iCut: an Integrative Cut Algorithm Enables Accurate Segmentation of Touching Cells
He, Yong; Gong, Hui; Xiong, Benyi; Xu, Xiaofeng; Li, Anan; Jiang, Tao; Sun, Qingtao; Wang, Simin; Luo, Qingming; Chen, Shangbin
2015-01-01
Individual cells play essential roles in the biological processes of the brain. The number of neurons changes during both normal development and disease progression. High-resolution imaging has made it possible to directly count cells. However, the automatic and precise segmentation of touching cells continues to be a major challenge for massive and highly complex datasets. Thus, an integrative cut (iCut) algorithm, which combines information regarding spatial location and intervening and concave contours with the established normalized cut, has been developed. iCut involves two key steps: (1) a weighting matrix is first constructed with the abovementioned information regarding the touching cells and (2) a normalized cut algorithm that uses the weighting matrix is implemented to separate the touching cells into isolated cells. This novel algorithm was evaluated using two types of data: the open SIMCEP benchmark dataset and our micro-optical imaging dataset from a Nissl-stained mouse brain. It has achieved a promising recall/precision of 91.2 ± 2.1%/94.1 ± 1.8% and 86.8 ± 4.1%/87.5 ± 5.7%, respectively, for the two datasets. As quantified using the harmonic mean of recall and precision, the accuracy of iCut is higher than that of some state-of-the-art algorithms. The better performance of this fully automated algorithm can benefit studies of brain cytoarchitecture. PMID:26168908
Accurate Finite Difference Algorithms
NASA Technical Reports Server (NTRS)
Goodrich, John W.
1996-01-01
Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.
A time-accurate multiple-grid algorithm
NASA Technical Reports Server (NTRS)
Jespersen, D. C.
1985-01-01
A time-accurate multiple-grid algorithm is described. The algorithm allows one to take much larger time steps with an explicit time-marching scheme than would otherwise be the case. Sample calculations of a scalar advection equation and the Euler equations for an oscillating airfoil are shown. For the oscillating airfoil, time steps an order of magnitude larger than the single-grid algorithm are possible.
Genomic-enabled prediction with classification algorithms.
Ornella, L; Pérez, P; Tapia, E; González-Camacho, J M; Burgueño, J; Zhang, X; Singh, S; Vicente, F S; Bonnett, D; Dreisigacker, S; Singh, R; Long, N; Crossa, J
2014-06-01
Pearson's correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait-environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen's kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets
Genomic-enabled prediction with classification algorithms
Ornella, L; Pérez, P; Tapia, E; González-Camacho, J M; Burgueño, J; Zhang, X; Singh, S; Vicente, F S; Bonnett, D; Dreisigacker, S; Singh, R; Long, N; Crossa, J
2014-01-01
Pearson's correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait–environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen's kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets
Nonexposure accurate location K-anonymity algorithm in LBS.
Jia, Jinying; Zhang, Fengli
2014-01-01
This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR. PMID:24605060
Nonexposure Accurate Location K-Anonymity Algorithm in LBS
2014-01-01
This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR. PMID:24605060
Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
Singh, Ritambhara; Kuscu, Cem; Quinlan, Aaron; Qi, Yanjun; Adli, Mazhar
2015-01-01
The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CRISPR/Cas9 Off-target Prediction and Identification Tool (CROP-IT) that performs improved off-target binding and cleavage site predictions. Unlike existing prediction programs that solely use DNA sequence information; CROP-IT integrates whole genome level biological information from existing Cas9 binding and cleavage data sets. Utilizing whole-genome chromatin state information from 125 human cell types further enhances its computational prediction power. Comparative analyses on experimentally validated datasets show that CROP-IT outperforms existing computational algorithms in predicting both Cas9 binding as well as cleavage sites. With a user-friendly web-interface, CROP-IT outputs scored and ranked list of potential off-targets that enables improved guide RNA design and more accurate prediction of Cas9 binding or cleavage sites. PMID:26032770
A spectrally accurate algorithm for electromagnetic scattering in three dimensions
NASA Astrophysics Data System (ADS)
Ganesh, M.; Hawkins, S.
2006-09-01
In this work we develop, implement and analyze a high-order spectrally accurate algorithm for computation of the echo area, and monostatic and bistatic radar cross-section (RCS) of a three dimensional perfectly conducting obstacle through simulation of the time-harmonic electromagnetic waves scattered by the conductor. Our scheme is based on a modified boundary integral formulation (of the Maxwell equations) that is tolerant to basis functions that are not tangential on the conductor surface. We test our algorithm with extensive computational experiments using a variety of three dimensional perfect conductors described in spherical coordinates, including benchmark radar targets such as the metallic NASA almond and ogive. The monostatic RCS measurements for non-convex conductors require hundreds of incident waves (boundary conditions). We demonstrate that the monostatic RCS of small (to medium) sized conductors can be computed using over one thousand incident waves within a few minutes (to a few hours) of CPU time. We compare our results with those obtained using method of moments based industrial standard three dimensional electromagnetic codes CARLOS, CICERO, FE-IE, FERM, and FISC. Finally, we prove the spectrally accurate convergence of our algorithm for computing the surface current, far-field, and RCS values of a class of conductors described globally in spherical coordinates.
Effective Echo Detection and Accurate Orbit Estimation Algorithms for Space Debris Radar
NASA Astrophysics Data System (ADS)
Isoda, Kentaro; Sakamoto, Takuya; Sato, Toru
Orbit estimation of space debris, objects of no inherent value orbiting the earth, is a task that is important for avoiding collisions with spacecraft. The Kamisaibara Spaceguard Center radar system was built in 2004 as the first radar facility in Japan devoted to the observation of space debris. In order to detect the smaller debris, coherent integration is effective in improving SNR (Signal-to-Noise Ratio). However, it is difficult to apply coherent integration to real data because the motions of the targets are unknown. An effective algorithm is proposed for echo detection and orbit estimation of the faint echoes from space debris. The characteristics of the evaluation function are utilized by the algorithm. Experiments show the proposed algorithm improves SNR by 8.32dB and enables estimation of orbital parameters accurately to allow for re-tracking with a single radar.
Depth-fused multi-focal plane displays enable accurate depth perception
NASA Astrophysics Data System (ADS)
Hua, Hong; Liu, Sheng
2010-11-01
Many different approaches to three-dimensional (3-D) displays have been explored, most of which are considered to be stereoscopic-type. The stereoscopic-type displays create depth perception by presenting two perspective images, one for each eye, of a 3D scene from two slightly different viewing positions. They have been the dominant technology adopted for many applications, spanning the fields of flight simulation, scientific visualization, medicine, engineering design, education and training, and entertainment systems. Existing stereoscopic displays, however, lack the ability to produce accurate focus cues, which have been suggested to contribute to various visual artifacts such as visual fatigue. This paper will review some recent work on vari- and multi-focal plane display technologies that are capable of rendering nearly correct focus cues for 3D objects and these technologies have great promise of enabling more accurate depth perception for 3D tasks.
Node Handprinting: A Scalable and Accurate Algorithm for Aligning Multiple Biological Networks.
Radu, Alex; Charleston, Michael
2015-07-01
Due to recent advancements in high-throughput sequencing technologies, progressively more protein-protein interactions have been identified for a growing number of species. Subsequently, the protein-protein interaction networks for these species have been further refined. The increase in the quality and availability of these networks has in turn brought a demand for efficient methods to analyze such networks. The pairwise alignment of these networks has been moderately investigated, with numerous algorithms available, but there is very little progress in the field of multiple network alignment. Multiple alignment of networks from different organisms is ideal at finding abnormally conserved or disparate subnetworks. We present a fast and accurate algorithmic approach, Node Handprinting (NH), based on our previous work with Node Fingerprinting, which enables quick and accurate alignment of multiple networks. We also propose two new metrics for the analysis of multiple alignments, as the current metrics are not as sophisticated as their pairwise alignment counterparts. To assess the performance of NH, we use previously aligned datasets as well as protein interaction networks generated from the public database BioGRID. Our results indicate that NH compares favorably with current methodologies and is the only algorithm capable of performing the more complex alignments. PMID:25695597
An accurate product SVD (singular value decomposition) algorithm
Bojanczyk, A.W.; Luk, F.T. . School of Electrical Engineering); Ewerbring, M. ); Van Dooren, P. )
1990-01-01
In this paper, we propose a new algorithm for computing a singular value decomposition of a product of three matrices. We show that our algorithm is numerically desirable in that all relevant residual elements will be numerically small. 12 refs., 1 tab.
Enabling accurate gate profile control with inline 3D-AFM
NASA Astrophysics Data System (ADS)
Bao, Tianming; Lopez, Andrew; Dawson, Dean
2009-05-01
The logic and memory semiconductor device technology strives to follow the aggressive ITRS roadmap. The ITRS calls for increased 3D metrology to meet the demand for tighter process control at 45nm and 32nm nodes. In particular, gate engineering has advanced to a level where conventional metrology by CD-SEM and optical scatterometry (OCD) faces fundamental limitations without involvement of 3D atomic force microscope (3D-AFM or CD-AFM). This paper reports recent progress in 3D-AFM to address the metrology need to control gate dimension in MOSFET transistor formation. 3D-AFM metrology measures the gate electrode at post-etch with the lowest measurement uncertainty for critical gate geometry, including linewidth, sidewall profile, sidewall angle (SWA), line width roughness (LWR), and line edge roughness (LER). 3D-AFM enables accurate gate profile control in three types of metrology applications: reference metrology to validate CD-SEM and OCD, inline depth or 3D monitoring, or replacing TEM for 3D characterization for engineering analysis.
