N(6)) method, where N is the number of basis functions, for thermochemistry and kinetics. The cost of the OMP2.5 method is comparable with that of CCSD for energy computations. However, for analytic gradient computations, the OMP2.5 method is only half as expensive as CCSD.

Purification and biochemical characterization of a novel ecto-apyrase, MP67, from Mimosa pudica.

PubMed

Okuhata, Riku; Takishima, Takeshi; Nishimura, Naoaki; Ueda, Shogo; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2011-09-01

We have previously reported the presence of an apyrase in Mimosa pudica. However, only limited information is available for this enzyme. Thus, in this study, the apyrase was purified to homogeneity. The purified enzyme had a molecular mass of around 67 kD and was able to hydrolyze both nucleotide triphosphate and nucleotide diphosphate as substrates. The ratio of ATP to ADP hydrolysis velocity of the purified protein was 0.01 in the presence of calcium ion, showing extremely high substrate specificity toward ADP. Thus, we designated this novel apyrase as MP67. A cDNA clone of MP67 was obtained using primers designed from the amino acid sequence of trypsin-digested fragments of the protein. In addition, rapid amplification of cDNA ends-polymerase chain reaction was performed to clone a conventional apyrase (MpAPY2). Comparison of the deduced amino acid sequences showed that MP67 is similar to ecto-apyrases; however, it was distinct from conventional apyrase based on phylogenetic classification. MP67 and MpAPY2 were expressed in Escherichia coli, and the recombinant proteins were purified. The recombinant MP67 showed high substrate specificity toward ADP rather than ATP. A polyclonal antibody raised against the recombinant MP67 was used to examine the tissue distribution and localization of native MP67 in the plant. The results showed that MP67 was ubiquitously distributed in various tissues, most abundantly in leaves, and was localized to plasma membranes. Thus, MP67 is a novel ecto-apyrase with extremely high substrate specificity for ADP.

Purification and Biochemical Characterization of a Novel Ecto-Apyrase, MP67, from Mimosa pudica1[C][W][OA

PubMed Central

Okuhata, Riku; Takishima, Takeshi; Nishimura, Naoaki; Ueda, Shogo; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2011-01-01

We have previously reported the presence of an apyrase in Mimosa pudica. However, only limited information is available for this enzyme. Thus, in this study, the apyrase was purified to homogeneity. The purified enzyme had a molecular mass of around 67 kD and was able to hydrolyze both nucleotide triphosphate and nucleotide diphosphate as substrates. The ratio of ATP to ADP hydrolysis velocity of the purified protein was 0.01 in the presence of calcium ion, showing extremely high substrate specificity toward ADP. Thus, we designated this novel apyrase as MP67. A cDNA clone of MP67 was obtained using primers designed from the amino acid sequence of trypsin-digested fragments of the protein. In addition, rapid amplification of cDNA ends-polymerase chain reaction was performed to clone a conventional apyrase (MpAPY2). Comparison of the deduced amino acid sequences showed that MP67 is similar to ecto-apyrases; however, it was distinct from conventional apyrase based on phylogenetic classification. MP67 and MpAPY2 were expressed in Escherichia coli, and the recombinant proteins were purified. The recombinant MP67 showed high substrate specificity toward ADP rather than ATP. A polyclonal antibody raised against the recombinant MP67 was used to examine the tissue distribution and localization of native MP67 in the plant. The results showed that MP67 was ubiquitously distributed in various tissues, most abundantly in leaves, and was localized to plasma membranes. Thus, MP67 is a novel ecto-apyrase with extremely high substrate specificity for ADP. PMID:21788364

Preclinical medical students’ understandings of academic and medical professionalism: visual analysis of mind maps

PubMed Central

Rees, Charlotte E

2017-01-01

Introduction Several studies have begun to explore medical students’ understandings of professionalism generally and medical professionalism specifically. Despite espoused relationships between academic (AP) and medical professionalism (MP), previous research has not yet investigated students’ conceptualisations of AP and MP and the relationships between the two. Objectives The current study, based on innovative visual analysis of mind maps, therefore aims to contribute to the developing literature on how professionalism is understood. Methods We performed a multilayered analysis of 98 mind maps from 262 first-year medical students, including analysing textual and graphical elements of AP, MP and the relationships between AP and MP. Results The most common textual attributes of AP were learning, lifestyle and personality, while attributes of MP were knowledge, ethics and patient-doctor relations. Images of books, academic caps and teachers were used most often to represent AP, while images of the stethoscope, doctor and red cross were used to symbolise MP. While AP-MP relations were sometimes indicated through co-occurring text, visual connections and higher-order visual metaphors, many students struggled to articulate the relationships between AP and MP. Conclusions While the mind maps’ textual attributes shared similarities with those found in previous research, suggesting the universality of some professionalism attributes, our study provides new insights into students’ conceptualisations of AP, MP and AP-MP relationships. We encourage medical educators to help students develop their understandings of AP, MP and AP-MP relationships, plus consider the feasibility and value of mind maps as a source of visual data for medical education research. PMID:28821520

Macular pigment and lutein supplementation in retinitis pigmentosa and Usher syndrome.

PubMed

Aleman, T S; Duncan, J L; Bieber, M L; de Castro, E; Marks, D A; Gardner, L M; Steinberg, J D; Cideciyan, A V; Maguire, M G; Jacobson, S G

2001-07-01

To determine macular pigment (MP) in patients with inherited retinal degeneration and the response of MP and vision to supplementation of lutein. Patients with retinitis pigmentosa (RP) or Usher syndrome and normal subjects had MP optical density profiles measured with heterochromatic flicker photometry. Serum carotenoids, visual acuity, foveal sensitivity, and retinal thickness (by optical coherence tomography [OCT]) were quantified. The effects on MP and central vision of 6 months of lutein supplementation at 20 mg/d were determined. MP density in the patients as a group did not differ from normal. Among patients with lower MP, there was a higher percentage of females, smokers, and light-colored irides. Disease expression tended to be more severe in patients with lower MP. Inner retinal thickness by OCT correlated positively with MP density in the patients. After supplementation, all participants showed an increase in serum lutein. Only approximately half the patients showed a statistically significant increase in MP. Retinal nonresponders had slightly greater disease severity but were otherwise not distinguishable from responders. Central vision was unchanged after supplementation. Factors previously associated with lower or higher MP density in normal subjects showed similar associations in RP and Usher syndrome. In addition, MP in patients may be affected by stage of retinal disease, especially that leading to abnormal foveal architecture. MP could be augmented by supplemental lutein in many but not all patients. There was no change in central vision after 6 months of lutein supplementation, but long-term influences on the natural history of these retinal degenerations require further study.

Assessment of the overlap metric in the context of RI-MP2 and atomic batched tensor decomposed MP2

NASA Astrophysics Data System (ADS)

Schmitz, Gunnar; Christiansen, Ove

2018-06-01

The resolution-of-the-identity approximation (RI) is a standard tool to accelerate the evaluation of two electron repulsion integrals. However introducing further approximations on top of for example RI-MP2, makes it important to check again the made choices. Usually the so called Coulomb metric is used. An alternative is the less accurate overlap metric, which has the benefit of a faster decay with distance. We encountered both choices in our atomic batched tensor decomposed MP2 (AB-MP2) and went with the Coulomb metric for the safe choice. In this work we re-investigate the choice of Coulomb and overlap metric for RI-MP2 and AB-MP2.

Recognition and characterization of unstructured environmental sounds

NASA Astrophysics Data System (ADS)

Chu, Selina

2011-12-01

Environmental sounds are what we hear everyday, or more generally sounds that surround us ambient or background audio. Humans utilize both vision and hearing to respond to their surroundings, a capability still quite limited in machine processing. The first step toward achieving multimodal input applications is the ability to process unstructured audio and recognize audio scenes (or environments). Such ability would have applications in content analysis and mining of multimedia data or improving robustness in context aware applications through multi-modality, such as in assistive robotics, surveillances, or mobile device-based services. The goal of this thesis is on the characterization of unstructured environmental sounds for understanding and predicting the context surrounding of an agent or device. Most research on audio recognition has focused primarily on speech and music. Less attention has been paid to the challenges and opportunities for using audio to characterize unstructured audio. My research focuses on investigating challenging issues in characterizing unstructured environmental audio and to develop novel algorithms for modeling the variations of the environment. The first step in building a recognition system for unstructured auditory environment was to investigate on techniques and audio features for working with such audio data. We begin by performing a study that explore suitable features and the feasibility of designing an automatic environment recognition system using audio information. In my initial investigation to explore the feasibility of designing an automatic environment recognition system using audio information, I have found that traditional recognition and feature extraction for audio were not suitable for environmental sound, as they lack any type of structures, unlike those of speech and music which contain formantic and harmonic structures, thus dispelling the notion that traditional speech and music recognition techniques can simply be used for realistic environmental sound. Natural unstructured environment sounds contain a large variety of sounds, which are in fact noise-like and are not effectively modeled by Mel-frequency cepstral coefficients (MFCCs) or other commonly-used audio features, e.g. energy, zero-crossing, etc. Due to the lack of appropriate features that is suitable for environmental audio and to achieve a more effective representation, I proposed a specialized feature extraction algorithm for environmental sounds that utilizes the matching pursuit (MP) algorithm to learn the inherent structure of each type of sounds, which we called MP-features. MP-features have shown to capture and represent sounds from different sources and different ranges, where frequency domain features (e.g., MFCCs) fail and can be advantageous when combining with MFCCs to improve the overall performance. The third component leads to our investigation on modeling and detecting the background audio. One of the goals of this research is to characterize an environment. Since many events would blend into the background, I wanted to look for a way to achieve a general model for any particular environment. Once we have an idea of the background, it will enable us to identify foreground events even if we havent seen these events before. Therefore, the next step is to investigate into learning the audio background model for each environment type, despite the occurrences of different foreground events. In this work, I presented a framework for robust audio background modeling, which includes learning the models for prediction, data knowledge and persistent characteristics of the environment. This approach has the ability to model the background and detect foreground events as well as the ability to verify whether the predicted background is indeed the background or a foreground event that protracts for a longer period of time. In this work, I also investigated the use of a semi-supervised learning technique to exploit and label new unlabeled audio data. The final components of my thesis will involve investigating on learning sound structures for generalization and applying the proposed ideas to context aware applications. The inherent nature of environmental sound is noisy and contains relatively large amounts of overlapping events between different environments. Environmental sounds contain large variances even within a single environment type, and frequently, there are no divisible or clear boundaries between some types. Traditional methods of classification are generally not robust enough to handle classes with overlaps. This audio, hence, requires representation by complex models. Using deep learning architecture provides a way to obtain a generative model-based method for classification. Specifically, I considered the use of Deep Belief Networks (DBNs) to model environmental audio and investigate its applicability with noisy data to improve robustness and generalization. A framework was proposed using composite-DBNs to discover high-level representations and to learn a hierarchical structure for different acoustic environments in a data-driven fashion. Experimental results on real data sets demonstrate its effectiveness over traditional methods with over 90% accuracy on recognition for a high number of environmental sound types.

Thigmomorphogenesis: the role of ethylene in the response of Pinus taeda and Abies fraseri to mechanical perturbation

NASA Technical Reports Server (NTRS)

Telewski, F. W.; Jaffe, M. J.

1986-01-01

Ethylene production was monitored for 48 h in two half-sibs of Pinus taeda L. grown in the greenhouse and given mechanical perturbation (MP) by flexing; and for 22 h in Abies fraseri (Pursh) Poir. grown in the field and exposed to wind-mediated MP. Both species produced a peak of ethylene 18 h after MP. Seedlings of P. taeda exposed to MP for the duration of the growing season (preconditioned) produced less ethylene compared to non-MP controls, with a peak production at 8 h. One half-sib which responded to MP by an increase in radial growth produced 16 times more ethylene than another half-sib which had no significant change in radial growth. Preconditioned A. fraseri produced no significant quantities of ethylene after MP. The production of wound ethylene appears to be different from MP-induced ethylene. When an ethylene-generating solution was applied to P. taeda seedlings, it mimicked many of the morphological and mechanical characteristics of MP seedlings. The putative role of ethylene in the thigmomorphogenetic response is addressed.

OpenMP 4.5 Validation and Verification Suite

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

Pophale, Swaroop S; Bernholdt, David E; Hernandez, Oscar R

2017-12-15

OpenMP, a directive-based programming API, introduce directives for accelerator devices that programmers are starting to use more frequently in production codes. To make sure OpenMP directives work correctly across architectures, it is critical to have a mechanism that tests for an implementation's conformance to the OpenMP standard. This testing process can uncover ambiguities in the OpenMP specification, which helps compiler developers and users make a better use of the standard. We fill this gap through our validation and verification test suite that focuses on the offload directives available in OpenMP 4.5.

Nonmydriatic fluorescence-based quantitative imaging of human macular pigment distributions

NASA Astrophysics Data System (ADS)

Sharifzadeh, Mohsen; Bernstein, Paul S.; Gellermann, Werner

2006-10-01

We have developed a CCD-camera-based nonmydriatic instrument that detects fluorescence from retinal lipofuscin chromophores ("autofluorescence") as a means to indirectly quantify and spatially image the distribution of macular pigment (MP). The lipofuscin fluorescence intensity is reduced at all retinal locations containing MP, since MP has a competing absorption in the blue-green wavelength region. Projecting a large diameter, 488 nm excitation spot onto the retina, centered on the fovea, but extending into the macular periphery, and comparing lipofuscin fluorescence intensities outside and inside the foveal area, it is possible to spatially map out the distribution of MP. Spectrally selective detection of the lipofuscin fluorescence reveals an important wavelength dependence of the obtainable image contrast and deduced MP optical density levels, showing that it is important to block out interfering fluorescence contributions in the detection setup originating from ocular media such as the lens. Measuring 70 healthy human volunteer subjects with no ocular pathologies, we find widely varying spatial extent of MP, distinctly differing distribution patterns of MP, and strongly differing absolute MP levels among individuals. Our population study suggests that MP imaging based on lipofuscin fluorescence is useful as a relatively simple, objective, and quantitative noninvasive optical technique suitable to rapidly screen MP levels and distributions in healthy humans with undilated pupils.

Regulation of IL-10 expression by upstream stimulating factor (USF-1) in glioma-associated microglia.

PubMed

Zhang, Leying; Handel, Michelle Van; Schartner, Jill M; Hagar, Aaron; Allen, Grant; Curet, Marjorie; Badie, Behnam

2007-03-01

Understanding the local CNS immune response to neoplasms is essential in the development of immune-based treatments for malignant brain tumors. Using rodent glioma models, we have recently found tumor-associated microglia/macrophages (MG/MP) to be less responsive to known MG/MP activators such as CpG, LPS and IFN-gamma. To understand the mechanism of MG/MP suppression, nuclear extracts from rodent intracranial C6 gliomas, C6 glioma-associated MG/MP, normal brain, and normal MG/MP were obtained and studied using Electrophoretic Mobility Shift Assay (EMSA). Among the nuclear factors studied (AP-1, IRF, USF-1 and Stat-1) only USF-1, which is constitutively expressed in most cells, was down-regulated in tumor-associated MG/MP, but not normal MG/MP. Because tumor-associated MG/MP had higher expression of IL-10 (but not TNF-alpha or TGF-beta), we evaluated the role of USF-1 on IL-10 expression. siRNA mediated inhibition of USF-1 expression in primary MG/MP cultures resulted in up-regulation of IL-10 mRNA but not TNF-alpha or TGF-beta. These findings suggest that USF-1 may play a role in IL-10 regulation in MG/MP in brain tumors.

Pharmacogenetic determinants of mercaptopurine disposition in children with acute lymphoblastic leukemia.

PubMed

Adam de Beaumais, Tiphaine; Jacqz-Aigrain, Evelyne

2012-09-01

The backbone of drug therapy used in acute lymphoblastic leukemia (ALL) in children includes 6-mercaptopurine (6-MP). Intracellular metabolism of this prodrug is a key component of the therapeutic response. Many metabolizing enzymes are involved in 6-MP disposition and active 6-MP metabolites are represented by 6-thioguanine nucleotides (6-TGN) and methylated metabolites primarily methylated by the thiopurine S-methyltransferase enzyme (TPMT). The genetic polymorphism affecting TPMT activity displays an important inter-subject variability in metabolites pharmacokinetics and influences the balance between 6-MP efficacy and toxicity: patients with high 6-TGN levels are at risk of myelosuppression while patients with high levels of methylated derivates are at hepatotoxic risk. However, the genetic TPMT polymorphism does not explain all 6-MP adverse events and some severe toxicities leading to life-threatening conditions remain unexplained. Additional single nucleotide polymorphisms (SNPs) in genes encoding enzymes involved in 6-MP metabolism and 6-MP transporters may also be responsible for this inter-individual 6-MP response variability. This review presents the pharmacogenetic aspects of 6-MP metabolism in great detail. We have focused on published data on ALL treatment supporting the great potential of 6-MP pharmacogenetics to improve efficacy, tolerance, and event-free survival rates in children with ALL.

Optimization of a GCaMP calcium indicator for neural activity imaging.