Consistent Multigroup Theory Enabling Accurate Course-Group Simulation of Gen IV Reactors
Rahnema, Farzad; Haghighat, Alireza; Ougouag, Abderrafi
2013-11-29
The objective of this proposal is the development of a consistent multi-group theory that accurately accounts for the energy-angle coupling associated with collapsed-group cross sections. This will allow for coarse-group transport and diffusion theory calculations that exhibit continuous energy accuracy and implicitly treat cross- section resonances. This is of particular importance when considering the highly heterogeneous and optically thin reactor designs within the Next Generation Nuclear Plant (NGNP) framework. In such reactors, ignoring the influence of anisotropy in the angular flux on the collapsed cross section, especially at the interface between core and reflector near which control rods are located, results in inaccurate estimates of the rod worth, a serious safety concern. The scope of this project will include the development and verification of a new multi-group theory enabling high-fidelity transport and diffusion calculations in coarse groups, as well as a methodology for the implementation of this method in existing codes. This will allow for a higher accuracy solution of reactor problems while using fewer groups and will reduce the computational expense. The proposed research represents a fundamental advancement in the understanding and improvement of multi- group theory for reactor analysis.
Accelerating universal Kriging interpolation algorithm using CUDA-enabled GPU
NASA Astrophysics Data System (ADS)
Cheng, Tangpei
2013-04-01
Kriging algorithms are a group of important interpolation methods, which are very useful in many geological applications. However, the algorithm based on traditional general purpose processors can be computationally expensive, especially when the problem scale expands. Inspired by the current trend in graphics processing technology, we proposed an efficient parallel scheme to accelerate the universal Kriging algorithm on the NVIDIA CUDA platform. Some high-performance mathematical functions have been introduced to calculate the compute-intensive steps in the Kriging algorithm, such as matrix-vector multiplication and matrix-matrix multiplication. To further optimize performance, we reduced the memory transfer overhead by reconstructing the time-consuming loops, specifically for the execution on GPU. In the numerical experiment, we compared the performances among different multi-core CPU and GPU implementations to interpolate a geological site. The improved CUDA implementation shows a nearly 18× speedup with respect to the sequential program and is 6.32 times faster compared to the OpenMP-based version running on Intel Xeon E5320 quad-cores CPU and scales well with the size of the system.
Li, Xiangrui; Lu, Zhong-Lin
2012-01-01
Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ (1) and DataPixx (2) use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher (3) described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network (4) and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements. Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect
A cooperative positioning algorithm for DSRC enabled vehicular networks
NASA Astrophysics Data System (ADS)
Efatmaneshnik, M.; Kealy, A.; Alam, N.; Dempster, A. G.
2011-12-01
Many of the safety related applications that can be facilitated by Dedicated Short Range Communications (DSRC), such as vehicle proximity warnings, automated braking (e.g. at level crossings), speed advisories, pedestrian alerts etc., rely on a robust vehicle positioning capability such as that provided by a Global Navigation Satellite System (GNSS). Vehicles in remote areas, entering tunnels, high rise areas or any high multipath/ weak signal environment will challenge the integrity of GNSS position solutions, and ultimately the safety application it underpins. To address this challenge, this paper presents an innovative application of Cooperative Positioning techniques within vehicular networks. CP refers to any method of integrating measurements from different positioning systems and sensors in order to improve the overall quality (accuracy and reliability) of the final position solution. This paper investigates the potential of the DSRC infrastructure itself to provide an inter-vehicular ranging signal that can be used as a measurement within the CP algorithm. In this paper, time-based techniques of ranging are introduced and bandwidth requirements are investigated and presented. The robustness of the CP algorithm to inter-vehicle connection failure as well as GNSS dropouts is also demonstrated using simulation studies. Finally, the performance of the Constrained Kalman Filter used to integrate GNSS measurements with DSRC derived range estimates within a typical VANET is described and evaluated.
SAR data exploitation: computational technology enabling SAR ATR algorithm development
NASA Astrophysics Data System (ADS)
Majumder, Uttam K.; Casteel, Curtis H., Jr.; Buxa, Peter; Minardi, Michael J.; Zelnio, Edmund G.; Nehrbass, John W.
2007-04-01
A fundamental issue with synthetic aperture radar (SAR) application development is data processing and exploitation in real-time or near real-time. The power of high performance computing (HPC) clusters, FPGA, and the IBM Cell processor presents new algorithm development possibilities that have not been fully leveraged. In this paper, we will illustrate the capability of SAR data exploitation which was impractical over the last decade due to computing limitations. We can envision that SAR imagery encompassing city size coverage at extremely high levels of fidelity could be processed at near-real time using the above technologies to empower the warfighter with access to critical information for the war on terror, homeland defense, as well as urban warfare.
Zhang, Hao; Zhao, Yan; Cao, Liangcai; Jin, Guofan
2015-02-23
We propose an algorithm based on fully computed holographic stereogram for calculating full-parallax computer-generated holograms (CGHs) with accurate depth cues. The proposed method integrates point source algorithm and holographic stereogram based algorithm to reconstruct the three-dimensional (3D) scenes. Precise accommodation cue and occlusion effect can be created, and computer graphics rendering techniques can be employed in the CGH generation to enhance the image fidelity. Optical experiments have been performed using a spatial light modulator (SLM) and a fabricated high-resolution hologram, the results show that our proposed algorithm can perform quality reconstructions of 3D scenes with arbitrary depth information. PMID:25836429
An accurate and efficient algorithm for Peptide and ptm identification by tandem mass spectrometry.
Ning, Kang; Ng, Hoong Kee; Leong, Hon Wai
2007-01-01
Peptide identification by tandem mass spectrometry (MS/MS) is one of the most important problems in proteomics. Recent advances in high throughput MS/MS experiments result in huge amount of spectra. Unfortunately, identification of these spectra is relatively slow, and the accuracies of current algorithms are not high with the presence of noises and post-translational modifications (PTMs). In this paper, we strive to achieve high accuracy and efficiency for peptide identification problem, with special concern on identification of peptides with PTMs. This paper expands our previous work on PepSOM with the introduction of two accurate modified scoring functions: Slambda for peptide identification and Slambda* for identification of peptides with PTMs. Experiments showed that our algorithm is both fast and accurate for peptide identification. Experiments on spectra with simulated and real PTMs confirmed that our algorithm is accurate for identifying PTMs. PMID:18546510
SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments
Eter, Wael A.; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin
2016-01-01
Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, 111In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of 111In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers. PMID:27080529
Eter, Wael A; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin
2016-01-01
Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, (111)In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of (111)In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers. PMID:27080529
Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics
NASA Technical Reports Server (NTRS)
Goodrich, John W.; Dyson, Rodger W.
1999-01-01
The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that
ASYMPTOTICALLY OPTIMAL HIGH-ORDER ACCURATE ALGORITHMS FOR THE SOLUTION OF CERTAIN ELLIPTIC PDEs
Leonid Kunyansky, PhD
2008-11-26
The main goal of the project, "Asymptotically Optimal, High-Order Accurate Algorithms for the Solution of Certain Elliptic PDE's" (DE-FG02-03ER25577) was to develop fast, high-order algorithms for the solution of scattering problems and spectral problems of photonic crystals theory. The results we obtained lie in three areas: (1) asymptotically fast, high-order algorithms for the solution of eigenvalue problems of photonics, (2) fast, high-order algorithms for the solution of acoustic and electromagnetic scattering problems in the inhomogeneous media, and (3) inversion formulas and fast algorithms for the inverse source problem for the acoustic wave equation, with applications to thermo- and opto- acoustic tomography.
Abate-Pella, Daniel; Freund, Dana M; Ma, Yan; Simón-Manso, Yamil; Hollender, Juliane; Broeckling, Corey D; Huhman, David V; Krokhin, Oleg V; Stoll, Dwight R; Hegeman, Adrian D; Kind, Tobias; Fiehn, Oliver; Schymanski, Emma L; Prenni, Jessica E; Sumner, Lloyd W; Boswell, Paul G
2015-09-18
Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) can be greatly improved if the chromatographic retention information is used along with mass spectral information to narrow down the lists of candidates. Linear retention indexing remains the standard for sharing retention data across labs, but it is unreliable because it cannot properly account for differences in the experimental conditions used by various labs, even when the differences are relatively small and unintentional. On the other hand, an approach called "retention projection" properly accounts for many intentional differences in experimental conditions, and when combined with a "back-calculation" methodology described recently, it also accounts for unintentional differences. In this study, the accuracy of this methodology is compared with linear retention indexing across eight different labs. When each lab ran a test mixture under a range of multi-segment gradients and flow rates they selected independently, retention projections averaged 22-fold more accurate for uncharged compounds because they properly accounted for these intentional differences, which were more pronounced in steep gradients. When each lab ran the test mixture under nominally the same conditions, which is the ideal situation to reproduce linear retention indices, retention projections still averaged 2-fold more accurate because they properly accounted for many unintentional differences between the LC systems. To the best of our knowledge, this is the most successful study to date aiming to calculate (or even just to reproduce) LC gradient retention across labs, and it is the only study in which retention was reliably calculated under various multi-segment gradients and flow rates chosen independently by labs. PMID:26292625
Smith, Matt J; Pascal, Carita E; Grauvogel, Zac; Habicht, Christopher; Seeb, James E; Seeb, Lisa W
2011-03-01
Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA. PMID:21429180
Enabling fast, stable and accurate peridynamic computations using multi-time-step integration
Lindsay, P.; Parks, M. L.; Prakash, A.
2016-04-13
Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less
FASTSIM2: a second-order accurate frictional rolling contact algorithm
NASA Astrophysics Data System (ADS)
Vollebregt, E. A. H.; Wilders, P.
2011-01-01
In this paper we consider the frictional (tangential) steady rolling contact problem. We confine ourselves to the simplified theory, instead of using full elastostatic theory, in order to be able to compute results fast, as needed for on-line application in vehicle system dynamics simulation packages. The FASTSIM algorithm is the leading technology in this field and is employed in all dominant railway vehicle system dynamics packages (VSD) in the world. The main contribution of this paper is a new version "FASTSIM2" of the FASTSIM algorithm, which is second-order accurate. This is relevant for VSD, because with the new algorithm 16 times less grid points are required for sufficiently accurate computations of the contact forces. The approach is based on new insights in the characteristics of the rolling contact problem when using the simplified theory, and on taking precise care of the contact conditions in the numerical integration scheme employed.
Puhakka, Pia H; Te Moller, Nikae C R; Tanska, Petri; Saarakkala, Simo; Tiitu, Virpi; Korhonen, Rami K; Brommer, Harold; Virén, Tuomas; Jurvelin, Jukka S; Töyräs, Juha
2016-08-01
Background and purpose - Arthroscopic estimation of articular cartilage thickness is important for scoring of lesion severity, and measurement of cartilage speed of sound (SOS)-a sensitive index of changes in cartilage composition. We investigated the accuracy of optical coherence tomography (OCT) in measurements of cartilage thickness and determined SOS by combining OCT thickness and ultrasound (US) time-of-flight (TOF) measurements. Material and methods - Cartilage thickness measurements from OCT and microscopy images of 94 equine osteochondral samples were compared. Then, SOS in cartilage was determined using simultaneous OCT thickness and US TOF measurements. SOS was then compared with the compositional, structural, and mechanical properties of cartilage. Results - Measurements of non-calcified cartilage thickness using OCT and microscopy were significantly correlated (ρ = 0.92; p < 0.001). With calcified cartilage included, the correlation was ρ = 0.85 (p < 0.001). The mean cartilage SOS (1,636 m/s) was in agreement with the literature. However, SOS and the other properties of cartilage lacked any statistically significant correlation. Interpretation - OCT can give an accurate measurement of articular cartilage thickness. Although SOS measurements lacked accuracy in thin equine cartilage, the concept of SOS measurement using OCT appears promising. PMID:27164159
Zhang, Xiujun; Zhao, Juan; Hao, Jin-Kao; Zhao, Xing-Ming; Chen, Luonan
2015-03-11
Mutual information (MI), a quantity describing the nonlinear dependence between two random variables, has been widely used to construct gene regulatory networks (GRNs). Despite its good performance, MI cannot separate the direct regulations from indirect ones among genes. Although the conditional mutual information (CMI) is able to identify the direct regulations, it generally underestimates the regulation strength, i.e. it may result in false negatives when inferring gene regulations. In this work, to overcome the problems, we propose a novel concept, namely conditional mutual inclusive information (CMI2), to describe the regulations between genes. Furthermore, with CMI2, we develop a new approach, namely CMI2NI (CMI2-based network inference), for reverse-engineering GRNs. In CMI2NI, CMI2 is used to quantify the mutual information between two genes given a third one through calculating the Kullback-Leibler divergence between the postulated distributions of including and excluding the edge between the two genes. The benchmark results on the GRNs from DREAM challenge as well as the SOS DNA repair network in Escherichia coli demonstrate the superior performance of CMI2NI. Specifically, even for gene expression data with small sample size, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the regulation strength between genes. As a case study, CMI2NI was also used to reconstruct cancer-specific GRNs using gene expression data from The Cancer Genome Atlas (TCGA). CMI2NI is freely accessible at http://www.comp-sysbio.org/cmi2ni. PMID:25539927
Ralph, Duncan K.; Matsen, Frederick A.
2016-01-01
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM “factorization” strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM. PMID:26751373
Zhang, Xiujun; Zhao, Juan; Hao, Jin-Kao; Zhao, Xing-Ming; Chen, Luonan
2015-01-01
Mutual information (MI), a quantity describing the nonlinear dependence between two random variables, has been widely used to construct gene regulatory networks (GRNs). Despite its good performance, MI cannot separate the direct regulations from indirect ones among genes. Although the conditional mutual information (CMI) is able to identify the direct regulations, it generally underestimates the regulation strength, i.e. it may result in false negatives when inferring gene regulations. In this work, to overcome the problems, we propose a novel concept, namely conditional mutual inclusive information (CMI2), to describe the regulations between genes. Furthermore, with CMI2, we develop a new approach, namely CMI2NI (CMI2-based network inference), for reverse-engineering GRNs. In CMI2NI, CMI2 is used to quantify the mutual information between two genes given a third one through calculating the Kullback–Leibler divergence between the postulated distributions of including and excluding the edge between the two genes. The benchmark results on the GRNs from DREAM challenge as well as the SOS DNA repair network in Escherichia coli demonstrate the superior performance of CMI2NI. Specifically, even for gene expression data with small sample size, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the regulation strength between genes. As a case study, CMI2NI was also used to reconstruct cancer-specific GRNs using gene expression data from The Cancer Genome Atlas (TCGA). CMI2NI is freely accessible at http://www.comp-sysbio.org/cmi2ni. PMID:25539927
Ralph, Duncan K; Matsen, Frederick A
2016-01-01
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM. PMID:26751373
Algorithms for Accurate and Fast Plotting of Contour Surfaces in 3D Using Hexahedral Elements
NASA Astrophysics Data System (ADS)
Singh, Chandan; Saini, Jaswinder Singh
2016-07-01
In the present study, Fast and accurate algorithms for the generation of contour surfaces in 3D are described using hexahedral elements which are popular in finite element analysis. The contour surfaces are described in the form of groups of boundaries of contour segments and their interior points are derived using the contour equation. The locations of contour boundaries and the interior points on contour surfaces are as accurate as the interpolation results obtained by hexahedral elements and thus there are no discrepancies between the analysis and visualization results.
Algorithms for Accurate and Fast Plotting of Contour Surfaces in 3D Using Hexahedral Elements
NASA Astrophysics Data System (ADS)
Singh, Chandan; Saini, Jaswinder Singh
2016-05-01
In the present study, Fast and accurate algorithms for the generation of contour surfaces in 3D are described using hexahedral elements which are popular in finite element analysis. The contour surfaces are described in the form of groups of boundaries of contour segments and their interior points are derived using the contour equation. The locations of contour boundaries and the interior points on contour surfaces are as accurate as the interpolation results obtained by hexahedral elements and thus there are no discrepancies between the analysis and visualization results.
A block-wise approximate parallel implementation for ART algorithm on CUDA-enabled GPU.
Fan, Zhongyin; Xie, Yaoqin
2015-01-01
Computed tomography (CT) has been widely used to acquire volumetric anatomical information in the diagnosis and treatment of illnesses in many clinics. However, the ART algorithm for reconstruction from under-sampled and noisy projection is still time-consuming. It is the goal of our work to improve a block-wise approximate parallel implementation for the ART algorithm on CUDA-enabled GPU to make the ART algorithm applicable to the clinical environment. The resulting method has several compelling features: (1) the rays are allotted into blocks, making the rays in the same block parallel; (2) GPU implementation caters to the actual industrial and medical application demand. We test the algorithm on a digital shepp-logan phantom, and the results indicate that our method is more efficient than the existing CPU implementation. The high computation efficiency achieved in our algorithm makes it possible for clinicians to obtain real-time 3D images. PMID:26405857
Efficient and Accurate Explicit Integration Algorithms with Application to Viscoplastic Models
NASA Technical Reports Server (NTRS)
Arya, Vinod K.
1994-01-01
Several explicit integration algorithms with self-adative time integration strategies are developed and investigated for efficiency and accuracy. These algorithms involve the Runge-Kutta second order, the lower Runge-Kutta method of orders one and two, and the exponential integration method. The algorithms are applied to viscoplastic models put forth by Freed and Verrilli and Bodner and Partom for thermal/mechanical loadings (including tensile, relaxation, and cyclic loadings). The large amount of computations performed showed that, for comparable accuracy, the efficiency of an integration algorithm depends significantly on the type of application (loading). However, in general, for the aforementioned loadings and viscoplastic models, the exponential integration algorithm with the proposed self-adaptive time integration strategy worked more (or comparably) efficiently and accurately than the other integration algorithms. Using this strategy for integrating viscoplastic models may lead to considerable savings in computer time (better efficiency) without adversely affecting the accuracy of the results. This conclusion should encourage the utilization of viscoplastic models in the stress analysis and design of structural components.
NASA Technical Reports Server (NTRS)
Cao, Fang; Fichot, Cedric G.; Hooker, Stanford B.; Miller, William L.
2014-01-01
Photochemical processes driven by high-energy ultraviolet radiation (UVR) in inshore, estuarine, and coastal waters play an important role in global bio geochemical cycles and biological systems. A key to modeling photochemical processes in these optically complex waters is an accurate description of the vertical distribution of UVR in the water column which can be obtained using the diffuse attenuation coefficients of down welling irradiance (Kd()). The Sea UV Sea UVc algorithms (Fichot et al., 2008) can accurately retrieve Kd ( 320, 340, 380,412, 443 and 490 nm) in oceanic and coastal waters using multispectral remote sensing reflectances (Rrs(), Sea WiFS bands). However, SeaUVSeaUVc algorithms are currently not optimized for use in optically complex, inshore waters, where they tend to severely underestimate Kd(). Here, a new training data set of optical properties collected in optically complex, inshore waters was used to re-parameterize the published SeaUVSeaUVc algorithms, resulting in improved Kd() retrievals for turbid, estuarine waters. Although the updated SeaUVSeaUVc algorithms perform best in optically complex waters, the published SeaUVSeaUVc models still perform well in most coastal and oceanic waters. Therefore, we propose a composite set of SeaUVSeaUVc algorithms, optimized for Kd() retrieval in almost all marine systems, ranging from oceanic to inshore waters. The composite algorithm set can retrieve Kd from ocean color with good accuracy across this wide range of water types (e.g., within 13 mean relative error for Kd(340)). A validation step using three independent, in situ data sets indicates that the composite SeaUVSeaUVc can generate accurate Kd values from 320 490 nm using satellite imagery on a global scale. Taking advantage of the inherent benefits of our statistical methods, we pooled the validation data with the training set, obtaining an optimized composite model for estimating Kd() in UV wavelengths for almost all marine waters. This
A new algorithm for generating highly accurate benchmark solutions to transport test problems
Azmy, Y.Y.