PubMed

Akerboom, Jasper; Chen, Tsai-Wen; Wardill, Trevor J; Tian, Lin; Marvin, Jonathan S; Mutlu, Sevinç; Calderón, Nicole Carreras; Esposti, Federico; Borghuis, Bart G; Sun, Xiaonan Richard; Gordus, Andrew; Orger, Michael B; Portugues, Ruben; Engert, Florian; Macklin, John J; Filosa, Alessandro; Aggarwal, Aman; Kerr, Rex A; Takagi, Ryousuke; Kracun, Sebastian; Shigetomi, Eiji; Khakh, Baljit S; Baier, Herwig; Lagnado, Leon; Wang, Samuel S-H; Bargmann, Cornelia I; Kimmel, Bruce E; Jayaraman, Vivek; Svoboda, Karel; Kim, Douglas S; Schreiter, Eric R; Looger, Loren L

2012-10-03

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of "GCaMP5" sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.

Perceptual learning modifies untrained pursuit eye movements.

PubMed

Szpiro, Sarit F A; Spering, Miriam; Carrasco, Marisa

2014-07-07

Perceptual learning improves detection and discrimination of relevant visual information in mature humans, revealing sensory plasticity. Whether visual perceptual learning affects motor responses is unknown. Here we implemented a protocol that enabled us to address this question. We tested a perceptual response (motion direction estimation, in which observers overestimate motion direction away from a reference) and a motor response (voluntary smooth pursuit eye movements). Perceptual training led to greater overestimation and, remarkably, it modified untrained smooth pursuit. In contrast, pursuit training did not affect overestimation in either pursuit or perception, even though observers in both training groups were exposed to the same stimuli for the same time period. A second experiment revealed that estimation training also improved discrimination, indicating that overestimation may optimize perceptual sensitivity. Hence, active perceptual training is necessary to alter perceptual responses, and an acquired change in perception suffices to modify pursuit, a motor response. © 2014 ARVO.

Perceptual learning modifies untrained pursuit eye movements

PubMed Central

Szpiro, Sarit F. A.; Spering, Miriam; Carrasco, Marisa

2014-01-01

Perceptual learning improves detection and discrimination of relevant visual information in mature humans, revealing sensory plasticity. Whether visual perceptual learning affects motor responses is unknown. Here we implemented a protocol that enabled us to address this question. We tested a perceptual response (motion direction estimation, in which observers overestimate motion direction away from a reference) and a motor response (voluntary smooth pursuit eye movements). Perceptual training led to greater overestimation and, remarkably, it modified untrained smooth pursuit. In contrast, pursuit training did not affect overestimation in either pursuit or perception, even though observers in both training groups were exposed to the same stimuli for the same time period. A second experiment revealed that estimation training also improved discrimination, indicating that overestimation may optimize perceptual sensitivity. Hence, active perceptual training is necessary to alter perceptual responses, and an acquired change in perception suffices to modify pursuit, a motor response. PMID:25002412

Memory and decision making in the frontal cortex during visual motion processing for smooth pursuit eye movements.

PubMed

Shichinohe, Natsuko; Akao, Teppei; Kurkin, Sergei; Fukushima, Junko; Kaneko, Chris R S; Fukushima, Kikuro

2009-06-11

Cortical motor areas are thought to contribute "higher-order processing," but what that processing might include is unknown. Previous studies of the smooth pursuit-related discharge of supplementary eye field (SEF) neurons have not distinguished activity associated with the preparation for pursuit from discharge related to processing or memory of the target motion signals. Using a memory-based task designed to separate these components, we show that the SEF contains signals coding retinal image-slip-velocity, memory, and assessment of visual motion direction, the decision of whether to pursue, and the preparation for pursuit eye movements. Bilateral muscimol injection into SEF resulted in directional errors in smooth pursuit, errors of whether to pursue, and impairment of initial correct eye movements. These results suggest an important role for the SEF in memory and assessment of visual motion direction and the programming of appropriate pursuit eye movements.

Purification, antitumor and immunomodulatory activity of polysaccharides from soybean residue fermented with Morchella esculenta.

PubMed

Li, Shuhong; Gao, Ang; Dong, Shuang; Chen, Ye; Sun, Shuang; Lei, Zhongfang; Zhang, Zhenya

2017-03-01

Crude polysaccharides (MPS) from soybean residue fermented with Morchella esculenta were extracted and purified by DEAE Sephadex A-50 chromatography and Sephadex G-100 size-exclusion chromatography in sequence. Three main fractions MP-1, MP-3 and MP-4 were obtained during the purification steps. The recovery rates based on MPS used were 26.2%, 29.1% and 18.7% for MP-1, MP-3 and MP-4 respectively. The monosaccharide composition, ultraviolet spectrum, infrared spectrum and NMR of the three fractions were analyzed. Furthermore, the influence of polysaccharides fractions upon activation of macrophage cells (RAW 264.7), antitumor activities of the human hepatocellular cell line (HepG-2) and human cervical carcinoma cells (Hela) in vitro were evaluated. The results indicated that the proliferation of MP-3 on RAW 264.7 was 313.57% at 25μg/mL, which is high while MP-1 had a higher growth inhibition effect on HepG-2 cells of 68.01% at concentration of 50μg/mL. The fractions of MP-1, MP-3 and MP-4 induced apoptosis in HepG-2 cells and Hela cells by arresting cell cycle progression at the G 0 /G 1 phase. These findings suggest that the purified polysaccharides fractions may be a potent candidate for human hepatocellular and cervical carcinoma treatment and prevention in functional foods and pharmacological fields. Copyright © 2016 Elsevier B.V. All rights reserved.

PD Trafficking of Potato Leaf Roll Virus Movement Protein in Arabidopsis Depends on Site-specific Protein Phosphorylation

PubMed Central

Sonnewald, Uwe

2011-01-01

Many plant viruses encode for specialized movement proteins (MP) to facilitate passage of viral material to and through plasmodesmata (PD). To analyze intracellular trafficking of potato leaf roll virus (PLRV) movement protein (MP17) we performed GFP fusion experiments with distinct deletion variants of MP17. These studies revealed that the C-terminus of MP17 is essential but not sufficient for PD targeting. Interestingly, fusion of GFP to three C-terminal MP17 deletion variants resulted in the accumulation of GFP in chloroplasts. This indicates that MP17 harbors hidden plastid targeting sequences. Previous studies showed that posttranslational protein phosphorylation influences PD targeting of MP and virus spread. Analysis of MP17-derived phospho-peptides by mass spectrometry revealed four phosphorylated serine residues (S71, S79, S137, and S140). Site-directed mutagenesis of S71/S79 and S137/S140 showed that the C-terminal serine residues S137/S140 are dispensable for PD targeting. However, exchange of S71/S79 to A71/A79 abolished PD targeting of the mutated MP17 protein. To mimic phosphorylation of S71/S79 both amino acids were substituted by aspartic acid. The resulting D71/D79 variant of MP17 was efficiently targeted to PD. Further deletion analysis showed that PD targeting of MP17 is dependent on the C-terminus, phosphorylation of S71 and/or S79 and a N-terminal domain. PMID:22645527

Sun light mediated synthesis of gold nanoparticles as carrier for 6-mercaptopurine: Preparation, characterization and toxicity studies in zebrafish embryo model

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

Ganeshkumar, Moorthy; Sastry, Thotapalli Parvathaleswara; Sathish Kumar, Muniram

2012-09-15

Highlights: ► Gold nanoparticles prepared using eco-friendly method with good in vitro stability. ► Can be used as drug delivery system. ► Did not show any toxicity in zebrafish embryo. ► More toxic to cancer cells when compared to N-Au-Mp and Mp. -- Abstract: The objective of this study is to synthesize green chemistry based gold nanoparticles by sun light irradiation method. The prepared gold nanoparticles (AuNPs) were modified using folic acid and then coupled with 6-mercaptopurine. These modified nanoparticles were used as a tool for targeted drug delivery to treat laryngeal cancer. In the present study, novel bionanocomposites containingmore » nutrient agar coated gold nano particles (N-AuNPs) coupled with 6-mercaptopurine (drug) (N-AuNPs-Mp), folic acid (ligand) (N-AuNPs-Mp-Fa) and rhodamine (dye) (N-AuNPs-Rd), a fluorescent agent, were prepared and characterized by IR, UV, TEM, Particle size analysis and in vitro stability. The toxicity and fluorescence of N-Au was studied using zebrafish embryo model. The in vitro cytotoxicity of free Mp, N-Au-Mp and N-Au-Mp-Fa against HEp-2 cells was compared and found that the amount of Mp required to achieve 50% of growth of inhibition (IC{sub 50}) was much lower in N-Au-Mp-Fa than in free Mp and N-Au-Mp.« less

Clinical application of eye movement tasks as an aid to understanding Parkinson's disease pathophysiology.

PubMed

Fukushima, Kikuro; Fukushima, Junko; Barnes, Graham R

2017-05-01

Parkinson's disease (PD) is a progressive neurodegenerative disorder of the basal ganglia. Most PD patients suffer from somatomotor and oculomotor disorders. The oculomotor system facilitates obtaining accurate information from the visual world. If a target moves slowly in the fronto-parallel plane, tracking eye movements occur that consist primarily of smooth-pursuit interspersed with corrective saccades. Efficient smooth-pursuit requires appropriate target selection and predictive compensation for inherent processing delays. Although pursuit impairment, e.g. as latency prolongation or low gain (eye velocity/target velocity), is well known in PD, normal aging alone results in such changes. In this article, we first briefly review some basic features of smooth-pursuit, then review recent results showing the specific nature of impaired pursuit in PD using a cue-dependent memory-based smooth-pursuit task. This task was initially used for monkeys to separate two major components of prediction (image-motion direction memory and movement preparation), and neural correlates were examined in major pursuit pathways. Most PD patients possessed normal cue-information memory but extra-retinal mechanisms for pursuit preparation and execution were dysfunctional. A minority of PD patients had abnormal cue-information memory or difficulty in understanding the task. Some PD patients with normal cue-information memory changed strategy to initiate smooth tracking. Strategy changes were also observed to compensate for impaired pursuit during whole body rotation while the target moved with the head. We discuss PD pathophysiology by comparing eye movement task results with neuropsychological and motor symptom evaluations of individual patients and further with monkey results, and suggest possible neural circuits for these functions/dysfunctions.

Compression of surface myoelectric signals using MP3 encoding.

PubMed

Chan, Adrian D C

2011-01-01

The potential of MP3 compression of surface myoelectric signals is explored in this paper. MP3 compression is a perceptual-based encoder scheme, used traditionally to compress audio signals. The ubiquity of MP3 compression (e.g., portable consumer electronics and internet applications) makes it an attractive option for remote monitoring and telemedicine applications. The effects of muscle site and contraction type are examined at different MP3 encoding bitrates. Results demonstrate that MP3 compression is sensitive to the myoelectric signal bandwidth, with larger signal distortion associated with myoelectric signals that have higher bandwidths. Compared to other myoelectric signal compression techniques reported previously (embedded zero-tree wavelet compression and adaptive differential pulse code modulation), MP3 compression demonstrates superior performance (i.e., lower percent residual differences for the same compression ratios).

Preclinical medical students' understandings of academic and medical professionalism: visual analysis of mind maps.

PubMed

Janczukowicz, Janusz; Rees, Charlotte E

2017-08-18

Several studies have begun to explore medical students' understandings of professionalism generally and medical professionalism specifically. Despite espoused relationships between academic (AP) and medical professionalism (MP), previous research has not yet investigated students' conceptualisations of AP and MP and the relationships between the two. The current study, based on innovative visual analysis of mind maps, therefore aims to contribute to the developing literature on how professionalism is understood. We performed a multilayered analysis of 98 mind maps from 262 first-year medical students, including analysing textual and graphical elements of AP, MP and the relationships between AP and MP. The most common textual attributes of AP were learning, lifestyle and personality, while attributes of MP were knowledge, ethics and patient-doctor relations. Images of books, academic caps and teachers were used most often to represent AP, while images of the stethoscope, doctor and red cross were used to symbolise MP. While AP-MP relations were sometimes indicated through co-occurring text, visual connections and higher-order visual metaphors, many students struggled to articulate the relationships between AP and MP. While the mind maps' textual attributes shared similarities with those found in previous research, suggesting the universality of some professionalism attributes, our study provides new insights into students' conceptualisations of AP, MP and AP-MP relationships. We encourage medical educators to help students develop their understandings of AP, MP and AP-MP relationships, plus consider the feasibility and value of mind maps as a source of visual data for medical education research. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Calciuric effects of protein and potassium bicarbonate but not of sodium chloride or phosphate can be detected acutely in adult women and men.

PubMed

Whiting, S J; Anderson, D J; Weeks, S J

1997-05-01

An acute load test was used to test the influence of dietary factors on urinary calcium excretion. In study 1, 10 fasting premenopausal women consumed test meals providing a moderate amount of protein (MP; 23 g), MP plus 23 mmol KHCO3 (MP+K), MP plus 23 mmol NaCl (MP+Na), and a high amount of protein (HP; 53 g), HP plus 70 mmol KHCO3 (HP+K), and HP plus 70 mmol NaCl (HP+Na). Protein was casein:lactalbumin (80:20), except for the treatments with added sodium chloride, to which only casein was added. In study 2, the effects of HP and HP plus 50 mmol KHCO3 (HP+K) were compared with those of MP or MP plus 7.5 mmol phosphate (MP+Pi), equaling the additional phosphate of HP, in 10 adult men. Subjects completed all treatments in random order. In study 1, the peak of calcium excretion was at 3 h for all treatments, except for HP+K, which indicated an acute hypocalciuric effect of potassium. Unexpectedly, there was no hypercalciuric effect of adding sodium chloride, nor was urine sodium increased. In study 2, calcium excretion was significantly higher with HP than with MP+Pi but not with MP at 3 h, indicating an acute hypercalciuric effect of protein alone. A hypocalciuric effect of potassium (HP+K compared with HP) but not of phosphate (MP compared with MP+Pi) was seen. An acute load test measuring changes 3 h postload was appropriate for examining the calciuric effects of protein and potassium bicarbonate, but not those of sodium chloride or phosphate in adults.

Data preprocessing for determining outer/inner parallelization in the nested loop problem using OpenMP

NASA Astrophysics Data System (ADS)

Handhika, T.; Bustamam, A.; Ernastuti, Kerami, D.

2017-07-01

Multi-thread programming using OpenMP on the shared-memory architecture with hyperthreading technology allows the resource to be accessed by multiple processors simultaneously. Each processor can execute more than one thread for a certain period of time. However, its speedup depends on the ability of the processor to execute threads in limited quantities, especially the sequential algorithm which contains a nested loop. The number of the outer loop iterations is greater than the maximum number of threads that can be executed by a processor. The thread distribution technique that had been found previously only be applied by the high-level programmer. This paper generates a parallelization procedure for low-level programmer in dealing with 2-level nested loop problems with the maximum number of threads that can be executed by a processor is smaller than the number of the outer loop iterations. Data preprocessing which is related to the number of the outer loop and the inner loop iterations, the computational time required to execute each iteration and the maximum number of threads that can be executed by a processor are used as a strategy to determine which parallel region that will produce optimal speedup.

A Localization Method for Underwater Wireless Sensor Networks Based on Mobility Prediction and Particle Swarm Optimization Algorithms

PubMed Central

Zhang, Ying; Liang, Jixing; Jiang, Shengming; Chen, Wei

2016-01-01

Due to their special environment, Underwater Wireless Sensor Networks (UWSNs) are usually deployed over a large sea area and the nodes are usually floating. This results in a lower beacon node distribution density, a longer time for localization, and more energy consumption. Currently most of the localization algorithms in this field do not pay enough consideration on the mobility of the nodes. In this paper, by analyzing the mobility patterns of water near the seashore, a localization method for UWSNs based on a Mobility Prediction and a Particle Swarm Optimization algorithm (MP-PSO) is proposed. In this method, the range-based PSO algorithm is used to locate the beacon nodes, and their velocities can be calculated. The velocity of an unknown node is calculated by using the spatial correlation of underwater object’s mobility, and then their locations can be predicted. The range-based PSO algorithm may cause considerable energy consumption and its computation complexity is a little bit high, nevertheless the number of beacon nodes is relatively smaller, so the calculation for the large number of unknown nodes is succinct, and this method can obviously decrease the energy consumption and time cost of localizing these mobile nodes. The simulation results indicate that this method has higher localization accuracy and better localization coverage rate compared with some other widely used localization methods in this field. PMID:26861348

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 5 : I-205 NB ramp flow & ML speed-flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ramp flow and ML speed-flow plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson C...

The Effects of Varying Ratios of Physical and Mental Practice, and Task Difficulty on Performance of a Tonal Pattern

ERIC Educational Resources Information Center

Cahn, Dan

2008-01-01

Sixty undergraduate students who had completed at least one semester of jazz improvisation were assigned to either: (a) physical practice (PP); (b) mental practice (MP); (c) combined 66 percent PP and 33 percent MP (66%PP:33%MP); and (d) combined 33 percent PP and 66 percent MP (33%PP:66%MP) groups. Subjects were to perform a 3-1-7-5 tonal pattern…

Apheresis platelet concentrates contain platelet-derived and endothelial cell-derived microparticles.