1997-06-01
We present a new algorithm for solving the neutron transport equation in its discrete-variable form. The new algorithm is based on computing the full matrix relating the scalar flux spatial moments in all cells to the fixed neutron source spatial moments, foregoing the need to compute the angular flux spatial moments, and thereby eliminating the need for sweeping the spatial mesh in each discrete-angular direction. The matrix equation is solved exactly in test cases, producing a solution vector that is free from iteration convergence error, and subject only to truncation and roundoff errors. Our algorithm is designed to provide method developers with a quick and simple solution scheme to test their new methods on difficult test problems without the need to develop sophisticated solution techniques, e.g. acceleration, before establishing the worthiness of their innovation. We demonstrate the utility of the new algorithm by applying it to the Arbitrarily High Order Transport Nodal (AHOT-N) method, and using it to solve two of Burre`s Suite of Test Problems (BSTP). Our results provide highly accurate benchmark solutions, that can be distributed electronically and used to verify the pointwise accuracy of other solution methods and algorithms.
PolyPole-1: An accurate numerical algorithm for intra-granular fission gas release
NASA Astrophysics Data System (ADS)
Pizzocri, D.; Rabiti, C.; Luzzi, L.; Barani, T.; Van Uffelen, P.; Pastore, G.
2016-09-01
The transport of fission gas from within the fuel grains to the grain boundaries (intra-granular fission gas release) is a fundamental controlling mechanism of fission gas release and gaseous swelling in nuclear fuel. Hence, accurate numerical solution of the corresponding mathematical problem needs to be included in fission gas behaviour models used in fuel performance codes. Under the assumption of equilibrium between trapping and resolution, the process can be described mathematically by a single diffusion equation for the gas atom concentration in a grain. In this paper, we propose a new numerical algorithm (PolyPole-1) to efficiently solve the fission gas diffusion equation in time-varying conditions. The PolyPole-1 algorithm is based on the analytic modal solution of the diffusion equation for constant conditions, combined with polynomial corrective terms that embody the information on the deviation from constant conditions. The new algorithm is verified by comparing the results to a finite difference solution over a large number of randomly generated operation histories. Furthermore, comparison to state-of-the-art algorithms used in fuel performance codes demonstrates that the accuracy of PolyPole-1 is superior to other algorithms, with similar computational effort. Finally, the concept of PolyPole-1 may be extended to the solution of the general problem of intra-granular fission gas diffusion during non-equilibrium trapping and resolution, which will be the subject of future work.
NASA Astrophysics Data System (ADS)
Diwakar, S. V.; Das, Sarit K.; Sundararajan, T.
2009-12-01
A new Quadratic Spline based Interface (QUASI) reconstruction algorithm is presented which provides an accurate and continuous representation of the interface in a multiphase domain and facilitates the direct estimation of local interfacial curvature. The fluid interface in each of the mixed cells is represented by piecewise parabolic curves and an initial discontinuous PLIC approximation of the interface is progressively converted into a smooth quadratic spline made of these parabolic curves. The conversion is achieved by a sequence of predictor-corrector operations enforcing function ( C0) and derivative ( C1) continuity at the cell boundaries using simple analytical expressions for the continuity requirements. The efficacy and accuracy of the current algorithm has been demonstrated using standard test cases involving reconstruction of known static interface shapes and dynamically evolving interfaces in prescribed flow situations. These benchmark studies illustrate that the present algorithm performs excellently as compared to the other interface reconstruction methods available in literature. Quadratic rate of error reduction with respect to grid size has been observed in all the cases with curved interface shapes; only in situations where the interface geometry is primarily flat, the rate of convergence becomes linear with the mesh size. The flow algorithm implemented in the current work is designed to accurately balance the pressure gradients with the surface tension force at any location. As a consequence, it is able to minimize spurious flow currents arising from imperfect normal stress balance at the interface. This has been demonstrated through the standard test problem of an inviscid droplet placed in a quiescent medium. Finally, the direct curvature estimation ability of the current algorithm is illustrated through the coupled multiphase flow problem of a deformable air bubble rising through a column of water.
Digitalized accurate modeling of SPCB with multi-spiral surface based on CPC algorithm
NASA Astrophysics Data System (ADS)
Huang, Yanhua; Gu, Lizhi
2015-09-01
The main methods of the existing multi-spiral surface geometry modeling include spatial analytic geometry algorithms, graphical method, interpolation and approximation algorithms. However, there are some shortcomings in these modeling methods, such as large amount of calculation, complex process, visible errors, and so on. The above methods have, to some extent, restricted the design and manufacture of the premium and high-precision products with spiral surface considerably. This paper introduces the concepts of the spatially parallel coupling with multi-spiral surface and spatially parallel coupling body. The typical geometry and topological features of each spiral surface forming the multi-spiral surface body are determined, by using the extraction principle of datum point cluster, the algorithm of coupling point cluster by removing singular point, and the "spatially parallel coupling" principle based on the non-uniform B-spline for each spiral surface. The orientation and quantitative relationships of datum point cluster and coupling point cluster in Euclidean space are determined accurately and in digital description and expression, coupling coalescence of the surfaces with multi-coupling point clusters under the Pro/E environment. The digitally accurate modeling of spatially parallel coupling body with multi-spiral surface is realized. The smooth and fairing processing is done to the three-blade end-milling cutter's end section area by applying the principle of spatially parallel coupling with multi-spiral surface, and the alternative entity model is processed in the four axis machining center after the end mill is disposed. And the algorithm is verified and then applied effectively to the transition area among the multi-spiral surface. The proposed model and algorithms may be used in design and manufacture of the multi-spiral surface body products, as well as in solving essentially the problems of considerable modeling errors in computer graphics and
Combinatorial Algorithms to Enable Computational Science and Engineering: The CSCAPES Institute
Pothen, Alex
2015-01-16
This final progress report summarizes the work accomplished at the Combinatorial Scientific Computing and Petascale Simulations Institute. We developed Zoltan, a parallel mesh partitioning library that made use of accurate hyeprgraph models to provide load balancing in mesh-based computations. We developed several graph coloring algorithms for computing Jacobian and Hessian matrices and organized them into a software package called ColPack. We developed parallel algorithms for graph coloring and graph matching problems, and also designed multi-scale graph algorithms. Three PhD students graduated, six more are continuing their PhD studies, and four postdoctoral scholars were advised. Six of these students and Fellows have joined DOE Labs (Sandia, Berkeley, as staff scientists or as postdoctoral scientists. We also organized the SIAM Workshop on Combinatorial Scientific Computing (CSC) in 2007, 2009, and 2011 to continue to foster the CSC community.
Joldes, Grand Roman; Wittek, Adam; Miller, Karol
2008-01-01
Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training. This requires algorithms that are fast, accurate and can handle material nonlinearities and large deformations. A set of such algorithms is presented in this paper, starting with the finite element formulation and the integration scheme used and addressing common problems such as hourglass control and locking. The computation examples presented prove that by using these algorithms, real time computations become possible without sacrificing the accuracy of the results. For a brain model having more than 7000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1000 Hz using a standard dual core PC. Similarly, we conducted simulation of brain shift using a model with more than 50 000 degrees of freedom in less than a minute. The speed benefits of our models results from combining the Total Lagrangian formulation with explicit time integration and low order finite elements. PMID:19152791
An accurate 3D inspection system using heterodyne multiple frequency phase-shifting algorithm
NASA Astrophysics Data System (ADS)
Xiao, Zhenzhong; Chee, Oichoo; Asundi, Anand
This paper presents an accurate 3D inspection system for industrial applications, which uses digital fringe projection technology. The system consists of two CCD cameras and a DLP projector. The mathematical model of the 3D inspection system with 10 distortion parameters for each camera is proposed. A heterodyne multiple frequency phase-shifting algorithm is employed for overcoming the unwrapping problem of phase functions and for a reliable unwrapping procedure. The redundant phase information is used to increase the accuracy of the 3D reconstruction. To demonstrate the effectiveness of our system, a standard sphere was used for testing. The verification test for the 3D inspection systems are based on the VDI standard 2634. The result shows the proposed system can be used for industrial quality inspection with high measurement precision.
A time-accurate algorithm for chemical non-equilibrium viscous flows at all speeds
NASA Technical Reports Server (NTRS)
Shuen, J.-S.; Chen, K.-H.; Choi, Y.
1992-01-01
A time-accurate, coupled solution procedure is described for the chemical nonequilibrium Navier-Stokes equations over a wide range of Mach numbers. This method employs the strong conservation form of the governing equations, but uses primitive variables as unknowns. Real gas properties and equilibrium chemistry are considered. Numerical tests include steady convergent-divergent nozzle flows with air dissociation/recombination chemistry, dump combustor flows with n-pentane-air chemistry, nonreacting flow in a model double annular combustor, and nonreacting unsteady driven cavity flows. Numerical results for both the steady and unsteady flows demonstrate the efficiency and robustness of the present algorithm for Mach numbers ranging from the incompressible limit to supersonic speeds.
A physics-enabled flow restoration algorithm for sparse PIV and PTV measurements
NASA Astrophysics Data System (ADS)
Vlasenko, Andrey; Steele, Edward C. C.; Nimmo-Smith, W. Alex M.
2015-06-01
The gaps and noise present in particle image velocimetry (PIV) and particle tracking velocimetry (PTV) measurements affect the accuracy of the data collected. Existing algorithms developed for the restoration of such data are only applicable to experimental measurements collected under well-prepared laboratory conditions (i.e. where the pattern of the velocity flow field is known), and the distribution, size and type of gaps and noise may be controlled by the laboratory set-up. However, in many cases, such as PIV and PTV measurements of arbitrarily turbid coastal waters, the arrangement of such conditions is not possible. When the size of gaps or the level of noise in these experimental measurements become too large, their successful restoration with existing algorithms becomes questionable. Here, we outline a new physics-enabled flow restoration algorithm (PEFRA), specially designed for the restoration of such velocity data. Implemented as a ‘black box’ algorithm, where no user-background in fluid dynamics is necessary, the physical structure of the flow in gappy or noisy data is able to be restored in accordance with its hydrodynamical basis. The use of this is not dependent on types of flow, types of gaps or noise in measurements. The algorithm will operate on any data time-series containing a sequence of velocity flow fields recorded by PIV or PTV. Tests with numerical flow fields established that this method is able to successfully restore corrupted PIV and PTV measurements with different levels of sparsity and noise. This assessment of the algorithm performance is extended with an example application to in situ submersible 3D-PTV measurements collected in the bottom boundary layer of the coastal ocean, where the naturally-occurring plankton and suspended sediments used as tracers causes an increase in the noise level that, without such denoising, will contaminate the measurements.