PubMed

Rank, A; Nieuwland, R; Liebhardt, S; Iberer, M; Grützner, S; Toth, B; Pihusch, R

2011-02-01

Microparticles (MP) are membrane vesicles with thrombogenic and immunomodulatory properties. We determined MP subgroups from resting platelets, activated platelets and endothelial cells in donors and apheresis platelet concentrates (PC). MP were double stained with annexin V and CD61 (platelet-derived MP; PMP), P-selectin or CD63 (MP from activated platelets) and CD144 plus E-selectin (endothelial cell-derived MP; EMP) and detected by flow cytometry in platelet donors (n=36) and apheresis PC (n=11; Trima™). PC contained MP, mainly from resting platelets [93% (90-95)], and minor fractions of PMP from activated platelets [P-selectin(+) or CD63(+); 4·8% (3·2-7·7) and 2·6% (2·0-4·0)]. Compared to donors, levels of annexin V+ MP, PMP, P-selectin(+) and CD63(+) MP were 1·7-, 2·3-, 8·6- and 3·1-fold higher in PC (all P<0·05). During storage (1-5 days), levels of annexin V+ MP and PMP did not increase, although small increases in the fraction of P-selectin(+) or CD63(+) MP occurred (both P<0·05). PC also contained EMP, which were 2·6- to 3·7-fold enriched in PC compared to donors (P<0·05). Transfusion of apheresis PC also results in transfusion of HLA-carrying PMP and EMP. This might counteract the aim of reducing transfused HLA load by leucodepletion. The increases in PMP exposing P-selectin or CD63 reflect mild platelet activation during storage. We conclude that in leucodepleted platelet apheresis using fluidized particle bed technology, MP are harvested mainly from the donor by apheresis. Improvement in apheresis technology might reduce MP load. © 2010 The Author(s). Vox Sanguinis © 2010 International Society of Blood Transfusion.

GPU accelerated dynamic functional connectivity analysis for functional MRI data.

PubMed

Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu

2015-07-01

Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

PubMed

Ruymgaart, A Peter; Elber, Ron

2012-11-13

We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported in our initial GPU implementation that did not include a water-specific code. Another optimization is the implementation of constrained dynamics entirely on the GPU. The routine, which enforces constraints of all bonds, runs in parallel on multiple Open-MP cores or entirely on the GPU. It is based on Conjugate Gradient solution of the Lagrange multipliers (CG SHAKE). The GPU implementation is partially in double precision and requires no communication with the CPU during the execution of the SHAKE algorithm. The (parallel) implementation of SHAKE allows an increase of the time step to 2.0fs while maintaining excellent energy conservation. Interestingly, CG SHAKE is faster than the usual bond relaxation algorithm even on a single core if high accuracy is expected. The significant speedup of the optimized components transfers the computational bottleneck of the MD calculation to the reciprocal part of Particle Mesh Ewald (PME).

Premotor neurons encode torsional eye velocity during smooth-pursuit eye movements

NASA Technical Reports Server (NTRS)

Angelaki, Dora E.; Dickman, J. David

2003-01-01

Responses to horizontal and vertical ocular pursuit and head and body rotation in multiple planes were recorded in eye movement-sensitive neurons in the rostral vestibular nuclei (VN) of two rhesus monkeys. When tested during pursuit through primary eye position, the majority of the cells preferred either horizontal or vertical target motion. During pursuit of targets that moved horizontally at different vertical eccentricities or vertically at different horizontal eccentricities, eye angular velocity has been shown to include a torsional component the amplitude of which is proportional to half the gaze angle ("half-angle rule" of Listing's law). Approximately half of the neurons, the majority of which were characterized as "vertical" during pursuit through primary position, exhibited significant changes in their response gain and/or phase as a function of gaze eccentricity during pursuit, as if they were also sensitive to torsional eye velocity. Multiple linear regression analysis revealed a significant contribution of torsional eye movement sensitivity to the responsiveness of the cells. These findings suggest that many VN neurons encode three-dimensional angular velocity, rather than the two-dimensional derivative of eye position, during smooth-pursuit eye movements. Although no clear clustering of pursuit preferred-direction vectors along the semicircular canal axes was observed, the sensitivity of VN neurons to torsional eye movements might reflect a preservation of similar premotor coding of visual and vestibular-driven slow eye movements for both lateral-eyed and foveate species.

Analysis of histological findings obtained combining US/mp-MRI fusion-guided biopsies with systematic US biopsies: mp-MRI role in prostate cancer detection and false negative.

PubMed

Faiella, Eliodoro; Santucci, Domiziana; Greco, Federico; Frauenfelder, Giulia; Giacobbe, Viola; Muto, Giovanni; Zobel, Bruno Beomonte; Grasso, Rosario Francesco

2018-02-01

To evaluate the diagnostic accuracy of mp-MRI correlating US/mp-MRI fusion-guided biopsy with systematic random US-guided biopsy in prostate cancer diagnosis. 137 suspected prostatic abnormalities were identified on mp-MRI (1.5T) in 96 patients and classified according to PI-RADS score v2. All target lesions underwent US/mp-MRI fusion biopsy and prostatic sampling was completed by US-guided systematic random 12-core biopsies. Histological analysis and Gleason score were established for all the samples, both target lesions defined by mp-MRI, and random biopsies. PI-RADS score was correlated with the histological results, divided in three groups (benign tissue, atypia and carcinoma) and with Gleason groups, divided in four categories considering the new Grading system of the ISUP 2014, using t test. Multivariate analysis was used to correlate PI-RADS and Gleason categories to PSA level and abnormalities axial diameter. When the random core biopsies showed carcinoma (mp-MRI false-negatives), PSA value and lesions Gleason median value were compared with those of carcinomas identified by mp-MRI (true-positives), using t test. There was statistically significant difference between PI-RADS score in carcinoma, atypia and benign lesions groups (4.41, 3.61 and 3.24, respectively) and between PI-RADS score in Gleason < 7 group and Gleason > 7 group (4.14 and 4.79, respectively). mp-MRI performance was more accurate for lesions > 15 mm and in patients with PSA > 6 ng/ml. In systematic sampling, 130 (11.25%) mp-MRI false-negative were identified. There was no statistic difference in Gleason median value (7.0 vs 7.06) between this group and the mp-MRI true-positives, but a significant lower PSA median value was demonstrated (7.08 vs 7.53 ng/ml). mp-MRI remains the imaging modality of choice to identify PCa lesions. Integrating US-guided random sampling with US/mp-MRI fusion target lesions sampling, 3.49% of false-negative were identified.

Cyanide binding to ferrous and ferric microperoxidase-11.

PubMed

Ascenzi, Paolo; Sbardella, Diego; Santucci, Roberto; Coletta, Massimo

2016-07-01

Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c (cytc). MP11 is characterized by a covalently linked solvent-exposed heme group, the heme-Fe atom being axially coordinated by a histidyl residue. Here, the reactions of ferrous and ferric MP11 (MP11-Fe(II) and MP11-Fe(III), respectively) with cyanide have been investigated from the kinetic and thermodynamic viewpoints, at pH 7.0 and 20.0 °C. Values of the second-order rate constant for cyanide binding to MP11-Fe(II) and MP11-Fe(III) are 4.5 M(-1) s(-1) and 8.9 × 10(3) M(-1) s(-1), respectively. Values of the first-order rate constant for cyanide dissociation from ligated MP11-Fe(II) and MP11-Fe(III) are 1.8 × 10(-1) s(-1) and 1.5 × 10(-3) s(-1), respectively. Values of the dissociation equilibrium constant for cyanide binding to MP11-Fe(II) and MP11-Fe(III) are 3.7 × 10(-2) and 1.7 × 10(-7) M, respectively, matching very well with those calculated from kinetic parameters so that no intermediate species seem to be involved in the ligand-binding process. The pH-dependence of cyanide binding to MP11-Fe(III) indicates that CN(-) is the only binding species. Present results have been analyzed in parallel with those of several heme-proteins, suggesting that (1) the ligand accessibility to the metal center and cyanide ionization may modulate the formation of heme-Fe-cyanide complexes, and (2) the general polarity of the heme pocket and/or hydrogen bonding of the heme-bound ligand may affect cyanide exit from the protein matrix. Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c. Penta-coordinated MP11 displays a very high reactivity towards cyanide, whereas the reactivity of hexa-coordinated horse heart cytochrome c is very low.

Association of Hospital Costs With Complications Following Total Gastrectomy for Gastric Adenocarcinoma.

PubMed

Selby, Luke V; Gennarelli, Renee L; Schnorr, Geoffrey C; Solomon, Stephen B; Schattner, Mark A; Elkin, Elena B; Bach, Peter B; Strong, Vivian E

2017-10-01

Postoperative complications are associated with increased hospital costs following major surgery, but the mechanism by which they increase cost and the categories of care that drive this increase are poorly described. To describe the association of postoperative complications with hospital costs following total gastrectomy for gastric adenocarcinoma. This retrospective analysis of a prospectively collected gastric cancer surgery database at a single National Cancer Institute-designated comprehensive cancer center included all patients undergoing curative-intent total gastrectomy for gastric adenocarcinoma between January 2009 and December 2012 and was conducted in 2015 and 2016. Ninety-day normalized postoperative costs. Hospital accounting system costs were normalized to reflect Medicare reimbursement levels using the ratio of hospital costs to Medicare reimbursement and categorized into major cost categories. Differences between costs in Medicare proportional dollars (MP $) can be interpreted as the amount that would be reimbursed to an average hospital by Medicare if it paid differentially based on types and extent of postoperative complications. In total, 120 patients underwent curative-intent total gastrectomy for stage I through III gastric adenocarcinoma between 2009 and 2012. Of these, 79 patients (65.8%) were men, and the median (interquartile range) age was 64 (52-70) years. The 51 patients (42.5%) who underwent an uncomplicated total gastrectomy had a mean (SD) normalized cost of MP $12 330 (MP $2500), predominantly owing to the cost of surgical care (mean [SD] cost, MP $6830 [MP $1600]). The 34 patients (28.3%) who had a major complication had a mean (SD) normalized cost of MP $37 700 (MP $28 090). Surgical care was more expensive in these patients (mean [SD] cost, MP $8970 [MP $2750]) but was a smaller contributor to total cost (24%) owing to increased costs from room and board (mean [SD] cost, MP $11 940 [MP $8820]), consultations (mean [SD] cost, MP $3530 [MP $2410]), and intensive care unit care (mean [SD] cost, MP $7770 [MP $14 310]). Major complications were associated with tripled normalized costs following curative-intent total gastrectomy. Most of the excess costs were related to the treatment of complications. Interventions that decrease the number or severity of postoperative complications could result in substantial cost savings.

Target representation of naturalistic echolocation sequences in single unit responses from the inferior colliculus of big brown bats

NASA Astrophysics Data System (ADS)

Sanderson, Mark I.; Simmons, James A.

2005-11-01

Echolocating big brown bats (Eptesicus fuscus) emit trains of frequency-modulated (FM) biosonar signals whose duration, repetition rate, and sweep structure change systematically during interception of prey. When stimulated with a 2.5-s sequence of 54 FM pulse-echo pairs that mimic sounds received during search, approach, and terminal stages of pursuit, single neurons (N=116) in the bat's inferior colliculus (IC) register the occurrence of a pulse or echo with an average of <1 spike/sound. Individual IC neurons typically respond to only a segment of the search or approach stage of pursuit, with fewer neurons persisting to respond in the terminal stage. Composite peristimulus-time-histogram plots of responses assembled across the whole recorded population of IC neurons depict the delay of echoes and, hence, the existence and distance of the simulated biosonar target, entirely as on-response latencies distributed across time. Correlated changes in pulse duration, repetition rate, and pulse or echo amplitude do modulate the strength of responses (probability of the single spike actually occurring for each sound), but registration of the target itself remains confined exclusively to the latencies of single spikes across cells. Modeling of echo processing in FM biosonar should emphasize spike-time algorithms to explain the content of biosonar images.

Sparse reconstruction localization of multiple acoustic emissions in large diameter pipelines

NASA Astrophysics Data System (ADS)

Dubuc, Brennan; Ebrahimkhanlou, Arvin; Salamone, Salvatore

2017-04-01

A sparse reconstruction localization method is proposed, which is capable of localizing multiple acoustic emission events occurring closely in time. The events may be due to a number of sources, such as the growth of corrosion patches or cracks. Such acoustic emissions may yield localization failure if a triangulation method is used. The proposed method is implemented both theoretically and experimentally on large diameter thin-walled pipes. Experimental examples are presented, which demonstrate the failure of a triangulation method when multiple sources are present in this structure, while highlighting the capabilities of the proposed method. The examples are generated from experimental data of simulated acoustic emission events. The data corresponds to helical guided ultrasonic waves generated in a 3 m long large diameter pipe by pencil lead breaks on its outer surface. Acoustic emission waveforms are recorded by six sparsely distributed low-profile piezoelectric transducers instrumented on the outer surface of the pipe. The same array of transducers is used for both the proposed and the triangulation method. It is demonstrated that the proposed method is able to localize multiple events occurring closely in time. Furthermore, the matching pursuit algorithm and the basis pursuit densoising approach are each evaluated as potential numerical tools in the proposed sparse reconstruction method.

Actions of 2-methylpiperidine (MP) and its interactions with (-)-nicotine (N) in the dog and rat

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

Sloan, J.W.; Martin, W.R.; Bostwick, M.

1986-03-01

(+/-)-MP is a highly specific drug for enhancing the binding of (+/-)-(/sup 3/H)N in the rat brain P/sub 2/ preparation. Competition studies employing (+/-)-(/sup 3/H)N as the labelled ligand show that this activity resides in the (+) isomer. Saturation studies employing (+/-)-(/sup 3/H)MP indicate that it binds to a very high affinity site which is presumed to be an up-regulatory site. Studies were conducted where (+/-)-MP was injected through an implanted cannula into the 4th ventricle of intact beagle-type dogs. (+/-)-MP, like low doses of (+)-N, another drug which has specificity in enhancing the binding of (+/-)-, and (-)- andmore » (+)-(/sup 3/H)N, produced EEG synchronization and miosis. (-)-N produced analgesia where as (+/-)-MP produced hyperalgesia. In the urethane-pentobarbital anethetized rats, the i.v. infusion of (+)-MP (600 ..mu..g/kg/min for 10 min), had no effect on heart rate, blood pressure or respiration. Pretreatment with (+)-MP delayed and decreased the bradycardia, vasodepression, and enhanced tidal volume produced by (-)-N infusion (60 ..mu..g/kg/min). These data show that the pharmacologic actions of MP are different from (-)-N and hexamethonium and that MP, which enhances the binding of (+/-)- and (-)-(/sup 3/H)N at the high affinity site, appears to exert opposite effects to and antagonistic effects against (-)-N.« less

Optimization of a GCaMP calcium indicator for neural activity imaging

PubMed Central

Akerboom, Jasper; Chen, Tsai-Wen; Wardill, Trevor J.; Tian, Lin; Marvin, Jonathan S.; Mutlu, Sevinç; Calderón, Nicole Carreras; Esposti, Federico; Borghuis, Bart G.; Sun, Xiaonan Richard; Gordus, Andrew; Orger, Michael B.; Portugues, Ruben; Engert, Florian; Macklin, John J.; Filosa, Alessandro; Aggarwal, Aman; Kerr, Rex; Takagi, Ryousuke; Kracun, Sebastian; Shigetomi, Eiji; Khakh, Baljit S.; Baier, Herwig; Lagnado, Leon; Wang, Samuel S.-H.; Bargmann, Cornelia I.; Kimmel, Bruce E.; Jayaraman, Vivek; Svoboda, Karel; Kim, Douglas S.; Schreiter, Eric R.; Looger, Loren L.

2012-01-01

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials (APs) in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by several-fold, creating a family of “GCaMP5” sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2–3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general. PMID:23035093

Rift Valley fever virus MP-12 vaccine encoding Toscana virus NSs retains neuroinvasiveness in mice.

PubMed

Indran, Sabarish V; Lihoradova, Olga A; Phoenix, Inaia; Lokugamage, Nandadeva; Kalveram, Birte; Head, Jennifer A; Tigabu, Bersabeh; Smith, Jennifer K; Zhang, Lihong; Juelich, Terry L; Gong, Bin; Freiberg, Alexander N; Ikegami, Tetsuro

2013-07-01

Rift Valley fever is a mosquito-borne zoonotic disease endemic to sub-Saharan Africa. Rift Valley fever virus (RVFV; genus Phlebovirus, family Bunyaviridae) causes high rates of abortion and fetal malformation in pregnant ruminants, and haemorrhagic fever, neurological disorders or blindness in humans. The MP-12 strain is a highly efficacious and safe live-attenuated vaccine candidate for both humans and ruminants. However, MP-12 lacks a marker to differentiate infected from vaccinated animals. In this study, we originally aimed to characterize the efficacy of a recombinant RVFV MP-12 strain encoding Toscana virus (TOSV) NSs gene in place of MP-12 NSs (rMP12-TOSNSs). TOSV NSs promotes the degradation of dsRNA-dependent protein kinase (PKR) and inhibits interferon-β gene up-regulation without suppressing host general transcription. Unexpectedly, rMP12-TOSNSs increased death in vaccinated outbred mice and inbred BALB/c or C57BL/6 mice. Immunohistochemistry showed diffusely positive viral antigens in the thalamus, hypothalamus and brainstem, including the medulla. No viral antigens were detected in spleen or liver, which is similar to the antigen distribution of moribund mice infected with MP-12. These results suggest that rMP12-TOSNSs retains neuroinvasiveness in mice. Our findings demonstrate that rMP12-TOSNSs causes neuroinvasion without any hepatic disease and will be useful for studying the neuroinvasion mechanism of RVFV and TOSV.

Loading cisplatin onto 6-mercaptopurine covalently modified MSNS: a nanomedicine strategy to improve the outcome of cisplatin therapy

PubMed Central

Lv, Xiaojie; Zhao, Ming; Wang, Yuiji; Hu, Xi; Wu, Jianhui; Jiang, Xueyun; Li, Shan; Cui, Chunying; Peng, Shiqi

2016-01-01

In the treatment of cancer patients, cisplatin (CDDP) exhibits serious cardiac and renal toxicities, while classical combinations related to CDDP are unable to solve these problems and may result in worse prognosis. Alternately, this study covalently conjugated 6-mercaptopurine (6MP) onto the surface of mercapto-modified mesoporous silica nanoparticles (MSNS) to form MSNS-6MP and loaded CDDP into the holes on the surface of MSNS-6MP to form MSNS-6MP/CDDP, a tumor-targeting nano-releasing regime for CDDP and 6MP specifically. In the S180 mouse model, the anti-tumor activity and overall survival of MSNS-6MP/CDDP (50 mg·kg−1·day−1, corresponding to 1 mg·kg−1·day−1 of 6MP and 5 mg·kg−1·day−1 of CDDP) were significantly higher than those of CDDP alone (5 mg·kg−1·day−1) or CDDP (5 mg·kg−1·day−1) plus 6MP (1 mg·kg−1·day−1). The assays of serum alanine aminotransferase, aspartate aminotransferase and creatinine, as well as the images of myocardium and kidney histology, support that MSNS-6MP/CDDP is able to completely eliminate liver, kidney and heart toxicities induced by CDDP alone or CDDP plus 6MP. PMID:27942204

Loading cisplatin onto 6-mercaptopurine covalently modified MSNS: a nanomedicine strategy to improve the outcome of cisplatin therapy.

PubMed

Lv, Xiaojie; Zhao, Ming; Wang, Yuiji; Hu, Xi; Wu, Jianhui; Jiang, Xueyun; Li, Shan; Cui, Chunying; Peng, Shiqi

2016-01-01

In the treatment of cancer patients, cisplatin (CDDP) exhibits serious cardiac and renal toxicities, while classical combinations related to CDDP are unable to solve these problems and may result in worse prognosis. Alternately, this study covalently conjugated 6-mercaptopurine (6MP) onto the surface of mercapto-modified mesoporous silica nanoparticles (MSNS) to form MSNS-6MP and loaded CDDP into the holes on the surface of MSNS-6MP to form MSNS-6MP/CDDP, a tumor-targeting nano-releasing regime for CDDP and 6MP specifically. In the S180 mouse model, the anti-tumor activity and overall survival of MSNS-6MP/CDDP (50 mg·kg -1 ·day -1 , corresponding to 1 mg·kg -1 ·day -1 of 6MP and 5 mg·kg -1 ·day -1 of CDDP) were significantly higher than those of CDDP alone (5 mg·kg -1 ·day -1 ) or CDDP (5 mg·kg -1 ·day -1 ) plus 6MP (1 mg·kg -1 ·day -1 ). The assays of serum alanine aminotransferase, aspartate aminotransferase and creatinine, as well as the images of myocardium and kidney histology, support that MSNS-6MP/CDDP is able to completely eliminate liver, kidney and heart toxicities induced by CDDP alone or CDDP plus 6MP.

Mercaptopurine metabolite levels are predictors of bone marrow toxicity following high-dose methotrexate therapy of childhood acute lymphoblastic leukaemia.

PubMed

Vang, Sophia Ingeborg; Schmiegelow, Kjeld; Frandsen, Thomas; Rosthøj, Susanne; Nersting, Jacob

2015-05-01

High-dose methotrexate (HD-MTX) courses with concurrent oral low-dose MTX/6-mercaptopurine (6MP) for childhood acute lymphoblastic leukaemia (ALL) are often followed by neutro- and thrombocytopenia necessitating treatment interruptions. Plasma MTX during HD-MTX therapy guides folinic acid rescue to prevent toxicities, but myelosuppression can also be prevented by pre-HD-MTX 6MP dose reductions. Accordingly, we monitored pre-HD-MTX erythrocyte levels of methylated 6MP metabolites (Ery-MeMP) and of thioguanine nucleotides (Ery-6TGN) as well as DNA-incorporated thioguanine nucleotides (DNA-TGN) in circulating leucocytes to identify patients at highest risk of post-HD-MTX myelosuppression. In multiple linear regression analyses of neutrophil and thrombocyte nadir values (adjusted for gender, age, risk group and 6MP dose) after 48 HD-MTX courses in 17 childhood ALL patients on MTX/6MP maintenance therapy, the pre-HD-MTX DNA-TGN levels in neutrophils (P < 0.0001), Ery-MeMP (P < 0.0001) and Ery-6TGN (P = 0.01) levels were significant predictors of post-HD-MTX neutrophil nadirs, whereas Ery-MeMP (P < 0.0001) was the only predictor of post-HD-MTX thrombocyte nadir. In conclusion, pre-HD-MTX 6MP metabolite levels may be applicable for 6MP dose adjustments to prevent HD-MTX-induced myelosuppression.

Mechanism of action of a novel recombinant peptide, MP1102, against Clostridium perfringens type C.

PubMed

Zong, Lifen; Teng, Da; Wang, Xiumin; Mao, Ruoyu; Yang, Na; Hao, Ya; Wang, Jianhua

2016-06-01

This work is the first to report the antibacterial characteristics and antibacterial mechanisms of MP1102, which is a variant of NZ2114, against pathogenic Clostridium perfringens. MP1102 exhibited strong antimicrobial activity against C. perfringens strains CVCC 61, CVCC 1163, and CVCC 2032 at a low minimal inhibitory concentration (MIC) of 0.91 μM. MP1102 showed anti-C. perfringens activity over a wide pH range of 2.0 and 10.0, high thermal stability from 20 to 80 °C, and remarkable resistance to pepsin. The fractional inhibitory concentration index (FICI) indicated an additive or synergic effect between MP1102 and bacitracin zinc, nisin, vancomycin, virginiamycin, aureomycin, and ampicillin against C. perfringens (FICI = 0.3125-1.0). To further elucidate the antibacterial mechanism of MP1102, its effect on the C. perfringens CVCC 61 cell membrane and intracellular DNA was studied. Flow cytometry and scanning electron microscopy (SEM) indicated that MP1102 treatment resulted in the release of cellular contents by damaging the membrane. A DNA gel retardation and circular dichroism analysis demonstrated that MP1102 interacted with DNA and intercalated into the DNA base pairs. A cell cycle assay demonstrated that MP1102 affected cellular functions, such as DNA synthesis. These results suggested that MP1102 exhibited potential as a new antimicrobial agent against C. perfringens infections.

Interaction of the Tobacco mosaic virus movement protein with microtubules during the cell cycle in tobacco BY-2 cells.

PubMed

Boutant, Emmanuel; Fitterer, Chantal; Ritzenthaler, Christophe; Heinlein, Manfred

2009-10-01

Cell-to-cell movement of Tobacco mosaic virus (TMV) involves the interaction of virus-encoded 30-kDa movement protein (MP) with microtubules. In cells behind the infection front that accumulate high levels of MP, this activity is reflected by the formation of stabilized MP/microtubule complexes. The ability of MP to bind along and stabilize microtubules is conserved upon expression in mammalian cells. In mammalian cells, the protein also leads to inhibition of mitosis and cell division through a microtubule-independent process correlated with the loss of centrosomal gamma-tubulin and of centrosomal microtubule-nucleation activity. Since MP has the capacity to interact with plant factors involved in microtubule nucleation and dynamics, we used inducible expression in BY-2 cells to test whether MP expression inhibits mitosis and cell division also in plants. We demonstrate that MP:GFP associates with all plant microtubule arrays and, unlike in mammalian cells, does not interfere with mitosis. Thus, MP function and the interaction of MP with factors of the cytoskeleton do not entail an inhibition of mitosis in plants. We also report that the protein targets primary plasmodesmata in BY-2 cells immediately upon or during cytokinesis and that the accumulation of MP in plasmodesmata occurs in the presence of inhibitors of the cytoskeleton and the secretory pathway.

Rift Valley fever virus MP-12 vaccine encoding Toscana virus NSs retains neuroinvasiveness in mice

PubMed Central

Indran, Sabarish V.; Lihoradova, Olga A.; Phoenix, Inaia; Lokugamage, Nandadeva; Kalveram, Birte; Head, Jennifer A.; Tigabu, Bersabeh; Smith, Jennifer K.; Zhang, Lihong; Juelich, Terry L.; Gong, Bin; Freiberg, Alexander N.

2013-01-01

Rift Valley fever is a mosquito-borne zoonotic disease endemic to sub-Saharan Africa. Rift Valley fever virus (RVFV; genus Phlebovirus, family Bunyaviridae) causes high rates of abortion and fetal malformation in pregnant ruminants, and haemorrhagic fever, neurological disorders or blindness in humans. The MP-12 strain is a highly efficacious and safe live-attenuated vaccine candidate for both humans and ruminants. However, MP-12 lacks a marker to differentiate infected from vaccinated animals. In this study, we originally aimed to characterize the efficacy of a recombinant RVFV MP-12 strain encoding Toscana virus (TOSV) NSs gene in place of MP-12 NSs (rMP12-TOSNSs). TOSV NSs promotes the degradation of dsRNA-dependent protein kinase (PKR) and inhibits interferon-β gene up-regulation without suppressing host general transcription. Unexpectedly, rMP12-TOSNSs increased death in vaccinated outbred mice and inbred BALB/c or C57BL/6 mice. Immunohistochemistry showed diffusely positive viral antigens in the thalamus, hypothalamus and brainstem, including the medulla. No viral antigens were detected in spleen or liver, which is similar to the antigen distribution of moribund mice infected with MP-12. These results suggest that rMP12-TOSNSs retains neuroinvasiveness in mice. Our findings demonstrate that rMP12-TOSNSs causes neuroinvasion without any hepatic disease and will be useful for studying the neuroinvasion mechanism of RVFV and TOSV. PMID:23515022

Low energy isomers of (H{sub 2}O){sub 25} from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations

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

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in, E-mail: sotiris.xantheas@pnnl.gov; Rakshit, Avijit

2014-10-28

We report new global minimum candidate structures for the (H{sub 2}O){sub 25} cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2more » level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H{sub 2}O){sub 25} cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.« less

Noah-MP-Crop: Introducing dynamic crop growth in the Noah-MP land surface model

NASA Astrophysics Data System (ADS)

Liu, Xing; Chen, Fei; Barlage, Michael; Zhou, Guangsheng; Niyogi, Dev

2016-12-01

Croplands are important in land-atmosphere interactions and in the modification of local and regional weather and climate; however, they are poorly represented in the current version of the coupled Weather Research and Forecasting/Noah with multiparameterization (Noah-MP) land surface modeling system. This study introduced dynamic corn (Zea mays) and soybean (Glycine max) growth simulations and field management (e.g., planting date) into Noah-MP and evaluated the enhanced model (Noah-MP-Crop) at field scales using crop biomass data sets, surface heat fluxes, and soil moisture observations. Compared to the generic dynamic vegetation and prescribed-leaf area index (LAI)-driven methods in Noah-MP, the Noah-MP-Crop showed improved performance in simulating leaf area index (LAI) and crop biomass. This model is able to capture the seasonal and annual variability of LAI and to differentiate corn and soybean in peak values of LAI as well as the length of growing seasons. Improved simulations of crop phenology in Noah-MP-Crop led to better surface heat flux simulations, especially in the early period of growing season where current Noah-MP significantly overestimated LAI. The addition of crop yields as model outputs expand the application of Noah-MP-Crop to regional agriculture studies. There are limitations in the use of current growing degree days (GDD) criteria to predict growth stages, and it is necessary to develop a new method that combines GDD with other environmental factors, to more accurately define crop growth stages. The capability introduced in Noah-MP allows further crop-related studies and development.

Image-guided filtering for improving photoacoustic tomographic image reconstruction.

PubMed

Awasthi, Navchetan; Kalva, Sandeep Kumar; Pramanik, Manojit; Yalavarthy, Phaneendra K

2018-06-01

Several algorithms exist to solve the photoacoustic image reconstruction problem depending on the expected reconstructed image features. These reconstruction algorithms promote typically one feature, such as being smooth or sharp, in the output image. Combining these features using a guided filtering approach was attempted in this work, which requires an input and guiding image. This approach act as a postprocessing step to improve commonly used Tikhonov or total variational regularization method. The result obtained from linear backprojection was used as a guiding image to improve these results. Using both numerical and experimental phantom cases, it was shown that the proposed guided filtering approach was able to improve (as high as 11.23 dB) the signal-to-noise ratio of the reconstructed images with the added advantage being computationally efficient. This approach was compared with state-of-the-art basis pursuit deconvolution as well as standard denoising methods and shown to outperform them. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Parallel eigenanalysis of finite element models in a completely connected architecture

NASA Technical Reports Server (NTRS)

Akl, F. A.; Morel, M. R.

1989-01-01

A parallel algorithm is presented for the solution of the generalized eigenproblem in linear elastic finite element analysis, (K)(phi) = (M)(phi)(omega), where (K) and (M) are of order N, and (omega) is order of q. The concurrent solution of the eigenproblem is based on the multifrontal/modified subspace method and is achieved in a completely connected parallel architecture in which each processor is allowed to communicate with all other processors. The algorithm was successfully implemented on a tightly coupled multiple-instruction multiple-data parallel processing machine, Cray X-MP. A finite element model is divided into m domains each of which is assumed to process n elements. Each domain is then assigned to a processor or to a logical processor (task) if the number of domains exceeds the number of physical processors. The macrotasking library routines are used in mapping each domain to a user task. Computational speed-up and efficiency are used to determine the effectiveness of the algorithm. The effect of the number of domains, the number of degrees-of-freedom located along the global fronts and the dimension of the subspace on the performance of the algorithm are investigated. A parallel finite element dynamic analysis program, p-feda, is documented and the performance of its subroutines in parallel environment is analyzed.

AthenaMT: upgrading the ATLAS software framework for the many-core world with multi-threading

NASA Astrophysics Data System (ADS)

Leggett, Charles; Baines, John; Bold, Tomasz; Calafiura, Paolo; Farrell, Steven; van Gemmeren, Peter; Malon, David; Ritsch, Elmar; Stewart, Graeme; Snyder, Scott; Tsulaia, Vakhtang; Wynne, Benjamin; ATLAS Collaboration

2017-10-01

ATLAS’s current software framework, Gaudi/Athena, has been very successful for the experiment in LHC Runs 1 and 2. However, its single threaded design has been recognized for some time to be increasingly problematic as CPUs have increased core counts and decreased available memory per core. Even the multi-process version of Athena, AthenaMP, will not scale to the range of architectures we expect to use beyond Run2. After concluding a rigorous requirements phase, where many design components were examined in detail, ATLAS has begun the migration to a new data-flow driven, multi-threaded framework, which enables the simultaneous processing of singleton, thread unsafe legacy Algorithms, cloned Algorithms that execute concurrently in their own threads with different Event contexts, and fully re-entrant, thread safe Algorithms. In this paper we report on the process of modifying the framework to safely process multiple concurrent events in different threads, which entails significant changes in the underlying handling of features such as event and time dependent data, asynchronous callbacks, metadata, integration with the online High Level Trigger for partial processing in certain regions of interest, concurrent I/O, as well as ensuring thread safety of core services. We also report on upgrading the framework to handle Algorithms that are fully re-entrant.

77 FR 43657 - Progressive Rail, Incorporated-Discontinuance of Service Exemption-in Barron County, WI

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-25

....05 at or near Rice Lake. The Lines are owned by WCL and have been operated by PGR since 2004 under...), Poskin (MP 85.4), Barron (MP 91.10), Cameron (MP 96.1), and Rice Lake (MP 56.05). \\1\\ See Progressive...

Quasi-Equilibrium Pairs in Pursuit Games on a Cyclic Graph: Some Modified Cases

DTIC Science & Technology

1989-05-01

CCS Research Report No. 627 QUASI-EQUILIBRIUM PAIRS IN PURSUIT GAMES ON A CYCLIC GRAPH: SOME MODIFIED CASES by A. Charnes D. Zhang i-0 00 CENTER FOR...CCS Research Report No. 627 QUASI-EQUILIBRIUM PAIRS IN PURSUIT GAMES ON A CYCLIC GRAPH: SOME MODIFIED CASES by A. Charnes D. Zhang May 1989 This...University of Texas at Austin Austin, Texas 78712-1177 II (512) 471-1821 APAWNJIZf ] ’ Api, k..s UsW , QUASI-EQUILIBRIUM PAIRS IN PURSUIT GAMES ON A

In Pursuit of LSST Science Requirements: A Comparison of Photometry Algorithms

NASA Astrophysics Data System (ADS)

Becker, Andrew C.; Silvestri, Nicole M.; Owen, Russell E.; Ivezić, Željko; Lupton, Robert H.

2007-12-01

We have developed an end-to-end photometric data-processing pipeline to compare current photometric algorithms commonly used on ground-based imaging data. This test bed is exceedingly adaptable and enables us to perform many research and development tasks, including image subtraction and co-addition, object detection and measurements, the production of photometric catalogs, and the creation and stocking of database tables with time-series information. This testing has been undertaken to evaluate existing photometry algorithms for consideration by a next-generation image-processing pipeline for the Large Synoptic Survey Telescope (LSST). We outline the results of our tests for four packages: the Sloan Digital Sky Survey's Photo package, DAOPHOT and ALLFRAME, DOPHOT, and two versions of Source Extractor (SExtractor). The ability of these algorithms to perform point-source photometry, astrometry, shape measurements, and star-galaxy separation and to measure objects at low signal-to-noise ratio is quantified. We also perform a detailed crowded-field comparison of DAOPHOT and ALLFRAME, and profile the speed and memory requirements in detail for SExtractor. We find that both DAOPHOT and Photo are able to perform aperture photometry to high enough precision to meet LSST's science requirements, and less adequately at PSF-fitting photometry. Photo performs the best at simultaneous point- and extended-source shape and brightness measurements. SExtractor is the fastest algorithm, and recent upgrades in the software yield high-quality centroid and shape measurements with little bias toward faint magnitudes. ALLFRAME yields the best photometric results in crowded fields.