Chen, Ying-ping; Chen, Chao-Hong
2010-01-01
An adaptive discretization method, called split-on-demand (SoD), enables estimation of distribution algorithms (EDAs) for discrete variables to solve continuous optimization problems. SoD randomly splits a continuous interval if the number of search points within the interval exceeds a threshold, which is decreased at every iteration. After the split operation, the nonempty intervals are assigned integer codes, and the search points are discretized accordingly. As an example of using SoD with EDAs, the integration of SoD and the extended compact genetic algorithm (ECGA) is presented and numerically examined. In this integration, we adopt a local search mechanism as an optional component of our back end optimization engine. As a result, the proposed framework can be considered as a memetic algorithm, and SoD can potentially be applied to other memetic algorithms. The numerical experiments consist of two parts: (1) a set of benchmark functions on which ECGA with SoD and ECGA with two well-known discretization methods: the fixed-height histogram (FHH) and the fixed-width histogram (FWH) are compared; (2) a real-world application, the economic dispatch problem, on which ECGA with SoD is compared to other methods. The experimental results indicate that SoD is a better discretization method to work with ECGA. Moreover, ECGA with SoD works quite well on the economic dispatch problem and delivers solutions better than the best known results obtained by other methods in existence. PMID:20210600
A high order accurate finite element algorithm for high Reynolds number flow prediction
NASA Technical Reports Server (NTRS)
Baker, A. J.
1978-01-01
A Galerkin-weighted residuals formulation is employed to establish an implicit finite element solution algorithm for generally nonlinear initial-boundary value problems. Solution accuracy, and convergence rate with discretization refinement, are quantized in several error norms, by a systematic study of numerical solutions to several nonlinear parabolic and a hyperbolic partial differential equation characteristic of the equations governing fluid flows. Solutions are generated using selective linear, quadratic and cubic basis functions. Richardson extrapolation is employed to generate a higher-order accurate solution to facilitate isolation of truncation error in all norms. Extension of the mathematical theory underlying accuracy and convergence concepts for linear elliptic equations is predicted for equations characteristic of laminar and turbulent fluid flows at nonmodest Reynolds number. The nondiagonal initial-value matrix structure introduced by the finite element theory is determined intrinsic to improved solution accuracy and convergence. A factored Jacobian iteration algorithm is derived and evaluated to yield a consequential reduction in both computer storage and execution CPU requirements while retaining solution accuracy.
Rawool-Sullivan, Mohini; Bounds, John Alan; Brumby, Steven P.; Prasad, Lakshman; Sullivan, John P.
2012-04-30
This is the final report of the project titled, 'Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes,' PMIS project number LA10-HUMANID-PD03. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). It summarizes work performed over the FY10 time period. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). Human analysts begin analyzing a spectrum based on features in the spectrum - lines and shapes that are present in a given spectrum. The proposed work was to carry out a feasibility study that will pick out all gamma ray peaks and other features such as Compton edges, bremsstrahlung, presence/absence of shielding and presence of neutrons and escape peaks. Ultimately success of this feasibility study will allow us to collectively explain identified features and form a realistic scenario that produced a given spectrum in the future. We wanted to develop and demonstrate machine learning algorithms that will qualitatively enhance the automated identification capabilities of portable radiological sensors that are currently being used in the field.
MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T
2014-01-01
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324
Towards fast and accurate algorithms for processing fuzzy data: interval computations revisited
NASA Astrophysics Data System (ADS)
Xiang, Gang; Kreinovich, Vladik
2013-02-01
In many practical applications, we need to process data, e.g. to predict the future values of different quantities based on their current values. Often, the only information that we have about the current values comes from experts, and is described in informal ('fuzzy') terms like 'small'. To process such data, it is natural to use fuzzy techniques, techniques specifically designed by Lotfi Zadeh to handle such informal information. In this survey, we start by revisiting the motivation behind Zadeh's formulae for processing fuzzy data, and explain how the algorithmic problem of processing fuzzy data can be described in terms of interval computations (α-cuts). Many fuzzy practitioners claim 'I tried interval computations, they did not work' - meaning that they got estimates which are much wider than the desired α-cuts. We show that such statements are usually based on a (widely spread) misunderstanding - that interval computations simply mean replacing each arithmetic operation with the corresponding operation with intervals. We show that while such straightforward interval techniques indeed often lead to over-wide estimates, the current advanced interval computations techniques result in estimates which are much more accurate. We overview such advanced interval computations techniques, and show that by using them, we can efficiently and accurately process fuzzy data. We wrote this survey with three audiences in mind. First, we want fuzzy researchers and practitioners to understand the current advanced interval computations techniques and to use them to come up with faster and more accurate algorithms for processing fuzzy data. For this 'fuzzy' audience, we explain these current techniques in detail. Second, we also want interval researchers to better understand this important application area for their techniques. For this 'interval' audience, we want to explain where fuzzy techniques come from, what are possible variants of these techniques, and what are the
Hu, Ranliang; Daftari Besheli, Laleh; Young, Joseph; Wu, Markus; Pomerantz, Stuart; Lev, Michael H; Gupta, Rajiv
2016-07-01
Purpose To evaluate the ability of dual-energy (DE) computed tomography (CT) to differentiate calcification from acute hemorrhage in the emergency department setting. Materials and Methods In this institutional review board-approved study, all unenhanced DE head CT examinations that were performed in the emergency department in November and December 2014 were retrospectively reviewed. Simulated 120-kVp single-energy CT images were derived from the DE CT acquisition via postprocessing. Patients with at least one focus of intraparenchymal hyperattenuation on single-energy CT images were included, and DE material decomposition postprocessing was performed. Each focal hyperattenuation was analyzed on the basis of the virtual noncalcium and calcium overlay images and classified as calcification or hemorrhage. Sensitivity, specificity, and accuracy were calculated for single-energy and DE CT by using a common reference standard established by relevant prior and follow-up imaging and clinical information. Results Sixty-two cases with 68 distinct intraparenchymal hyperattenuating lesions in which the reference standards were available were included in the study, of which 41 (60%) were confirmed as calcification and 27 (40%) were confirmed as hemorrhage. Sensitivity, specificity, and accuracy of DE CT for the detection of hemorrhage were 96% (95% confidence interval [CI]: 81%, 100%), 100% (95% CI: 91%, 100%), and 99% (95% CI: 92%, 100%) and those of single-energy CT were 74% (95% CI: 54%, 89%), 95% (95% CI: 83%, 99%), and 87% (95% CI: 76%, 94%), respectively. Six of 68 (9%) lesions were classified as indeterminate and three (4%) were misinterpreted with single-energy CT alone and were correctly classified with DE CT. Conclusion DE CT by using material decomposition enables accurate differentiation between calcification and hemorrhage in patients presenting for emergency head imaging and can be especially useful in problem-solving complex cases that are difficult to
Adaptive switching detection algorithm for iterative-MIMO systems to enable power savings
NASA Astrophysics Data System (ADS)
Tadza, N.; Laurenson, D.; Thompson, J. S.
2014-11-01
This paper attempts to tackle one of the challenges faced in soft input soft output Multiple Input Multiple Output (MIMO) detection systems, which is to achieve optimal error rate performance with minimal power consumption. This is realized by proposing a new algorithm design that comprises multiple thresholds within the detector that, in real time, specify the receiver behavior according to the current channel in both slow and fast fading conditions, giving it adaptivity. This adaptivity enables energy savings within the system since the receiver chooses whether to accept or to reject the transmission, according to the success rate of detecting thresholds. The thresholds are calculated using the mutual information of the instantaneous channel conditions between the transmitting and receiving antennas of iterative-MIMO systems. In addition, the power saving technique, Dynamic Voltage and Frequency Scaling, helps to reduce the circuit power demands of the adaptive algorithm. This adaptivity has the potential to save up to 30% of the total energy when it is implemented on Xilinx®Virtex-5 simulation hardware. Results indicate the benefits of having this "intelligence" in the adaptive algorithm due to the promising performance-complexity tradeoff parameters in both software and hardware codesign simulation.
Chen, Weizhong; Liu, Yi; Zhu, Shanshan; Green, Christopher D; Wei, Gang; Han, Jing-Dong Jackie
2014-01-01
Accurate determination of genome-wide nucleosome positioning can provide important insights into global gene regulation. Here, we describe the development of an improved nucleosome-positioning algorithm-iNPS-which achieves significantly better performance than the widely used NPS package. By determining nucleosome boundaries more precisely and merging or separating shoulder peaks based on local MNase-seq signals, iNPS can unambiguously detect 60% more nucleosomes. The detected nucleosomes display better nucleosome 'widths' and neighbouring centre-centre distance distributions, giving rise to sharper patterns and better phasing of average nucleosome profiles and higher consistency between independent data subsets. In addition to its unique advantage in classifying nucleosomes by shape to reveal their different biological properties, iNPS also achieves higher significance and lower false positive rates than previously published methods. The application of iNPS to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process. PMID:25233085
NASA Astrophysics Data System (ADS)
Peng, Qin; Jinbo, Li; Jian, Kang; Xiaoyong, Li; Jianjun, Zhou
2014-09-01
A low noise phase locked loop (PLL) frequency synthesizer implemented in 65 nm CMOS technology is introduced. A VCO noise reduction method suited for short channel design is proposed to minimize PLL output phase noise. A self-calibrated voltage controlled oscillator is proposed in cooperation with the automatic frequency calibration circuit, whose accurate binary search algorithm helps reduce the VCO tuning curve coverage, which reduces the VCO noise contribution at PLL output phase noise. A low noise, charge pump is also introduced to extend the tuning voltage range of the proposed VCO, which further reduces its phase noise contribution. The frequency synthesizer generates 9.75-11.5 GHz high frequency wide band local oscillator (LO) carriers. Tested 11.5 GHz LO bears a phase noise of-104 dBc/Hz at 1 MHz frequency offset. The total power dissipation of the proposed frequency synthesizer is 48 mW. The area of the proposed frequency synthesizer is 0.3 mm2, including bias circuits and buffers.