Asteroid detection using a single multi-wavelength CCD scan

NASA Astrophysics Data System (ADS)

Melton, Jonathan

2016-09-01

Asteroid detection is a topic of great interest due to the possibility of diverting possibly dangerous asteroids or mining potentially lucrative ones. Currently, asteroid detection is generally performed by taking multiple images of the same patch of sky separated by 10-15 minutes, then subtracting the images to find movement. However, this is time consuming because of the need to revisit the same area multiple times per night. This paper describes an algorithm that can detect asteroids using a single CCD camera scan, thus cutting down on the time and cost of an asteroid survey. The algorithm is based on the fact that some telescopes scan the sky at multiple wavelengths with a small time separation between the wavelength components. As a result, an object moving with sufficient speed will appear in different places in different wavelength components of the same image. Using image processing techniques we detect the centroids of points of light in the first component and compare these positions to the centroids in the other components using a nearest neighbor algorithm. The algorithm was used on a test set of 49 images obtained from the Sloan telescope in New Mexico and found 100% of known asteroids with only 3 false positives. This algorithm has the advantage of decreasing the amount of time required to perform an asteroid scan, thus allowing more sky to be scanned in the same amount of time or freeing a telescope for other pursuits.

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

Hornung, Richard D.; Hones, Holger E.

The RAJA Performance Suite is designed to evaluate performance of the RAJA performance portability library on a wide variety of important high performance computing (HPC) algorithmic lulmels. These kernels assess compiler optimizations and various parallel programming model backends accessible through RAJA, such as OpenMP, CUDA, etc. The Initial version of the suite contains 25 computational kernels, each of which appears in 6 variants: Baseline SequcntiaJ, RAJA SequentiaJ, Baseline OpenMP, RAJA OpenMP, Baseline CUDA, RAJA CUDA. All variants of each kernel perform essentially the same mathematical operations and the loop body code for each kernel is identical across all variants. Theremore » are a few kernels, such as those that contain reduction operations, that require CUDA-specific coding for their CUDA variants. ActuaJ computer instructions executed and how they run in parallel differs depending on the parallel programming model backend used and which optimizations are perfonned by the compiler used to build the Perfonnance Suite executable. The Suite will be used primarily by RAJA developers to perform regular assessments of RAJA performance across a range of hardware platforms and compilers as RAJA features are being developed. It will also be used by LLNL hardware and software vendor panners for new defining requirements for future computing platform procurements and acceptance testing. In particular, the RAJA Performance Suite will be used for compiler acceptance testing of the upcoming CORAUSierra machine {initial LLNL delivery expected in late-2017/early 2018) and the CORAL-2 procurement. The Suite will aJso be used to generate concise source code reproducers of compiler and runtime issues we uncover so that we may provide them to relevant vendors to be fixed.« less

Tensor hypercontraction. II. Least-squares renormalization

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Hohenstein, Edward G.; Martínez, Todd J.; Sherrill, C. David

2012-12-01

The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)], 10.1063/1.4732310. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1/r12 operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N^5) effort if exact integrals are decomposed, or O(N^4) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N^4) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

Online Continuous Trace Process Analytics Using Multiplexing Gas Chromatography.

PubMed

Wunsch, Marco R; Lehnig, Rudolf; Trapp, Oliver

2017-04-04

The analysis of impurities at a trace level in chemical products, nutrition additives, and drugs is highly important to guarantee safe products suitable for consumption. However, trace analysis in the presence of a dominating component can be a challenging task because of noncompatible linear detection ranges or strong signal overlap that suppresses the signal of interest. Here, we developed a technique for quantitative analysis using multiplexing gas chromatography (mpGC) for continuous and completely automated process trace analytics exemplified for the analysis of a CO 2 stream in a production plant for detection of benzene, toluene, ethylbenzene, and the three structural isomers of xylene (BTEX) in the concentration range of 0-10 ppb. Additional minor components are methane and methanol with concentrations up to 100 ppm. The sample is injected up to 512 times according to a pseudorandom binary sequence (PRBS) with a mean frequency of 0.1 Hz into a gas chromatograph equipped with a flame ionization detector (FID). A superimposed chromatogram is recorded which is deconvoluted into an averaged chromatogram with Hadamard transformation. Novel algorithms to maintain the data acquisition rate of the detector by application of Hadamard transformation and to suppress correlation noise induced by components with much higher concentrations than the target substances are shown. Compared to conventional GC-FID, the signal-to-noise ratio has been increased by a factor of 10 with mpGC-FID. Correspondingly, the detection limits for BTEX in CO 2 have been lowered from 10 to 1 ppb each. This has been achieved despite the presence of detectable components (methane and methanol) with a concentration about 1000 times higher than the target substances. The robustness and reliability of mpGC has been proven in a two-month field test in a chemical production plant.

Tensor hypercontraction. II. Least-squares renormalization.

PubMed

Parrish, Robert M; Hohenstein, Edward G; Martínez, Todd J; Sherrill, C David

2012-12-14

The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)]. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1∕r(12) operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N(5)) effort if exact integrals are decomposed, or O(N(4)) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N(4)) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

Motion coherence affects human perception and pursuit similarly.

PubMed

Beutter, B R; Stone, L S

2000-01-01

Pursuit and perception both require accurate information about the motion of objects. Recovering the motion of objects by integrating the motion of their components is a difficult visual task. Successful integration produces coherent global object motion, while a failure to integrate leaves the incoherent local motions of the components unlinked. We compared the ability of perception and pursuit to perform motion integration by measuring direction judgments and the concomitant eye-movement responses to line-figure parallelograms moving behind stationary rectangular apertures. The apertures were constructed such that only the line segments corresponding to the parallelogram's sides were visible; thus, recovering global motion required the integration of the local segment motion. We investigated several potential motion-integration rules by using stimuli with different object, vector-average, and line-segment terminator-motion directions. We used an oculometric decision rule to directly compare direction discrimination for pursuit and perception. For visible apertures, the percept was a coherent object, and both the pursuit and perceptual performance were close to the object-motion prediction. For invisible apertures, the percept was incoherently moving segments, and both the pursuit and perceptual performance were close to the terminator-motion prediction. Furthermore, both psychometric and oculometric direction thresholds were much higher for invisible apertures than for visible apertures. We constructed a model in which both perception and pursuit are driven by a shared motion-processing stage, with perception having an additional input from an independent static-processing stage. Model simulations were consistent with our perceptual and oculomotor data. Based on these results, we propose the use of pursuit as an objective and continuous measure of perceptual coherence. Our results support the view that pursuit and perception share a common motion-integration stage, perhaps within areas MT or MST.

Smooth Pursuit Eye Movement Deficits in Patients With Whiplash and Neck Pain are Modulated by Target Predictability.

PubMed

Janssen, Malou; Ischebeck, Britta K; de Vries, Jurryt; Kleinrensink, Gert-Jan; Frens, Maarten A; van der Geest, Jos N

2015-10-01

This is a cross-sectional study. The purpose of this study is to support and extend previous observations on oculomotor disturbances in patients with neck pain and whiplash-associated disorders (WADs) by systematically investigating the effect of static neck torsion on smooth pursuit in response to both predictably and unpredictably moving targets using video-oculography. Previous studies showed that in patients with neck complaints, for instance due to WAD, extreme static neck torsion deteriorates smooth pursuit eye movements in response to predictably moving targets compared with healthy controls. Eye movements in response to a smoothly moving target were recorded with video-oculography in a heterogeneous group of 55 patients with neck pain (including 11 patients with WAD) and 20 healthy controls. Smooth pursuit performance was determined while the trunk was fixed in 7 static rotations relative to the head (from 45° to the left to 45° to right), using both predictably and unpredictably moving stimuli. Patients had reduced smooth pursuit gains and smooth pursuit gain decreased due to neck torsion. Healthy controls showed higher gains for predictably moving targets compared with unpredictably moving targets, whereas patients with neck pain had similar gains in response to both types of target movements. In 11 patients with WAD, increased neck torsion decreased smooth pursuit performance, but only for predictably moving targets. Smooth pursuit of patients with neck pain is affected. The previously reported WAD-specific decline in smooth pursuit due to increased neck torsion seems to be modulated by the predictability of the movement of the target. The observed oculomotor disturbances in patients with WAD are therefore unlikely to be induced by impaired neck proprioception alone. 3.

Motion coherence affects human perception and pursuit similarly

NASA Technical Reports Server (NTRS)

Beutter, B. R.; Stone, L. S.

2000-01-01

Pursuit and perception both require accurate information about the motion of objects. Recovering the motion of objects by integrating the motion of their components is a difficult visual task. Successful integration produces coherent global object motion, while a failure to integrate leaves the incoherent local motions of the components unlinked. We compared the ability of perception and pursuit to perform motion integration by measuring direction judgments and the concomitant eye-movement responses to line-figure parallelograms moving behind stationary rectangular apertures. The apertures were constructed such that only the line segments corresponding to the parallelogram's sides were visible; thus, recovering global motion required the integration of the local segment motion. We investigated several potential motion-integration rules by using stimuli with different object, vector-average, and line-segment terminator-motion directions. We used an oculometric decision rule to directly compare direction discrimination for pursuit and perception. For visible apertures, the percept was a coherent object, and both the pursuit and perceptual performance were close to the object-motion prediction. For invisible apertures, the percept was incoherently moving segments, and both the pursuit and perceptual performance were close to the terminator-motion prediction. Furthermore, both psychometric and oculometric direction thresholds were much higher for invisible apertures than for visible apertures. We constructed a model in which both perception and pursuit are driven by a shared motion-processing stage, with perception having an additional input from an independent static-processing stage. Model simulations were consistent with our perceptual and oculomotor data. Based on these results, we propose the use of pursuit as an objective and continuous measure of perceptual coherence. Our results support the view that pursuit and perception share a common motion-integration stage, perhaps within areas MT or MST.

Genetic Instability of Breast Cancer Cells Induced by Aberrant Expression of hMpS1

DTIC Science & Technology

2004-09-01

and function of the mitotic spindle is dependent on the MpS1 protein kinase. The components of mitotic spindle checkpoints were first identified in...yeast and their homologs of higher organisms were then identified and characterized. These include Bubl, Bub2, Bub3, Madl, Mad2, Mad3 and MpS1 . MpS 1...spindle checkpoint and centrosome duplication (1-6). Although several recent reports demonstrated that vertebrate MpS1 proteins regulate the spindle

Expansion of direction space around the cardinal axes revealed by smooth pursuit eye movements.

PubMed

Krukowski, Anton E; Stone, Leland S

2005-01-20

It is well established that perceptual direction discrimination shows an oblique effect; thresholds are higher for motion along diagonal directions than for motion along cardinal directions. Here, we compare simultaneous direction judgments and pursuit responses for the same motion stimuli and find that both pursuit and perceptual thresholds show similar anisotropies. The pursuit oblique effect is robust under a wide range of experimental manipulations, being largely resistant to changes in trajectory (radial versus tangential motion), speed (10 versus 25 deg/s), directional uncertainty (blocked versus randomly interleaved), and cognitive state (tracking alone versus concurrent tracking and perceptual tasks). Our data show that the pursuit oblique effect is caused by an effective expansion of direction space surrounding the cardinal directions and the requisite compression of space for other directions. This expansion suggests that the directions around the cardinal directions are in some way overrepresented in the visual cortical pathways that drive both smooth pursuit and perception.

Expansion of direction space around the cardinal axes revealed by smooth pursuit eye movements

NASA Technical Reports Server (NTRS)

Krukowski, Anton E.; Stone, Leland S.

2005-01-01

It is well established that perceptual direction discrimination shows an oblique effect; thresholds are higher for motion along diagonal directions than for motion along cardinal directions. Here, we compare simultaneous direction judgments and pursuit responses for the same motion stimuli and find that both pursuit and perceptual thresholds show similar anisotropies. The pursuit oblique effect is robust under a wide range of experimental manipulations, being largely resistant to changes in trajectory (radial versus tangential motion), speed (10 versus 25 deg/s), directional uncertainty (blocked versus randomly interleaved), and cognitive state (tracking alone versus concurrent tracking and perceptual tasks). Our data show that the pursuit oblique effect is caused by an effective expansion of direction space surrounding the cardinal directions and the requisite compression of space for other directions. This expansion suggests that the directions around the cardinal directions are in some way overrepresented in the visual cortical pathways that drive both smooth pursuit and perception.

Azathioprine suppresses the mixed lymphocyte reaction of patients with Lesch-Nyhan syndrome.

PubMed Central

Szawlowski, P W; Al-Safi, S A; Dooley, T; Maddocks, J L

1985-01-01

The mixed lymphocyte reaction of Lesch-Nyhan patients (HGPRT deficient) was used to study the immunosuppressive effects of azathioprine and 6-mercaptopurine (6-MP). Mitogen stimulated lymphocytes of these patients are highly resistant to azathioprine and 6-MP. When both stimulator and responder lymphocytes in the MLR were HGPRT deficient, azathioprine (36 microM) was much more inhibitory than 6-MP (100 microM). Azathioprine produced inhibition of 98.2% and 78.5% compared with the values of 63.9% and 30.6% for 6-MP. The difference in inhibitory activity between azathioprine and 6-MP was reduced when normal stimulator lymphocytes were cultured with HGPRT deficient responder lymphocytes in the MLR. These results provide very strong evidence that the nucleotide metabolites of azathioprine and 6-MP are unnecessary for immunosuppression. They also suggest that azathioprine and 6-MP interfere with antigenic triggering of the MLR. PMID:2934083

Visual sensitivity for luminance and chromatic stimuli during the execution of smooth pursuit and saccadic eye movements.

PubMed

Braun, Doris I; Schütz, Alexander C; Gegenfurtner, Karl R

2017-07-01

Visual sensitivity is dynamically modulated by eye movements. During saccadic eye movements, sensitivity is reduced selectively for low-spatial frequency luminance stimuli and largely unaffected for high-spatial frequency luminance and chromatic stimuli (Nature 371 (1994), 511-513). During smooth pursuit eye movements, sensitivity for low-spatial frequency luminance stimuli is moderately reduced while sensitivity for chromatic and high-spatial frequency luminance stimuli is even increased (Nature Neuroscience, 11 (2008), 1211-1216). Since these effects are at least partly of different polarity, we investigated the combined effects of saccades and smooth pursuit on visual sensitivity. For the time course of chromatic sensitivity, we found that detection rates increased slightly around pursuit onset. During saccades to static and moving targets, detection rates dropped briefly before the saccade and reached a minimum at saccade onset. This reduction of chromatic sensitivity was present whenever a saccade was executed and it was not modified by subsequent pursuit. We also measured contrast sensitivity for flashed high- and low-spatial frequency luminance and chromatic stimuli during saccades and pursuit. During saccades, the reduction of contrast sensitivity was strongest for low-spatial frequency luminance stimuli (about 90%). However, a significant reduction was also present for chromatic stimuli (about 58%). Chromatic sensitivity was increased during smooth pursuit (about 12%). These results suggest that the modulation of visual sensitivity during saccades and smooth pursuit is more complex than previously assumed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Health Information in Modern Standard Arabic (al-ʻArabīyat ul-fuṣḥá)

MedlinePlus

... fuṣḥá (Modern Standard Arabic) MP4 Healthy Roads Media Tornadoes - English MP3 Tornadoes - al-ʻArabīyat ul-fuṣḥá (Modern Standard Arabic) MP3 Tornadoes - English MP4 Tornadoes - al-ʻArabīyat ul-fuṣḥá (Modern ...

Registration of Mp718 and Mp719 germplasm lines of maize

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays L.) germplasm lines Mp718 (Reg. No. GP-xxxx, PI 662045) and Mp719 (Reg. No. GP-xxxx, PI 662046) were developed and released by USDA-ARS in cooperation with the Mississippi Agricultural and Forestry Experiment Station, Mississippi State, Mississippi, as sources of resistance to aflat...

Changes in the structural and gel properties of pork myofibrillar protein induced by catechin modification.

PubMed

Jia, Na; Wang, Letian; Shao, Junhua; Liu, Dengyong; Kong, Baohua

2017-05-01

Different concentrations of catechin (0, 10, 50, 100 and 200μmol/g protein) were added to pork myofibrillar protein (MP) suspensions, and the related changes in protein conformational and gel properties were investigated. The results showed that catechin at 200μmol/g protein led to the greatest increase in the surface hydrophobicity of MP. A significant loss of thiols (SH) content was observed in MP in the presence of catechin. The low concentration of catechin of 10μmol/g led to slight changes in the MP gel strength and water-holding capacity. However, catechin at higher concentrations (50, 100 and 200μmol/g protein) caused severe deterioration of MP gelation. The microstructure and dynamic rheological properties confirmed the unfavorable effect of catechin on the MP gel properties. The results indicate that catechin caused changes in MP conformational and gel properties, which may be due to the catechin-MP covalent interactions and the exposure of hydrophobic domains caused by catechin. Copyright © 2017 Elsevier Ltd. All rights reserved.

Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

NASA Astrophysics Data System (ADS)

Calafiura, Paolo; Leggett, Charles; Seuster, Rolf; Tsulaia, Vakhtang; Van Gemmeren, Peter

2015-12-01

AthenaMP is a multi-process version of the ATLAS reconstruction, simulation and data analysis framework Athena. By leveraging Linux fork and copy-on-write mechanisms, it allows for sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain configurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows the running of AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of AthenaMP in the diversity of ATLAS event processing workloads on various computing resources: Grid, opportunistic resources and HPC.

Effects of polystyrene microbeads in marine planktonic crustaceans.

PubMed

Gambardella, Chiara; Morgana, Silvia; Ferrando, Sara; Bramini, Mattia; Piazza, Veronica; Costa, Elisa; Garaventa, Francesca; Faimali, Marco

2017-11-01

Plastic debris accumulates in the marine environment, fragmenting into microplastics (MP), causing concern about their potential toxic effects when ingested by marine organisms. The aim of this study was to verify whether 0.1µm polystyrene beads are likely to trigger lethal and sub-lethal responses in marine planktonic crustaceans. MP build-up, mortality, swimming speed alteration and enzyme activity (cholinesterases, catalase) were investigated in the larval stages of Amphibalanus amphitrite barnacle and of Artemia franciscana brine shrimp exposed to a wide range of MP concentrations (from 0.001 to 10mgL -1 ) for 24 and 48h. The results show that MP were accumulated in crustaceans, without affecting mortality. Swimming activity was significantly altered in crustaceans exposed to high MP concentrations (> 1mgL -1 ) after 48h. Enzyme activities were significantly affected in all organisms exposed to all the above MP concentrations, indicating that neurotoxic effects and oxidative stress were induced after MP treatment. These findings provide new insight into sub-lethal MP effects on marine crustaceans. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantification of microplastic mass and removal rates at wastewater treatment plants applying Focal Plane Array (FPA)-based Fourier Transform Infrared (FT-IR) imaging.

PubMed

Simon, Márta; van Alst, Nikki; Vollertsen, Jes

2018-05-17

This paper presents a method for microplastic (MP) mass quantification using a Focal Plane Array-based Fourier Transform Infrared imaging technique. It discusses the issue that particle number is not a conserved base quantity and hence less suited than mass to compare independent studies on MP in the environment. It concludes that MP mass should be included when quantifying MP pollution in the environment, supplementing the conventional approach of reporting particle numbers. Applying mass as the unit of MP measurement, the paper presents data showing that Danish wastewater treatment plants discharge around 3 t/year of MP in the size range 10-500 μm. This value corresponds to an annual per capita emission from these plants of 0.56 g MP/(capita year). The distribution of polymer types by mass and particle number differed because the size of MP particles of the different material types varied. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

The effect of tailor-made additives on crystal growth of methyl paraben: Experiments and modelling

NASA Astrophysics Data System (ADS)

Cai, Zhihui; Liu, Yong; Song, Yang; Guan, Guoqiang; Jiang, Yanbin

2017-03-01

In this study, methyl paraben (MP) was selected as the model component, and acetaminophen (APAP), p-methyl acetanilide (PMAA) and acetanilide (ACET), which share the similar molecular structure as MP, were selected as the three tailor-made additives to study the effect of tailor-made additives on the crystal growth of MP. HPLC results indicated that the MP crystals induced by the three additives contained MP only. Photographs of the single crystals prepared indicated that the morphology of the MP crystals was greatly changed by the additives, but PXRD and single crystal diffraction results illustrated that the MP crystals were the same polymorph only with different crystal habits, and no new crystal form was found compared with other references. To investigate the effect of the additives on the crystal growth, the interaction between additives and facets was discussed in detail using the DFT methods and MD simulations. The results showed that APAP, PMAA and ACET would be selectively adsorbed on the growth surfaces of the crystal facets, which induced the change in MP crystal habits.

Immuno-analysis of microparticles: probing at the limits of detection

PubMed Central

Latham, Sharissa L.; Tiberti, Natalia; Gokoolparsadh, Naveena; Holdaway, Karen; Olivier Couraud, Pierre; Grau, Georges E. R.; Combes, Valery

2015-01-01

Microparticle (MP) research is clouded by debate regarding the accuracy and validity of flow cytometry (FCM) as an analytical methodology, as it is influenced by many variables including the pre-analytical conditions, instruments physical capabilities and detection parameters. This study utilises a simplistic in vitro system for generating MP, and through comparative analysis with immuno-electron microscopy (Immuno-EM) assesses the strengths and limitations of probe selection and high-sensitivity FCM. Of the markers examined, MP were most specifically labelled with phosphatidylserine ligands, annexin V and lactadherin, although only ~60% MP are PS positive. Whilst these two ligands detect comparable absolute MP numbers, they interact with the same population in distinct manners; annexin V binding is enhanced on TNF induced MP. CD105 and CD54 expression were, as expected, consistent and enhanced following TNF activation respectively. Their labelling however accounted for as few as 30–40% of MP. The greatest discrepancies between FCM and I-EM were observed in the population solely labelled for the surface antigen. These findings demonstrate that despite significant improvements in resolution, high-sensitivity FCM remains limited in detecting small-size MP expressing low antigen levels. This study highlights factors to consider when selecting endothelial MP probes, as well as interpreting and representing data. PMID:26553743

Functional diversification of cerato-platanins in Moniliophthora perniciosa as seen by differential expression and protein function specialization.

PubMed

de O Barsottini, Mario R; de Oliveira, Juliana F; Adamoski, Douglas; Teixeira, Paulo J P L; do Prado, Paula F V; Tiezzi, Henrique O; Sforça, Mauricio L; Cassago, Alexandre; Portugal, Rodrigo V; de Oliveira, Paulo S L; de M Zeri, Ana C; Dias, Sandra M G; Pereira, Gonçalo A G; Ambrosio, Andre L B

2013-11-01

Cerato-platanins (CP) are small, cysteine-rich fungal-secreted proteins involved in the various stages of the host-fungus interaction process, acting as phytotoxins, elicitors, and allergens. We identified 12 CP genes (MpCP1 to MpCP12) in the genome of Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, and showed that they present distinct expression profiles throughout fungal development and infection. We determined the X-ray crystal structures of MpCP1, MpCP2, MpCP3, and MpCP5, representative of different branches of a phylogenetic tree and expressed at different stages of the disease. Structure-based biochemistry, in combination with nuclear magnetic resonance and mass spectrometry, allowed us to define specialized capabilities regarding self-assembling and the direct binding to chitin and N-acetylglucosamine (NAG) tetramers, a fungal cell wall building block, and to map a previously unknown binding region in MpCP5. Moreover, fibers of MpCP2 were shown to act as expansin and facilitate basidiospore germination whereas soluble MpCP5 blocked NAG6-induced defense response. The correlation between these roles, the fungus life cycle, and its tug-of-war interaction with cacao plants is discussed.

Orbital-optimized third-order Møller-Plesset perturbation theory and its spin-component and spin-opposite scaled variants: application to symmetry breaking problems.

PubMed

Bozkaya, Uğur

2011-12-14

In this research, orbital-optimized third-order Møller-Plesset perturbation theory (OMP3) and its spin-component and spin-opposite scaled variants (SCS-OMP3 and SOS-OMP3) are introduced. Using a Lagrangian-based approach, an efficient, quadratically convergent algorithm for variational optimization of the molecular orbitals (MOs) for third-order Møller-Plesset perturbation theory (MP3) is presented. Explicit equations for response density matrices, the MO gradient, and Hessian are reported in spin-orbital form. The OMP3, SCS-OMP3, and SOS-OMP3 approaches are compared with the second-order Møller-Plesset perturbation theory (MP2), MP3, coupled-cluster doubles (CCD), optimized-doubles (OD), and coupled-cluster singles and doubles (CCSD) methods. All these methods are applied to the O(4)(+), O(3), and seven diatomic molecules. Results demonstrate that the OMP3 and its variants provide significantly better vibrational frequencies than MP3, CCSD, and OD for the molecules where the symmetry-breaking problems are observed. For O(4)(+), the OMP3 prediction, 1343 cm(-1), for ω(6) (b(3u)) mode, where symmetry-breaking appears, is even better than presumably more reliable methods such as Brueckner doubles (BD), 1194 cm(-1), and OD, 1193 cm(-1), methods (the experimental value is 1320 cm(-1)). For O(3), the predictions of SCS-OMP3 (1143 cm(-1)) and SOS-OMP3 (1165 cm(-1)) are remarkably better than the more robust OD method (1282 cm(-1)); the experimental value is 1089 cm(-1). For the seven diatomics, again the SCS-OMP3 and SOS-OMP3 methods provide the lowest average errors, ∣Δω(e)∣ = 44 and ∣Δω(e)∣ = 35 cm(-1), respectively, while for OD, ∣Δω(e)∣ = 161 cm(-1)and CCSD ∣Δω(e)∣ = 106 cm(-1). Hence, the OMP3 and especially its spin-scaled variants perform much better than the MP3, CCSD, and more robust OD approaches for considered test cases. Therefore, considering both the computational cost and the reliability, SCS-OMP3 and SOS-OMP3 appear to be the best methods for the symmetry-breaking cases, based on present application results. The OMP3 method offers certain advantages: it provides reliable vibrational frequencies in case of symmetry-breaking problems, especially with spin-scaling tricks, its analytic gradients are easier to compute since there is no need to solve the coupled-perturbed equations for the orbital response, and the computation of one-electron properties are easier because there is no response contribution to the particle density matrices. The OMP3 has further advantages over standard MP3, making it promising for excited state properties via linear response theory. © 2011 American Institute of Physics

Changing patterns of localization of the tobacco mosaic virus movement protein and replicase to the endoplasmic reticulum and microtubules during infection

NASA Technical Reports Server (NTRS)

Heinlein, M.; Padgett, H. S.; Gens, J. S.; Pickard, B. G.; Casper, S. J.; Epel, B. L.; Beachy, R. N.; Evans, M. L. (Principal Investigator)

1998-01-01

Tobacco mosaic virus (TMV) derivatives that encode movement protein (MP) as a fusion to the green fluorescent protein (MP:GFP) were used in combination with antibody staining to identify host cell components to which MP and replicase accumulate in cells of infected Nicotiana benthamiana leaves and in infected BY-2 protoplasts. MP:GFP and replicase colocalized to the endoplasmic reticulum (ER; especially the cortical ER) and were present in large, irregularly shaped, ER-derived structures that may represent "viral factories." The ER-derived structures required an intact cytoskeleton, and microtubules appeared to redistribute MP:GFP from these sites during late stages of infection. In leaves, MP:GFP accumulated in plasmodesmata, whereas in protoplasts, the MP:GFP was targeted to distinct, punctate sites near the plasma membrane. Treating protoplasts with cytochalasin D and brefeldin A at the time of inoculation prevented the accumulation of MP:GFP at these sites. It is proposed that the punctate sites anchor the cortical ER to plasma membrane and are related to sites at which plasmodesmata form in walled cells. Hairlike structures containing MP:GFP appeared on the surface of some of the infected protoplasts and are reminiscent of similar structures induced by other plant viruses. We present a model that postulates the role of the ER and cytoskeleton in targeting the MP and viral ribonucleoprotein from sites of virus synthesis to the plasmodesmata through which infection is spread.

6-Mercaptopurine, an activator of Nur77, enhances transcriptional activity of HIF-1alpha resulting in new vessel formation.

PubMed

Yoo, Y-G; Na, T-Y; Yang, W-K; Kim, H-J; Lee, I-K; Kong, G; Chung, J-H; Lee, M-O

2007-05-31

Hypoxia-inducible factor-1alpha (HIF-1alpha) plays a central role in oxygen homeostasis. Previously, we reported that the orphan nuclear receptor Nur77 functions in stabilizing HIF-1alpha. Here, we demonstrate that 6-mercaptopurine (6-MP), an activator of the NR4A family members, enhances transcriptional activity of HIF-1. 6-MP enhanced the protein-level of HIF-1alpha as well as vascular endothelial growth factor (VEGF) in a dose- and time-dependent manner. The induction of HIF-1alpha was abolished by the transfection of either a dominant-negative Nur77 mutant or si-Nur77, indicating a critical role of Nur77 in the 6-MP action. The HIF-1alpha protein level remained up to 60 min in the presence of 6-MP when de novo protein synthesis was blocked by cycloheximide, suggesting that 6-MP induces stabilization of the HIF-1alpha protein. The fact that 6-MP decreased the association of HIF-1alpha with von Hippel-Lindau protein and the acetylation of HIF-1alpha, may explain how 6-MP induced stability of HIF-1alpha. Further, 6-MP induced the transactivation function of HIF-1alpha by recruiting co-activator cyclic-AMP-response-element-binding protein. Finally, 6-MP enhanced the expression of HIF-1alpha and VEGF, and the formation of capillary tubes in human umbilical vascular endothelial cells. Together, our results provide a new insight for 6-MP action in the stabilization of HIF-1alpha and imply a potential application of 6-MP in hypoxia-associated human vascular diseases.

High hydrostatic pressure processing reduces the glycemic index of fresh mango puree in healthy subjects.

PubMed

Elizondo-Montemayor, Leticia; Hernández-Brenes, Carmen; Ramos-Parra, Perla A; Moreno-Sánchez, Diana; Nieblas, Bianca; Rosas-Pérez, Aratza M; Lamadrid-Zertuche, Ana C

2015-04-01

Dietary guidelines recommend the daily consumption of fruits; however, healthy and type 2 diabetes mellitus (T2DM) subjects receive conflicting messages regarding ingestion of fruits, such as mango, because of its sugar content. We investigated the effects of high hydrostatic pressure (HHP) processing of fresh mango puree (MP) on the glycemic indexes (GIs) and postprandial glycemic responses of 38 healthy Mexican subjects in a randomized cross-over clinical trial. Physicochemical characterization of MP included sugar profiles by HPLC-ELSD, starch, fibers, moisture, viscosity, swelling capacity and solubility properties of alcohol insoluble residue (AIR). The mean GI for HHP-MP was significantly lower (32.7 ± 13.4) than that of unprocessed-MP (42.7 ± 19.5). A significantly higher proportion of subjects showed a low GI following the consumption of HHP-MP compared to unprocessed-MP and none of them showed a high GI for the HHP-MP, compared to a significantly higher proportion for the unprocessed-MP. The viscosity and AIR solubility values of HHP-MP samples were significantly higher, which influenced glucose peaking later (Tmax) at 45 minutes and induced 20% lower AUC values than unprocessed-MP, corresponding to greater retardation indexes. The study findings support data stating that low GI fruits are appropriate for glycemic control and that mango may be included as part of healthy subjects' diets and potentially T2DM subjects' diets. Furthermore, HHP processing of mango may offer additional benefits for glycemic control, as its performance regarding GI, AUC and Tmax was significantly better than that of the unprocessed-MP. To our knowledge, this is the first report on the impact of this commercial non-thermal pasteurization technology on glucose metabolism.

Phosphatidylserine lipids and membrane order precisely regulate the activity of Polybia-MP1 peptide.

PubMed

Alvares, Dayane S; Ruggiero Neto, João; Ambroggio, Ernesto E

2017-06-01

Polybia-MP1 (IDWKKLLDAAKQIL-NH 2 ) is a lytic peptide from the Brazilian wasp venom with known anti-cancer properties. Previous evidence indicates that phosphatidylserine (PS) lipids are relevant for the lytic activity of MP1. In agreement with this requirement, phosphatidylserine lipids are translocated to the outer leaflet of cells, and are available for MP1 binding, depending on the presence of liquid-ordered domains. Here, we investigated the effect of PS on MP1 activity when this lipid is reconstituted in membranes of giant or large liposomes with different lipid-phase states. By monitoring the membrane and soluble luminal content of giant unilamellar vesicles (GUVs), using fluorescence confocal microscopy, we were able to determine that MP1 has a pore-forming activity at the membrane level. Liquid-ordered domains, which were phase-separated within the membrane of GUVs, influenced the pore-forming activity of MP1. Experiments evaluating the membrane-binding and lytic activity of MP1 on large unilamellar vesicles (LUVs), with the same lipid composition as GUVs, demonstrated that there was synergy between liquid-ordered domains and PS, which enhanced both activities. Based on our findings, we propose that the physicochemical properties of cancer cell membranes, which possess a much higher concentration of PS than normal cells, renders them susceptible to MP1 binding and lytic pore formation. These results can be correlated with MP1's potent and selective anti-cancer activity and pave the way for future research to develop cancer therapies that harness and exploit the properties of MP1. Copyright © 2017 Elsevier B.V. All rights reserved.

The accuracy of quantum chemical methods for large noncovalent complexes

PubMed Central

Pitoňák, Michal; Řezáč, Jan; Pulay, Peter

2013-01-01

We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable “accuracy/cost” ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent. PMID:24098094

A method to assess the migration properties of cell-derived microparticles within a living tissue.