Xiao, Heng; Chen, Yuqi; Yuan, Erfeng; Li, Wei; Jiang, Zhuoran; Wei, Lai; Su, Haomiao; Zeng, Weiwu; Gan, Yunjiu; Wang, Zijing; Yuan, Bifeng; Qin, Shanshan; Leng, Xiaohua; Zhou, Xin; Liu, Songmei; Zhou, Xiang
2016-09-14
Early cancer diagnosis is of great significance to relative cancer prevention and clinical therapy, and it is crucial to efficiently recognize cancerous tumor sites at the molecular level. Herein, we proposed a versatile and efficient strategy based on aptamer recognition and photoactivation imaging for cancer diagnosis. This is the first time that a visible light-controlled photoactivatable aptamer-based platform has been applied for cancer diagnosis. The photoactivatable aptamer-based strategy can accurately detect nucleolin-overexpressed tumor cells and can be used for highly selective cancer cell screening and tissue imaging. This strategy is available for both formalin-fixed paraffin-embedded tissue specimens and frozen sections. Moreover, the photoactivation techniques showed great progress in more accurate and persistent imaging to the use of traditional fluorophores. Significantly, the application of this strategy can produce the same accurate results in tissue specimen analysis as with classical hematoxylin-eosin staining and immunohistochemical technology. PMID:27550088
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.
Zheng, Mo; Li, Xiaoxia; Guo, Li
2013-04-01
Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. PMID:23454611
Fast and accurate image recognition algorithms for fresh produce food safety sensing
NASA Astrophysics Data System (ADS)
Yang, Chun-Chieh; Kim, Moon S.; Chao, Kuanglin; Kang, Sukwon; Lefcourt, Alan M.
2011-06-01
This research developed and evaluated the multispectral algorithms derived from hyperspectral line-scan fluorescence imaging under violet LED excitation for detection of fecal contamination on Golden Delicious apples. The algorithms utilized the fluorescence intensities at four wavebands, 680 nm, 684 nm, 720 nm, and 780 nm, for computation of simple functions for effective detection of contamination spots created on the apple surfaces using four concentrations of aqueous fecal dilutions. The algorithms detected more than 99% of the fecal spots. The effective detection of feces showed that a simple multispectral fluorescence imaging algorithm based on violet LED excitation may be appropriate to detect fecal contamination on fast-speed apple processing lines.
Kapp, Eugene; Schutz, Frederick; Connolly, Lisa M.; Chakel, John A.; Meza, Jose E.; Miller, Christine A.; Fenyo, David; Eng, Jimmy K.; Adkins, Joshua N.; Omenn, Gilbert; Simpson, Richard
2005-08-01
MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X-Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, Peptide Prophet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X-Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of ''consensus scoring'', i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.
Xie, Minzhu; Wang, Jianxin; Chen, Xin
2015-01-01
Phased haplotype information is crucial in our complete understanding of differences between individuals at the genetic level. Given a collection of DNA fragments sequenced from a homologous pair of chromosomes, the problem of single individual haplotyping (SIH) aims to reconstruct a pair of haplotypes using a computer algorithm. In this paper, we encode the information of aligned DNA fragments into a two-locus linkage graph and approach the SIH problem by vertex labeling of the graph. In order to find a vertex labeling with the minimum sum of weights of incompatible edges, we develop a fast and accurate heuristic algorithm. It starts with detecting error-tolerant components by an adapted breadth-first search. A proper labeling of vertices is then identified for each component, with which sequencing errors are further corrected and edge weights are adjusted accordingly. After contracting each error-tolerant component into a single vertex, the above procedure is iterated on the resulting condensed linkage graph until error-tolerant components are no longer detected. The algorithm finally outputs a haplotype pair based on the vertex labeling. Extensive experiments on simulated and real data show that our algorithm is more accurate and faster than five existing algorithms for single individual haplotyping. PMID:26671798
Spectrally-accurate algorithm for the analysis of flows in two-dimensional vibrating channels
NASA Astrophysics Data System (ADS)
Zandi, S.; Mohammadi, A.; Floryan, J. M.
2015-11-01
A spectral algorithm based on the immersed boundary conditions (IBC) concept has been developed for the analysis of flows in channels bounded by vibrating walls. The vibrations take the form of travelling waves of arbitrary profile. The algorithm uses a fixed computational domain with the flow domain immersed in its interior. Boundary conditions enter the algorithm in the form of constraints. The spatial discretization uses a Fourier expansion in the stream-wise direction and a Chebyshev expansion in the wall-normal direction. Use of the Galileo transformation converts the unsteady problem into a steady one. An efficient solver which takes advantage of the structure of the coefficient matrix has been used. It is demonstrated that the method can be extended to more extreme geometries using the overdetermined formulation. Various tests confirm the spectral accuracy of the algorithm.
A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.
Liu, Jian; Li, Dezhang; Liu, Xinzijian
2016-07-14
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used. PMID:27421393
A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat
NASA Astrophysics Data System (ADS)
Liu, Jian; Li, Dezhang; Liu, Xinzijian
2016-07-01
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.
Sharma, Ashok; Podolsky, Robert; Zhao, Jieping; McIndoe, Richard A.
2009-01-01
Motivation: As the number of publically available microarray experiments increases, the ability to analyze extremely large datasets across multiple experiments becomes critical. There is a requirement to develop algorithms which are fast and can cluster extremely large datasets without affecting the cluster quality. Clustering is an unsupervised exploratory technique applied to microarray data to find similar data structures or expression patterns. Because of the high input/output costs involved and large distance matrices calculated, most of the algomerative clustering algorithms fail on large datasets (30 000 + genes/200 + arrays). In this article, we propose a new two-stage algorithm which partitions the high-dimensional space associated with microarray data using hyperplanes. The first stage is based on the Balanced Iterative Reducing and Clustering using Hierarchies algorithm with the second stage being a conventional k-means clustering technique. This algorithm has been implemented in a software tool (HPCluster) designed to cluster gene expression data. We compared the clustering results using the two-stage hyperplane algorithm with the conventional k-means algorithm from other available programs. Because, the first stage traverses the data in a single scan, the performance and speed increases substantially. The data reduction accomplished in the first stage of the algorithm reduces the memory requirements allowing us to cluster 44 460 genes without failure and significantly decreases the time to complete when compared with popular k-means programs. The software was written in C# (.NET 1.1). Availability: The program is freely available and can be downloaded from http://www.amdcc.org/bioinformatics/bioinformatics.aspx. Contact: rmcindoe@mail.mcg.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19261720
NASA Astrophysics Data System (ADS)
Oh, Jieun; Cho, Hyosung; Je, Uikyu; Lee, Minsik; Kim, Hyojeong; Hong, Daeki; Park, Yeonok; Lee, Seonhwa; Cho, Heemoon; Choi, Sungil; Koo, Yangseo
2013-03-01
In practical applications of three-dimensional (3D) tomographic imaging, there are often challenges for image reconstruction from insufficient data. In computed tomography (CT); for example, image reconstruction from few views would enable fast scanning with reduced doses to the patient. In this study, we investigated and implemented an efficient reconstruction method based on a compressed-sensing (CS) algorithm, which exploits the sparseness of the gradient image with substantially high accuracy, for accurate, low-dose dental cone-beam CT (CBCT) reconstruction. We applied the algorithm to a commercially-available dental CBCT system (Expert7™, Vatech Co., Korea) and performed experimental works to demonstrate the algorithm for image reconstruction in insufficient sampling problems. We successfully reconstructed CBCT images from several undersampled data and evaluated the reconstruction quality in terms of the universal-quality index (UQI). Experimental demonstrations of the CS-based reconstruction algorithm appear to show that it can be applied to current dental CBCT systems for reducing imaging doses and improving the image quality.
NASA Astrophysics Data System (ADS)
Wang, Wei; Huang, Peter
2016-02-01
Evanescent wave nano-velocimetry offers a unique three-dimensional measurement capability that allows for inferring tracer position distribution through the imaged particle intensities. Our previous study suggested that tracer polydispersity and failure to account for a near-wall tracer depletion layer would lead to compromised measurement accuracy. In this work, we report on a hybrid algorithm that converts the measured tracer intensities as a whole into their overall position distribution. The algorithm achieves a superior accuracy by using tracer size variation as a statistical analysis parameter.
An accurate dynamical electron diffraction algorithm for reflection high-energy electron diffraction
NASA Astrophysics Data System (ADS)
Huang, J.; Cai, C. Y.; Lv, C. L.; Zhou, G. W.; Wang, Y. G.
2015-12-01
The conventional multislice method (CMS) method, one of the most popular dynamical electron diffraction calculation procedures in transmission electron microscopy, was introduced to calculate reflection high-energy electron diffraction (RHEED) as it is well adapted to deal with the deviations from the periodicity in the direction parallel to the surface. However, in the present work, we show that the CMS method is no longer sufficiently accurate for simulating RHEED with the accelerating voltage 3-100 kV because of the high-energy approximation. An accurate multislice (AMS) method can be an alternative for more accurate RHEED calculations with reasonable computing time. A detailed comparison of the numerical calculation of the AMS method and the CMS method is carried out with respect to different accelerating voltages, surface structure models, Debye-Waller factors and glancing angles.