PubMed

Hoang, Thang Q; Rampon, Christine; Freyssinet, Jean-Marie; Vriz, Sophie; Kerbiriou-Nabias, Danièle

2011-09-01

Cells undergoing activation or apoptosis exhibit plasma membrane changes, leading to the formation of shed vesicles (microparticles, MP). Although their effects on recipient cells in vitro, and their ability to support inflammatory or thrombotic events in the circulation have been studied, the spreading of such vesicles in tissues is still elusive. Our aim was to set up a method to examine the behavior of these vesicles in vivo. We examined the persistence of green-fluorescent microparticles (fMP), prepared after Ca2+ ionophore activation (iono-fMP) or apoptogenic treatment (eto-fMP) of human Jurkat T lymphoblastic or non-hematopoietic embryonic kidney (HEK) cell lines, following injection in zebrafish embryos 2h after egg fertilization. One hour post-injection, iono-fMP issued from both cell types formed a fluorescent dispersal in the intercellular space of embryos. In contrast, eto-fMP or MP deprived of sialic acid at their membrane, gathered together at the site of injection. We propose a method characterizing the abilities of MP to spread in the intercellular space. We showed that MP produced by apoptosis of T cells and those deprived of sialic acid at their membrane do not diffuse within the living cells. On the contrary, MP shed upon calcium induced activation of T and HEK cells, diffuse at a distance and spread in the intercellular space. The fate of injected MP relies on the type of induction rather than the cell species and results provide a model to test the ability of vesicles to interact locally or to spread outside of the site of production. Copyright © 2011 Elsevier B.V. All rights reserved.

Oral administration of non-absorbable delayed release 6-mercaptopurine is locally active in the gut, exerts a systemic immune effect and alleviates Crohn’s disease with low rate of side effects: results of double blind Phase II clinical trial

PubMed Central

Israeli, E; Goldin, E; Fishman, S; Konikoff, F; Lavy, A; Chowers, Y; Melzer, E; Lahat, A; Mahamid, M; Shirin, H; Nussinson, E; Segol, O; Ya’acov, A Ben; Shabbat, Y; Ilan, Y

2015-01-01

Therapy for Crohn’s disease (CD) with thiopurines is limited by systemic side effects. A novel formulation of fixed-dose, delayed-release 6-mercaptopurine (DR-6MP) was developed, with local effect on the gut immune system and minimal absorption. The aim of this study was to evaluate the safety and efficacy of DR-6MP in patients with moderately severe CD compared to systemically delivered 6-mercaptopurine (Purinethol). Seventy CD patients were enrolled into a 12-week, double-blind controlled trial. The primary end-point was the percentage of subjects with clinical remission [Crohn’s Disease Activity Index (CDAI) < 150] or clinical response (100-point CDAI reduction). Twenty-six (56·5%) and 13 (54·2%) subjects from the DR-6MP and Purinethol cohorts, respectively, completed the study. DR-6MP had similar efficacy to Purinethol following 12 weeks of treatment. However, the time to maximal clinical response was 8 weeks for DR-6MP versus 12 weeks for Purinethol. A higher proportion of patients on DR-6MP showed clinical remission at week 8. A greater improvement in Inflammatory Bowel Disease Questionnaire (IBDQ) score was noted in the DR-6MP group. DR-6MP led to a decrease of CD62+ expression on T cells, implying a reduction of lymphocyte adhesion to site of inflammation. DR-6MP was safer than Purinethol, with significantly fewer adverse events (AEs). There was no evidence of drug-induced leucopenia in the DR-6MP group; the proportion of subjects who developed hepatotoxicity was lower for the DR-6MP. Non-absorbable DR-6MP is safe and biologically active in the gut. It is clinically effective, exerting a systemic immune response with low systemic bioavailability and a low incidence of side effects. PMID:25846055

Oral administration of non-absorbable delayed release 6-mercaptopurine is locally active in the gut, exerts a systemic immune effect and alleviates Crohn's disease with low rate of side effects: results of double blind Phase II clinical trial.

PubMed

Israeli, E; Goldin, E; Fishman, S; Konikoff, F; Lavy, A; Chowers, Y; Melzer, E; Lahat, A; Mahamid, M; Shirin, H; Nussinson, E; Segol, O; Ya'acov, A Ben; Shabbat, Y; Ilan, Y

2015-08-01

Therapy for Crohn's disease (CD) with thiopurines is limited by systemic side effects. A novel formulation of fixed-dose, delayed-release 6-mercaptopurine (DR-6MP) was developed, with local effect on the gut immune system and minimal absorption. The aim of this study was to evaluate the safety and efficacy of DR-6MP in patients with moderately severe CD compared to systemically delivered 6-mercaptopurine (Purinethol). Seventy CD patients were enrolled into a 12-week, double-blind controlled trial. The primary end-point was the percentage of subjects with clinical remission [Crohn's Disease Activity Index (CDAI) < 150] or clinical response (100-point CDAI reduction). Twenty-six (56·5%) and 13 (54·2%) subjects from the DR-6MP and Purinethol cohorts, respectively, completed the study. DR-6MP had similar efficacy to Purinethol following 12 weeks of treatment. However, the time to maximal clinical response was 8 weeks for DR-6MP versus 12 weeks for Purinethol. A higher proportion of patients on DR-6MP showed clinical remission at week 8. A greater improvement in Inflammatory Bowel Disease Questionnaire (IBDQ) score was noted in the DR-6MP group. DR-6MP led to a decrease of CD62(+) expression on T cells, implying a reduction of lymphocyte adhesion to site of inflammation. DR-6MP was safer than Purinethol, with significantly fewer adverse events (AEs). There was no evidence of drug-induced leucopenia in the DR-6MP group; the proportion of subjects who developed hepatotoxicity was lower for the DR-6MP. Non-absorbable DR-6MP is safe and biologically active in the gut. It is clinically effective, exerting a systemic immune response with low systemic bioavailability and a low incidence of side effects. © 2015 British Society for Immunology.

Genetic stability of Rift Valley fever virus MP-12 vaccine during serial passages in culture cells.

PubMed

Lokugamage, Nandadeva; Ikegami, Tetsuro

2017-01-01

Rift Valley fever (RVF) is a mosquito-borne zoonotic disease endemic to Africa which affects both ruminants and humans. RVF causes serious damage to the livestock industry and is also a threat to public health. The Rift Valley fever virus has a segmented negative-stranded RNA genome consisting of Large (L)-, Medium (M)-, and Small (S)-segments. The live-attenuated MP-12 vaccine is immunogenic in livestock and humans, and is conditionally licensed for veterinary use in the U.S. The MP-12 strain encodes 23 mutations (nine amino acid substitutions) and is attenuated through a combination of mutations in the L-, M-, and S-segments. Among them, the M-U795C, M-A3564G, and L-G3104A mutations contribute to viral attenuation through the L- and M-segments. The M-U795C, M-A3564G, L-U533C, and L-G3750A mutations are also independently responsible for temperature-sensitive (ts) phenotype. We hypothesized that a serial passage of the MP-12 vaccine in culture cells causes reversions of the MP-12 genome. The MP-12 vaccine and recombinant rMP12-ΔNSs16/198 were serially passaged 25 times. Droplet digital PCR analysis revealed that the reversion occurred at L-G3750A during passages of MP-12 in Vero or MRC-5 cells. The reversion also occurred at M-A3564G and L-U533C of rMP12-ΔNSs16/198 in Vero cells. Reversion mutations were not found in MP-12 or the variant, rMP12-TOSNSs, in the brains of mice with encephalitis. This study characterized genetic stability of the MP-12 vaccine and the potential risk of reversion mutation at the L-G3750A ts mutation after excessive viral passages in culture cells.

Concordance of macular pigment measurements obtained using customized heterochromatic flicker photometry, dual-wavelength autofluorescence, and single-wavelength reflectance.

PubMed

Dennison, Jessica L; Stack, Jim; Beatty, Stephen; Nolan, John M

2013-11-01

This study compares in vivo measurements of macular pigment (MP) obtained using customized heterochromatic flicker photometry (cHFP; Macular Metrics Densitometer(™)), dual-wavelength fundus autofluorescence (Heidelberg Spectralis(®) HRA + OCT MultiColor) and single-wavelength fundus reflectance (Zeiss Visucam(®) 200). MP was measured in one eye of 62 subjects on each device. Data from 49 subjects (79%) was suitable for analysis. Agreement between the Densitometer and Spectralis was investigated at various eccentricities using a variety of quantitative and graphical methods, including: Pearson correlation coefficient to measure degree of scatter (precision), accuracy coefficient, concordance correlation coefficient (ccc), paired t-test, scatter and Bland-Altman plots. The relationship between max MP from the Visucam and central MP from the Spectralis and Densitometer was investigated using regression methods. Agreement was strong between the Densitometer and Spectralis at all central eccentricities (e.g. at 0.25° eccentricity: accuracy = 0.97, precision = 0.90, ccc = 0.87). Regression analysis showed a very weak relationship between the Visucam and Densitometer (e.g. Visucam max on Densitometer central MP: R(2) = 0.008, p = 0.843). Regression analysis also demonstrated a weak relationship between MP measured by the Spectralis and Visucam (e.g. Visucam max on Spectralis central MP: R(2) = 0.047, p = 0.348). MP values obtained using the Heidelberg Spectralis are comparable to MP values obtained using the Densitometer. In contrast, MP values obtained using the Zeiss Visucam are not comparable with either the Densitometer or the Spectralis MP measuring devices. Taking cHFP as the current standard to which other MP measuring devices should be compared, the Spectralis is suitable for use in a clinical and research setting, whereas the Visucam is not. Copyright © 2013 Elsevier Ltd. All rights reserved.

Analysis of Levodopa Content in Commercial Mucuna pruriens Products Using High-Performance Liquid Chromatography with Fluorescence Detection.

PubMed

Soumyanath, Amala; Denne, Tanya; Hiller, Amie; Ramachandran, Shaila; Shinto, Lynne

2018-02-01

Mucuna pruriens (MP) seeds contain levodopa (up to 2% by weight) and have been used in traditional Indian medicine to treat an illness named "Kampavata," now understood to be Parkinson's disease (PD). Studies have shown MP to be beneficial, and even superior, to levodopa alone in treating PD symptoms. Commercial products containing MP are readily available from online and retail sources to patients and physicians. Products often contain extracts of MP seeds, with significantly higher levodopa content than the seeds. However, MP products have limited regulatory controls with respect to quality and content of active ingredient. The aim of this study was to apply a quantitative method to determine levodopa content in readily available MP products that might be used by patients or in research studies. Levodopa present in six commercial MP products was quantified by solvent extraction followed by reversed-phase high-performance liquid chromatography (HPLC) coupled to fluorescence detection (FD). Certificates of analysis (COA) were obtained, from manufacturers of MP products, to assess the existence and implementation of specifications for levodopa content. HPLC-FD analysis revealed that the levodopa content of the six commercial MP products varied from 6% to 141% of individual label claims. No product contained levodopa within normal pharmacopeial limits of 90%-110% label claim. The maximum daily dose of levodopa delivered by the products varied from 14.4 to 720 mg/day. COAs were inconsistent in specifications for and verification of levodopa content. The commercial products tested varied widely in levodopa content, sometimes deviating widely from the label claim. These deficiencies could impact efficacy and safety of MP products used by PD patients and compromise the results of scientific studies on MP products. The HPLC-FD method described in this study could be utilized by both manufacturers and scientific researchers to verify levodopa content of MP products.

Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha

PubMed Central

Kato, Hirotaka; Ishizaki, Kimitsune; Kouno, Masaru; Shirakawa, Makoto; Bowman, John L.; Nishihama, Ryuichi; Kohchi, Takayuki

2015-01-01

The plant hormone auxin regulates many aspects of plant growth and development. Recent progress in Arabidopsis provided a scheme that auxin receptors, TIR1/AFBs, target transcriptional co-repressors, AUX/IAAs, for degradation, allowing ARFs to regulate transcription of auxin responsive genes. The mechanism of auxin-mediated transcriptional regulation is considered to have evolved around the time plants adapted to land. However, little is known about the role of auxin-mediated transcription in basal land plant lineages. We focused on the liverwort Marchantia polymorpha, which belongs to the earliest diverging lineage of land plants. M. polymorpha has only a single TIR1/AFB (MpTIR1), a single AUX/IAA (MpIAA), and three ARFs (MpARF1, MpARF2, and MpARF3) in the genome. Expression of a dominant allele of MpIAA with mutations in its putative degron sequence conferred an auxin resistant phenotype and repressed auxin-dependent expression of the auxin response reporter proGH3:GUS. We next established a system for DEX-inducible auxin-response repression by expressing the putatively stabilized MpIAA protein fused with the glucocorticoid receptor domain (MpIAAmDII-GR). Repression of auxin responses in proMpIAA:MpIAAmDII-GR plants caused severe defects in various developmental processes, including gemmaling development, dorsiventrality, organogenesis, and tropic responses. Transient transactivation assays showed that the three MpARFs had different transcriptional activities, each corresponding to their phylogenetic classifications. Moreover, MpIAA and MpARF proteins interacted with each other with different affinities. This study provides evidence that pleiotropic auxin responses can be achieved by a minimal set of auxin signaling factors and suggests that the transcriptional regulation mediated by TIR1/AFB, AUX/IAA, and three types of ARFs might have been a key invention to establish body plans of land plants. We propose that M. polymorpha is a good model to investigate the principles and the evolution of auxin-mediated transcriptional regulation and its roles in land plant morphogenesis. PMID:26020919

Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha.

PubMed

Kato, Hirotaka; Ishizaki, Kimitsune; Kouno, Masaru; Shirakawa, Makoto; Bowman, John L; Nishihama, Ryuichi; Kohchi, Takayuki

2015-05-01

The plant hormone auxin regulates many aspects of plant growth and development. Recent progress in Arabidopsis provided a scheme that auxin receptors, TIR1/AFBs, target transcriptional co-repressors, AUX/IAAs, for degradation, allowing ARFs to regulate transcription of auxin responsive genes. The mechanism of auxin-mediated transcriptional regulation is considered to have evolved around the time plants adapted to land. However, little is known about the role of auxin-mediated transcription in basal land plant lineages. We focused on the liverwort Marchantia polymorpha, which belongs to the earliest diverging lineage of land plants. M. polymorpha has only a single TIR1/AFB (MpTIR1), a single AUX/IAA (MpIAA), and three ARFs (MpARF1, MpARF2, and MpARF3) in the genome. Expression of a dominant allele of MpIAA with mutations in its putative degron sequence conferred an auxin resistant phenotype and repressed auxin-dependent expression of the auxin response reporter proGH3:GUS. We next established a system for DEX-inducible auxin-response repression by expressing the putatively stabilized MpIAA protein fused with the glucocorticoid receptor domain (MpIAA(mDII)-GR). Repression of auxin responses in (pro)MpIAA:MpIAA(mDII)-GR plants caused severe defects in various developmental processes, including gemmaling development, dorsiventrality, organogenesis, and tropic responses. Transient transactivation assays showed that the three MpARFs had different transcriptional activities, each corresponding to their phylogenetic classifications. Moreover, MpIAA and MpARF proteins interacted with each other with different affinities. This study provides evidence that pleiotropic auxin responses can be achieved by a minimal set of auxin signaling factors and suggests that the transcriptional regulation mediated by TIR1/AFB, AUX/IAA, and three types of ARFs might have been a key invention to establish body plans of land plants. We propose that M. polymorpha is a good model to investigate the principles and the evolution of auxin-mediated transcriptional regulation and its roles in land plant morphogenesis.

Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study.

PubMed

Al-Otaibi, Jamelah S

2015-01-01

2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP). Møller-Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000-400 cm(-1)). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra. Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.

Mucuna pruriens (L.) DC chemo sensitize human breast cancer cells via downregulation of prolactin-mediated JAK2/STAT5A signaling.