French, Dustin D; Gill, Manjot; Mitchell, Christopher; Jackson, Kathryn; Kho, Abel; Bryar, Paul J
2016-01-01
Background Visual acuity is the primary measure used in ophthalmology to determine how well a patient can see. Visual acuity for a single eye may be recorded in multiple ways for a single patient visit (eg, Snellen vs. Jäger units vs. font print size), and be recorded for either distance or near vision. Capturing the best documented visual acuity (BDVA) of each eye in an individual patient visit is an important step for making electronic ophthalmology clinical notes useful in research. Objective Currently, there is limited methodology for capturing BDVA in an efficient and accurate manner from electronic health record (EHR) notes. We developed an algorithm to detect BDVA for right and left eyes from defined fields within electronic ophthalmology clinical notes. Methods We designed an algorithm to detect the BDVA from defined fields within 295,218 ophthalmology clinical notes with visual acuity data present. About 5668 unique responses were identified and an algorithm was developed to map all of the unique responses to a structured list of Snellen visual acuities. Results Visual acuity was captured from a total of 295,218 ophthalmology clinical notes during the study dates. The algorithm identified all visual acuities in the defined visual acuity section for each eye and returned a single BDVA for each eye. A clinician chart review of 100 random patient notes showed a 99% accuracy detecting BDVA from these records and 1% observed error. Conclusions Our algorithm successfully captures best documented Snellen distance visual acuity from ophthalmology clinical notes and transforms a variety of inputs into a structured Snellen equivalent list. Our work, to the best of our knowledge, represents the first attempt at capturing visual acuity accurately from large numbers of electronic ophthalmology notes. Use of this algorithm can benefit research groups interested in assessing visual acuity for patient centered outcome. All codes used for this study are currently
Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm
Manzer, Samuel; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Martin
2015-01-01
Construction of the exact exchange matrix, K, is typically the rate-determining step in hybrid density functional theory, and therefore, new approaches with increased efficiency are highly desirable. We present a framework with potential for greatly improved efficiency by computing a compressed exchange matrix that yields the exact exchange energy, gradient, and direct inversion of the iterative subspace (DIIS) error vector. The compressed exchange matrix is constructed with one index in the compact molecular orbital basis and the other index in the full atomic orbital basis. To illustrate the advantages, we present a practical algorithm that uses this framework in conjunction with the resolution of the identity (RI) approximation. We demonstrate that convergence using this method, referred to hereafter as occupied orbital RI-K (occ-RI-K), in combination with the DIIS algorithm is well-behaved, that the accuracy of computed energetics is excellent (identical to conventional RI-K), and that significant speedups can be obtained over existing integral-direct and RI-K methods. For a 4400 basis function C68H22 hydrogen-terminated graphene fragment, our algorithm yields a 14 × speedup over the conventional algorithm and a speedup of 3.3 × over RI-K. PMID:26178096
Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm
Manzer, Samuel; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Martin
2015-07-14
Construction of the exact exchange matrix, K, is typically the rate-determining step in hybrid density functional theory, and therefore, new approaches with increased efficiency are highly desirable. We present a framework with potential for greatly improved efficiency by computing a compressed exchange matrix that yields the exact exchange energy, gradient, and direct inversion of the iterative subspace (DIIS) error vector. The compressed exchange matrix is constructed with one index in the compact molecular orbital basis and the other index in the full atomic orbital basis. To illustrate the advantages, we present a practical algorithm that uses this framework in conjunction with the resolution of the identity (RI) approximation. We demonstrate that convergence using this method, referred to hereafter as occupied orbital RI-K (occ-RI-K), in combination with the DIIS algorithm is well-behaved, that the accuracy of computed energetics is excellent (identical to conventional RI-K), and that significant speedups can be obtained over existing integral-direct and RI-K methods. For a 4400 basis function C{sub 68}H{sub 22} hydrogen-terminated graphene fragment, our algorithm yields a 14 × speedup over the conventional algorithm and a speedup of 3.3 × over RI-K.
Novel Algorithms Enabling Rapid, Real-Time Earthquake Monitoring and Tsunami Early Warning Worldwide
NASA Astrophysics Data System (ADS)
Lomax, A.; Michelini, A.
2012-12-01
We have introduced recently new methods to determine rapidly the tsunami potential and magnitude of large earthquakes (e.g., Lomax and Michelini, 2009ab, 2011, 2012). To validate these methods we have implemented them along with other new algorithms within the Early-est earthquake monitor at INGV-Rome (http://early-est.rm.ingv.it, http://early-est.alomax.net). Early-est is a lightweight software package for real-time earthquake monitoring (including phase picking, phase association and event detection, location, magnitude determination, first-motion mechanism determination, ...), and for tsunami early warning based on discriminants for earthquake tsunami potential. In a simulation using archived broadband seismograms for the devastating M9, 2011 Tohoku earthquake and tsunami, Early-est determines: the epicenter within 3 min after the event origin time, discriminants showing very high tsunami potential within 5-7 min, and magnitude Mwpd(RT) 9.0-9.2 and a correct shallow-thrusting mechanism within 8 min. Real-time monitoring with Early-est givess similar results for most large earthquakes using currently available, real-time seismogram data. Here we summarize some of the key algorithms within Early-est that enable rapid, real-time earthquake monitoring and tsunami early warning worldwide: >>> FilterPicker - a general purpose, broad-band, phase detector and picker (http://alomax.net/FilterPicker); >>> Robust, simultaneous association and location using a probabilistic, global-search; >>> Period-duration discriminants TdT0 and TdT50Ex for tsunami potential available within 5 min; >>> Mwpd(RT) magnitude for very large earthquakes available within 10 min; >>> Waveform P polarities determined on broad-band displacement traces, focal mechanisms obtained with the HASH program (Hardebeck and Shearer, 2002); >>> SeisGramWeb - a portable-device ready seismogram viewer using web-services in a browser (http://alomax.net/webtools/sgweb/info.html). References (see also: http
A hybrid reconstruction algorithm for fast and accurate 4D cone-beam CT imaginga)
Yan, Hao; Zhen, Xin; Folkerts, Michael; Li, Yongbao; Pan, Tinsu; Cervino, Laura; Jiang, Steve B.; Jia, Xun
2014-01-01
Purpose: 4D cone beam CT (4D-CBCT) has been utilized in radiation therapy to provide 4D image guidance in lung and upper abdomen area. However, clinical application of 4D-CBCT is currently limited due to the long scan time and low image quality. The purpose of this paper is to develop a new 4D-CBCT reconstruction method that restores volumetric images based on the 1-min scan data acquired with a standard 3D-CBCT protocol. Methods: The model optimizes a deformation vector field that deforms a patient-specific planning CT (p-CT), so that the calculated 4D-CBCT projections match measurements. A forward-backward splitting (FBS) method is invented to solve the optimization problem. It splits the original problem into two well-studied subproblems, i.e., image reconstruction and deformable image registration. By iteratively solving the two subproblems, FBS gradually yields correct deformation information, while maintaining high image quality. The whole workflow is implemented on a graphic-processing-unit to improve efficiency. Comprehensive evaluations have been conducted on a moving phantom and three real patient cases regarding the accuracy and quality of the reconstructed images, as well as the algorithm robustness and efficiency. Results: The proposed algorithm reconstructs 4D-CBCT images from highly under-sampled projection data acquired with 1-min scans. Regarding the anatomical structure location accuracy, 0.204 mm average differences and 0.484 mm maximum difference are found for the phantom case, and the maximum differences of 0.3–0.5 mm for patients 1–3 are observed. As for the image quality, intensity errors below 5 and 20 HU compared to the planning CT are achieved for the phantom and the patient cases, respectively. Signal-noise-ratio values are improved by 12.74 and 5.12 times compared to results from FDK algorithm using the 1-min data and 4-min data, respectively. The computation time of the algorithm on a NVIDIA GTX590 card is 1–1.5 min per phase
A hybrid reconstruction algorithm for fast and accurate 4D cone-beam CT imaging
Yan, Hao; Folkerts, Michael; Jiang, Steve B. E-mail: steve.jiang@UTSouthwestern.edu; Jia, Xun E-mail: steve.jiang@UTSouthwestern.edu; Zhen, Xin; Li, Yongbao; Pan, Tinsu; Cervino, Laura
2014-07-15
Purpose: 4D cone beam CT (4D-CBCT) has been utilized in radiation therapy to provide 4D image guidance in lung and upper abdomen area. However, clinical application of 4D-CBCT is currently limited due to the long scan time and low image quality. The purpose of this paper is to develop a new 4D-CBCT reconstruction method that restores volumetric images based on the 1-min scan data acquired with a standard 3D-CBCT protocol. Methods: The model optimizes a deformation vector field that deforms a patient-specific planning CT (p-CT), so that the calculated 4D-CBCT projections match measurements. A forward-backward splitting (FBS) method is invented to solve the optimization problem. It splits the original problem into two well-studied subproblems, i.e., image reconstruction and deformable image registration. By iteratively solving the two subproblems, FBS gradually yields correct deformation information, while maintaining high image quality. The whole workflow is implemented on a graphic-processing-unit to improve efficiency. Comprehensive evaluations have been conducted on a moving phantom and three real patient cases regarding the accuracy and quality of the reconstructed images, as well as the algorithm robustness and efficiency. Results: The proposed algorithm reconstructs 4D-CBCT images from highly under-sampled projection data acquired with 1-min scans. Regarding the anatomical structure location accuracy, 0.204 mm average differences and 0.484 mm maximum difference are found for the phantom case, and the maximum differences of 0.3–0.5 mm for patients 1–3 are observed. As for the image quality, intensity errors below 5 and 20 HU compared to the planning CT are achieved for the phantom and the patient cases, respectively. Signal-noise-ratio values are improved by 12.74 and 5.12 times compared to results from FDK algorithm using the 1-min data and 4-min data, respectively. The computation time of the algorithm on a NVIDIA GTX590 card is 1–1.5 min per phase
A novel approach for accurate identification of splice junctions based on hybrid algorithms.