PubMed

Sinha, Sonam; Sharma, Sonal; Vora, Jaykant; Shah, Heta; Srivastava, Anshu; Shrivastava, Neeta

2018-05-10

Mucuna pruriens (L.) DC (MP) is an ancient Indian medicinal plant traditionally used to treat Parkinson's disease. L-Dopa (LD), precursor of dopamine is abundantly found in the seeds of MP. L-dopa is a natural inhibitor of prolactin (PRL) hormone which is required to maintain lactation in women but it's over production (hyperprolactinemia) plays critical role in advancement of breast cancer. We aim to examine the pharmacological effect of LD and MP on this hyperprolactinemia associated breast cancer and related signaling for effective management of the disease. We also investigated chemo-sensitizing effect of MP on hyperprolactinemia-mediated cisplatin resistance. Methanolic seed extract of MP were prepared and analysed using HPLC. Effect of LD and MP on the cellular viability of breast cancer cells (T47D, MCF-7, MDA-MB-468 and MDA-MB-231) were evaluated using MTT assay. Further, effect of LD and MP on colony forming potential, DNA damage, cell cycle distribution and apoptosis was determined using agar/agarose method, comet assay and annexin and PI method followed by FACS analysis. To reveal the molecular mechanism involved in the anti-cancer activity of MP, transcriptional and translational level analysis of the key proteins involved in the PRL-mediated signaling, was performed using RT-PCR and western blot analysis. The effect of MP extract on PRL-mediated signaling was validated using dopaminergic agonist bromocriptine. MP extract and cisplatin was given in different combination with appropriate controls to check their effect on chemo-resistivity of breast cancer cells. Our results demonstrated that MP seed extract has the potential to inhibit cellular proliferation of PRL expressing T47D and MCF-7 breast cancer cells via induction of DNA damage, G1 phase of cell cycle arrest and apoptosis more effectively as compare to LD. Further, MP-mediated anti-cancerous effect was associated with the downregulation of PRL expression, further suppressing the JAK2/STAT5A/Cyclin D1 signaling pathway which has been validated using dopaminergic agonist bromocriptine. Cancer-related hyperprolactinemia confers cisplatin resistance, we observed that MP via PRL inhibition, enhances cisplatin efficacy after their combinatorial treatment in breast cancer cells. Collectively, our study suggests that MP could be recommended as dietary supplement along with the chemotherapeutic agents against breast cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Zamzam, Ahmed, S.; Zhaoy, Changhong; Dall'Anesey, Emiliano

This paper examines the AC Optimal Power Flow (OPF) problem for multiphase distribution networks featuring renewable energy resources (RESs). We start by outlining a power flow model for radial multiphase systems that accommodates wye-connected and delta-connected RESs and non-controllable energy assets. We then formalize an AC OPF problem that accounts for both types of connections. Similar to various AC OPF renditions, the resultant problem is a non convex quadratically-constrained quadratic program. However, the so-called Feasible Point Pursuit-Successive Convex Approximation algorithm is leveraged to obtain a feasible and yet locally-optimal solution. The merits of the proposed solution approach are demonstrated usingmore » two unbalanced multiphase distribution feeders with both wye and delta connections.« less

BI-sparsity pursuit for robust subspace recovery

DOE PAGES

Bian, Xiao; Krim, Hamid

2015-09-01

Here, the success of sparse models in computer vision and machine learning in many real-world applications, may be attributed in large part, to the fact that many high dimensional data are distributed in a union of low dimensional subspaces. The underlying structure may, however, be adversely affected by sparse errors, thus inducing additional complexity in recovering it. In this paper, we propose a bi-sparse model as a framework to investigate and analyze this problem, and provide as a result , a novel algorithm to recover the union of subspaces in presence of sparse corruptions. We additionally demonstrate the effectiveness ofmore » our method by experiments on real-world vision data.« less

An Improved B+ Tree for Flash File Systems

NASA Astrophysics Data System (ADS)

Havasi, Ferenc

Nowadays mobile devices such as mobile phones, mp3 players and PDAs are becoming evermore common. Most of them use flash chips as storage. To store data efficiently on flash, it is necessary to adapt ordinary file systems because they are designed for use on hard disks. Most of the file systems use some kind of search tree to store index information, which is very important from a performance aspect. Here we improved the B+ search tree algorithm so as to make flash devices more efficient. Our implementation of this solution saves 98%-99% of the flash operations, and is now the part of the Linux kernel.

Processing-in-Memory Technology for Knowledge Discovery Algorithms

DTIC Science & Technology

2006-07-01

e MP EG 2-d ist1 EP IC -u nq ua nti ze GS M- Ca lcu lat ion Sp ee du p ov er b as el in e MIT-SLP SLP SLPCF SLPCF+SLL 15 8 our infrastructure...to non-threat groups as well. Figure 15: Summary of ARDA/Eagle Data Sets. D at as et #o f N od es (P eo pl e ) #o f L in ks A vg . F an ou t Ph...on e C al ls Te le co ns Te le co n R es po nd en ts A vg . T el ec on Pa rt

DWT-Based High Capacity Audio Watermarking

NASA Astrophysics Data System (ADS)

Fallahpour, Mehdi; Megías, David

This letter suggests a novel high capacity robust audio watermarking algorithm by using the high frequency band of the wavelet decomposition, for which the human auditory system (HAS) is not very sensitive to alteration. The main idea is to divide the high frequency band into frames and then, for embedding, the wavelet samples are changed based on the average of the relevant frame. The experimental results show that the method has very high capacity (about 5.5kbps), without significant perceptual distortion (ODG in [-1, 0] and SNR about 33dB) and provides robustness against common audio signal processing such as added noise, filtering, echo and MPEG compression (MP3).

Input/output behavior of supercomputing applications

NASA Technical Reports Server (NTRS)

Miller, Ethan L.

1991-01-01

The collection and analysis of supercomputer I/O traces and their use in a collection of buffering and caching simulations are described. This serves two purposes. First, it gives a model of how individual applications running on supercomputers request file system I/O, allowing system designer to optimize I/O hardware and file system algorithms to that model. Second, the buffering simulations show what resources are needed to maximize the CPU utilization of a supercomputer given a very bursty I/O request rate. By using read-ahead and write-behind in a large solid stated disk, one or two applications were sufficient to fully utilize a Cray Y-MP CPU.

Mercaptopurine Ingestion Habits, Red Cell Thioguanine Nucleotide Levels, and Relapse Risk in Children With Acute Lymphoblastic Leukemia: A Report From the Children’s Oncology Group Study AALL03N1

PubMed Central

Landier, Wendy; Hageman, Lindsey; Chen, Yanjun; Kornegay, Nancy; Evans, William E.; Bostrom, Bruce C.; Casillas, Jacqueline; Dickens, David S.; Angiolillo, Anne L.; Lew, Glen; Maloney, Kelly W.; Mascarenhas, Leo; Ritchey, A. Kim; Termuhlen, Amanda M.; Carroll, William L.; Relling, Mary V.; Wong, F. Lennie

2017-01-01

Purpose Children with acute lymphoblastic leukemia (ALL) are generally instructed to take mercaptopurine (6-MP) in the evening and without food or dairy products. This study examines the association between 6-MP ingestion habits and 6-MP adherence, red cell thioguanine nucleotide (TGN) levels, and risk of relapse in children with TMPT wild-type genotype. Methods Participants included 441 children with ALL receiving oral 6-MP for maintenance. Adherence was monitored over 48,086 patient-days using the Medication Event Monitoring System; nonadherence was defined as adherence rate < 95%. 6-MP ingestion habits examined included: takes 6-MP with versus never with food, takes 6-MP with versus never with dairy, and takes 6-MP in the evening versus morning versus varying times. Results Median age at study was 6 years (range, 2 to 20 years); 43.8% were nonadherent. Certain 6-MP ingestion habits were associated with nonadherence (taking 6-MP with dairy [odds ratio (OR), 1.9; 95% CI, 1.3 to 2.9; P = .003] and at varying times [OR, 3.4; 95% CI, 1.8 to 6.3; P = .0001]). After adjusting for adherence and other prognosticators, there was no association between 6-MP ingestion habits and relapse risk (6-MP with food: hazard ratio [HR], 0.7; 95% CI, 0.3 to 1.9; P = .5; with dairy: HR, 0.3; 95% CI, 0.07 to 1.5; P = .2; taken in evening/night: HR, 1.1; 95% CI, 0.2 to 7.8; P = .9; at varying times: HR, 0.3; 95% CI, 0.04 to 2.7; P = .3). Among adherent patients, there was no association between red cell TGN levels and taking 6-MP with food versus without (206.1 ± 107.1 v 220.6 ± 121.6; P = .5), with dairy versus without (220.1 ± 87.8 v 216.3 ± 121.3; P =.7), or in the evening/night versus morning/midday versus varying times (218.8 ± 119.7 v 195.5 ± 82.3 v 174.8 ± 93.4; P = .6). Conclusion Commonly practiced restrictions surrounding 6-MP ingestion might not influence outcome but may hinder adherence. Future recommendations regarding 6-MP intake during maintenance therapy for childhood ALL should aim to simplify administration. PMID:28339328

Mercaptopurine Ingestion Habits, Red Cell Thioguanine Nucleotide Levels, and Relapse Risk in Children With Acute Lymphoblastic Leukemia: A Report From the Children's Oncology Group Study AALL03N1.

PubMed

Landier, Wendy; Hageman, Lindsey; Chen, Yanjun; Kornegay, Nancy; Evans, William E; Bostrom, Bruce C; Casillas, Jacqueline; Dickens, David S; Angiolillo, Anne L; Lew, Glen; Maloney, Kelly W; Mascarenhas, Leo; Ritchey, A Kim; Termuhlen, Amanda M; Carroll, William L; Relling, Mary V; Wong, F Lennie; Bhatia, Smita

2017-05-20

Purpose Children with acute lymphoblastic leukemia (ALL) are generally instructed to take mercaptopurine (6-MP) in the evening and without food or dairy products. This study examines the association between 6-MP ingestion habits and 6-MP adherence, red cell thioguanine nucleotide (TGN) levels, and risk of relapse in children with TMPT wild-type genotype. Methods Participants included 441 children with ALL receiving oral 6-MP for maintenance. Adherence was monitored over 48,086 patient-days using the Medication Event Monitoring System; nonadherence was defined as adherence rate < 95%. 6-MP ingestion habits examined included: takes 6-MP with versus never with food, takes 6-MP with versus never with dairy, and takes 6-MP in the evening versus morning versus varying times. Results Median age at study was 6 years (range, 2 to 20 years); 43.8% were nonadherent. Certain 6-MP ingestion habits were associated with nonadherence (taking 6-MP with dairy [odds ratio (OR), 1.9; 95% CI, 1.3 to 2.9; P = .003] and at varying times [OR, 3.4; 95% CI, 1.8 to 6.3; P = .0001]). After adjusting for adherence and other prognosticators, there was no association between 6-MP ingestion habits and relapse risk (6-MP with food: hazard ratio [HR], 0.7; 95% CI, 0.3 to 1.9; P = .5; with dairy: HR, 0.3; 95% CI, 0.07 to 1.5; P = .2; taken in evening/night: HR, 1.1; 95% CI, 0.2 to 7.8; P = .9; at varying times: HR, 0.3; 95% CI, 0.04 to 2.7; P = .3). Among adherent patients, there was no association between red cell TGN levels and taking 6-MP with food versus without (206.1 ± 107.1 v 220.6 ± 121.6; P = .5), with dairy versus without (220.1 ± 87.8 v 216.3 ± 121.3; P =.7), or in the evening/night versus morning/midday versus varying times (218.8 ± 119.7 v 195.5 ± 82.3 v 174.8 ± 93.4; P = .6). Conclusion Commonly practiced restrictions surrounding 6-MP ingestion might not influence outcome but may hinder adherence. Future recommendations regarding 6-MP intake during maintenance therapy for childhood ALL should aim to simplify administration.

Impact of microbial efficiency to predict MP supply when estimating protein requirements of growing beef cattle from performance.

PubMed

Watson, A K; Klopfenstein, T J; Erickson, G E; MacDonald, J C; Wilkerson, V A

2017-07-01

Data from 16 trials were compiled to calculate microbial CP (MCP) production and MP requirements of growing cattle on high-forage diets. All cattle were individually fed diets with 28% to 72% corn cobs in addition to either alfalfa, corn silage, or sorghum silage at 18% to 60% of the diet (DM basis). The remainder of the diet consisted of protein supplement. Source of protein within the supplement varied and included urea, blood meal, corn gluten meal, dry distillers grains, feather meal, meat and bone meal, poultry by-product meal, soybean meal, and wet distillers grains. All trials included a urea-only treatment. Intake of all cattle within an experiment was held constant, as a percentage of BW, established by the urea-supplemented group. In each trial the base diet (forage and urea supplement) was MP deficient. Treatments consisted of increasing amounts of test protein replacing the urea supplement. As protein in the diet increased, ADG plateaued. Among experiments, ADG ranged from 0.11 to 0.73 kg. Three methods of calculating microbial efficiency were used to determine MP supply. Gain was then regressed against calculated MP supply to determine MP requirement for maintenance and gain. Method 1 (based on a constant 13% microbial efficiency as used by the beef NRC model) predicted an MP maintenance requirement of 3.8 g/kg BW and 385 g MP/kg gain. Method 2 calculated microbial efficiency using low-quality forage diets and predicted MP requirements of 3.2 g/kg BW for maintenance and 448 g/kg for gain. Method 3 (based on an equation predicting MCP yield from TDN intake, proposed by the Beef Cattle Nutrient Requirements Model [BCNRM]) predicted MP requirements of 3.1 g/kg BW for maintenance and 342 g/kg for gain. The factorial method of calculating MP maintenance requirements accounts for scurf, endogenous urinary, and metabolic fecal protein losses and averaged 4.2 g/kg BW. Cattle performance data demonstrate formulating diets to meet the beef NRC model recommended MP maintenance requirement (3.8 g/kg S) works well when using 13% microbial efficiency. Therefore, a change in how microbial efficiency is calculated necessitates a change in the proposed MP maintenance requirement to not oversupply or undersupply RUP. Using the 2016 BCNRM to predict MCP production and formulate diets to meet MP requirements also requires changing the MP maintenance requirement to 3.1 g/kg BW.

Melicope ptelefolia leaf extracts exhibit antioxidant activity and exert anti-proliferative effect with apoptosis induction on four different cancer cell lines.

PubMed

Kabir, Mohammad Faujul; Mohd Ali, Johari; Abolmaesoomi, Mitra; Hashim, Onn Haji

2017-05-05

Melicope ptelefolia is a well-known herb in a number of Asian countries. It is often used as vegetable salad and traditional medicine to address various ailments. However, not many studies have been currently done to evaluate the medicinal benefits of M. ptelefolia (MP). The present study reports antioxidant, anti-proliferative, and apoptosis induction activities of MP leaf extracts. Young MP leaves were dried, powdered and extracted sequentially using hexane (HX), ethyl acetate (EA), methanol (MeOH) and water (W). Antioxidant activity was evaluated using ferric reducing antioxidant power (FRAP), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) radicals scavenging and cellular antioxidant activity (CAA) assays. Anti-proliferative activity was evaluated through cell viability assay, using the following four human cancer cell lines: breast (HCC1937, MDA-MB-231), colorectal (HCT116) and liver (HepG2). The anti-proliferative activity was further confirmed through cell cycle and apoptosis assays, including annexin-V/7-aminoactinomycin D staining and measurements of caspase enzymes activation and inhibition. Overall, MP-HX extract exhibited the highest antioxidant potential, with IC 50 values of 267.73 ± 5.58 and 327.40 ± 3.80 μg/mL for ABTS and DPPH radical-scavenging assays, respectively. MP-HX demonstrated the highest CAA activity in Hs27 cells, with EC 50 of 11.30 ± 0.68 μg/mL, while MP-EA showed EC 50 value of 37.32 ± 0.68 μg/mL. MP-HX and MP-EA showed promising anti-proliferative activity towards the four cancer cell lines, with IC 50 values that were mostly below 100 μg/mL. MP-HX showed the most notable anti-proliferative activity against MDA-MB-231 (IC 50  = 57.81 ± 3.49 μg/mL) and HCT116 (IC 50  = 58.04 ± 0.96 μg/mL) while MP-EA showed strongest anti-proliferative activity in HCT116 (IC 50  = 64.69 ± 0.72 μg/mL). The anticancer potential of MP-HX and MP-EA were also demonstrated by their ability to induce caspase-dependent apoptotic cell death in all of the cancer cell lines tested. Cell cycle analysis suggested that both the MP-HX and MP-EA extracts were able to disrupt the cell cycle in most of the cancer cell lines. MP-HX and MP-EA extracts demonstrated notable antioxidant, anti-proliferative, apoptosis induction and cancer cell cycle inhibition activities. These findings reflect the promising potentials of MP to be a source of novel phytochemical(s) with health promoting benefits that are also valuable for nutraceutical industry and cancer therapy.

Two-level structural sparsity regularization for identifying lattices and defects in noisy images

DOE PAGES

Li, Xin; Belianinov, Alex; Dyck, Ondrej E.; ...

2018-03-09

Here, this paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives.more » To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. In conclusion, we believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.« less

Two-level structural sparsity regularization for identifying lattices and defects in noisy images

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

Li, Xin; Belianinov, Alex; Dyck, Ondrej E.

Here, this paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives.more » To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. In conclusion, we believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.« less

Sparse Regression as a Sparse Eigenvalue Problem

NASA Technical Reports Server (NTRS)

Moghaddam, Baback; Gruber, Amit; Weiss, Yair; Avidan, Shai

2008-01-01

We extend the l0-norm "subspectral" algorithms for sparse-LDA [5] and sparse-PCA [6] to general quadratic costs such as MSE in linear (kernel) regression. The resulting "Sparse Least Squares" (SLS) problem is also NP-hard, by way of its equivalence to a rank-1 sparse eigenvalue problem (e.g., binary sparse-LDA [7]). Specifically, for a general quadratic cost we use a highly-efficient technique for direct eigenvalue computation using partitioned matrix inverses which leads to dramatic x103 speed-ups over standard eigenvalue decomposition. This increased efficiency mitigates the O(n4) scaling behaviour that up to now has limited the previous algorithms' utility for high-dimensional learning problems. Moreover, the new computation prioritizes the role of the less-myopic backward elimination stage which becomes more efficient than forward selection. Similarly, branch-and-bound search for Exact Sparse Least Squares (ESLS) also benefits from partitioned matrix inverse techniques. Our Greedy Sparse Least Squares (GSLS) generalizes Natarajan's algorithm [9] also known as Order-Recursive Matching Pursuit (ORMP). Specifically, the forward half of GSLS is exactly equivalent to ORMP but more efficient. By including the backward pass, which only doubles the computation, we can achieve lower MSE than ORMP. Experimental comparisons to the state-of-the-art LARS algorithm [3] show forward-GSLS is faster, more accurate and more flexible in terms of choice of regularization

38 CFR 21.310 - Rate of pursuit of a rehabilitation program.

Code of Federal Regulations, 2011 CFR

2011-07-01

... rehabilitation program. 21.310 Section 21.310 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Vocational Rehabilitation and Employment Under 38 U.S.C. Chapter 31 Rate of Pursuit § 21.310 Rate of pursuit of a rehabilitation program. (a...