Mandal, Indrajit
2015-01-01
The precise prediction of splice junctions as 'exon-intron' or 'intron-exon' boundaries in a given DNA sequence is an important task in Bioinformatics. The main challenge is to determine the splice sites in the coding region. Due to the intrinsic complexity and the uncertainty in gene sequence, the adoption of data mining methods is increasingly becoming popular. There are various methods developed on different strategies in this direction. This article focuses on the construction of new hybrid machine learning ensembles that solve the splice junction task more effectively. A novel supervised feature reduction technique is developed using entropy-based fuzzy rough set theory optimized by greedy hill-climbing algorithm. The average prediction accuracy achieved is above 98% with 95% confidence interval. The performance of the proposed methods is evaluated using various metrics to establish the statistical significance of the results. The experiments are conducted using various schemes with human DNA sequence data. The obtained results are highly promising as compared with the state-of-the-art approaches in literature. PMID:25203504
NASA Astrophysics Data System (ADS)
Alexandre, E.; Cuadra, L.; Nieto-Borge, J. C.; Candil-García, G.; del Pino, M.; Salcedo-Sanz, S.
2015-08-01
Wave parameters computed from time series measured by buoys (significant wave height Hs, mean wave period, etc.) play a key role in coastal engineering and in the design and operation of wave energy converters. Storms or navigation accidents can make measuring buoys break down, leading to missing data gaps. In this paper we tackle the problem of locally reconstructing Hs at out-of-operation buoys by using wave parameters from nearby buoys, based on the spatial correlation among values at neighboring buoy locations. The novelty of our approach for its potential application to problems in coastal engineering is twofold. On one hand, we propose a genetic algorithm hybridized with an extreme learning machine that selects, among the available wave parameters from the nearby buoys, a subset FnSP with nSP parameters that minimizes the Hs reconstruction error. On the other hand, we evaluate to what extent the selected parameters in subset FnSP are good enough in assisting other machine learning (ML) regressors (extreme learning machines, support vector machines and gaussian process regression) to reconstruct Hs. The results show that all the ML method explored achieve a good Hs reconstruction in the two different locations studied (Caribbean Sea and West Atlantic).
NASA Astrophysics Data System (ADS)
Singh, Malkiat; Bettenhausen, Michael H.
2011-08-01
Faraday rotation changes the polarization plane of linearly polarized microwaves which propagate through the ionosphere. To correct for ionospheric polarization error, it is necessary to have electron density profiles on a global scale that represent the ionosphere in real time. We use raytrace through the combined models of ionospheric conductivity and electron density (ICED), Bent, and Gallagher models (RIBG model) to specify the ionospheric conditions by ingesting the GPS data from observing stations that are as close as possible to the observation time and location of the space system for which the corrections are required. To accurately calculate Faraday rotation corrections, we also utilize the raytrace utility of the RIBG model instead of the normal shell model assumption for the ionosphere. We use WindSat data, which exhibits a wide range of orientations of the raypath and a high data rate of observations, to provide a realistic data set for analysis. The standard single-shell models at 350 and 400 km are studied along with a new three-shell model and compared with the raytrace method for computation time and accuracy. We have compared the Faraday results obtained with climatological (International Reference Ionosphere and RIBG) and physics-based (Global Assimilation of Ionospheric Measurements) ionospheric models. We also study the impact of limitations in the availability of GPS data on the accuracy of the Faraday rotation calculations.
Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; Macnaught, Gillian; Semple, Scott I.; Boardman, James P.
2016-01-01
Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238
Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P
2016-01-01
Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238
NASA Astrophysics Data System (ADS)
Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; MacNaught, Gillian; Semple, Scott I.; Boardman, James P.
2016-03-01
Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.
Petascale Orbital-Free Density Functional Theory Enabled by Small-Box Algorithms.
Chen, Mohan; Jiang, Xiang-Wei; Zhuang, Houlong; Wang, Lin-Wang; Carter, Emily A
2016-06-14
Orbital-free density functional theory (OFDFT) is a quantum-mechanics-based method that utilizes electron density as its sole variable. The main computational cost in OFDFT is the ubiquitous use of the fast Fourier transform (FFT), which is mainly adopted to evaluate the kinetic energy density functional (KEDF) and electron-electron Coulomb interaction terms. We design and implement a small-box FFT (SBFFT) algorithm to overcome the parallelization limitations of conventional FFT algorithms. We also propose real-space truncation of the nonlocal Wang-Teter KEDF kernel. The scalability of the SBFFT is demonstrated by efficiently simulating one full optimization step (electron density, energies, forces, and stresses) of 1,024,000 lithium (Li) atoms on up to 65,536 cores. We perform other tests using Li as a test material, including calculations of physical properties of different phases of bulk Li, geometry optimizations of nanocrystalline Li, and molecular dynamics simulations of liquid Li. All of the tests yield excellent agreement with the original OFDFT results, suggesting that the OFDFT-SBFFT algorithm opens the door to efficient first-principles simulations of materials containing millions of atoms. PMID:27145175
Note: Fast imaging of DNA in atomic force microscopy enabled by a local raster scan algorithm
Huang, Peng; Andersson, Sean B.
2014-06-15
Approaches to high-speed atomic force microscopy typically involve some combination of novel mechanical design to increase the physical bandwidth and advanced controllers to take maximum advantage of the physical capabilities. For certain classes of samples, however, imaging time can be reduced on standard instruments by reducing the amount of measurement that is performed to image the sample. One such technique is the local raster scan algorithm, developed for imaging of string-like samples. Here we provide experimental results on the use of this technique to image DNA samples, demonstrating the efficacy of the scheme and illustrating the order-of-magnitude improvement in imaging time that it provides.
Note: Fast imaging of DNA in atomic force microscopy enabled by a local raster scan algorithm
Huang, Peng; Andersson, Sean B.
2014-01-01
Approaches to high-speed atomic force microscopy typically involve some combination of novel mechanical design to increase the physical bandwidth and advanced controllers to take maximum advantage of the physical capabilities. For certain classes of samples, however, imaging time can be reduced on standard instruments by reducing the amount of measurement that is performed to image the sample. One such technique is the local raster scan algorithm, developed for imaging of string-like samples. Here we provide experimental results on the use of this technique to image DNA samples, demonstrating the efficacy of the scheme and illustrating the order-of-magnitude improvement in imaging time that it provides. PMID:24985865
Ergül, Özgür; Gürel, Levent
2013-03-01
Accurate electromagnetic modeling of complicated optical structures poses several challenges. Optical metamaterial and plasmonic structures are composed of multiple coexisting dielectric and/or conducting parts. Such composite structures may possess diverse values of conductivities and dielectric constants, including negative permittivity and permeability. Further challenges are the large sizes of the structures with respect to wavelength and the complexities of the geometries. In order to overcome these challenges and to achieve rigorous and efficient electromagnetic modeling of three-dimensional optical composite structures, we have developed a parallel implementation of the multilevel fast multipole algorithm (MLFMA). Precise formulation of composite structures is achieved with the so-called "electric and magnetic current combined-field integral equation." Surface integral equations are carefully discretized with piecewise linear basis functions, and the ensuing dense matrix equations are solved iteratively with parallel MLFMA. The hierarchical strategy is used for the efficient parallelization of MLFMA on distributed-memory architectures. In this paper, fast and accurate solutions of large-scale canonical and complicated real-life problems, such as optical metamaterials, discretized with tens of millions of unknowns are presented in order to demonstrate the capabilities of the proposed electromagnetic solver. PMID:23456127
Shi, Haixiang; Schmidt, Bertil; Liu, Weiguo; Müller-Wittig, Wolfgang
2010-04-01
Emerging DNA sequencing technologies open up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, produced reads are significantly shorter and more error-prone compared to the traditional Sanger shotgun sequencing method. This poses challenges for de novo DNA fragment assembly algorithms in terms of both accuracy (to deal with short, error-prone reads) and scalability (to deal with very large input data sets). In this article, we present a scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly, which is of high importance to many graph-based short-read assembly tools. The algorithm is based on spectral alignment and uses the Compute Unified Device Architecture (CUDA) programming model. To gain efficiency we are taking advantage of the CUDA texture memory using a space-efficient Bloom filter data structure for spectrum membership queries. We have tested the runtime and accuracy of our algorithm using real and simulated Illumina data for different read lengths, error rates, input sizes, and algorithmic parameters. Using a CUDA-enabled mass-produced GPU (available for less than US$400 at any local computer outlet), this results in speedups of 12-84 times for the parallelized error correction, and speedups of 3-63 times for both sequential preprocessing and parallelized error correction compared to the publicly available Euler-SR program. Our implementation is freely available for download from http://cuda-ec.sourceforge.net . PMID:20426693
A genetic algorithm enabled ensemble for unsupervised medical term extraction from clinical letters.
Liu, Wei; Chung, Bo Chuen; Wang, Rui; Ng, Jonathon; Morlet, Nigel
2015-01-01
Despite the rapid global movement towards electronic health records, clinical letters written in unstructured natural languages are still the preferred form of inter-practitioner communication about patients. These letters, when archived over a long period of time, provide invaluable longitudinal clinical details on individual and populations of patients. In this paper we present three unsupervised approaches, sequential pattern mining (PrefixSpan); frequency linguistic based C-Value; and keyphrase extraction from co-occurrence graphs (TextRank), to automatically extract single and multi-word medical terms without domain-specific knowledge. Because each of the three approaches focuses on different aspects of the language feature space, we propose a genetic algorithm to learn the best parameters of linearly integrating the three extractors for optimal performance against domain expert annotations. Around 30,000 clinical letters sent over the past decade from ophthalmology specialists to general practitioners at an eye clinic are anonymised as the corpus to evaluate the effectiveness of the ensemble against individual extractors. With minimal annotation, the ensemble achieves an average F-measure of 65.65 % when considering only complex medical terms, and a F-measure of 72.47 % if we take single word terms (i.e. unigrams) into consideration, markedly better than the three term extraction techniques when used alone. PMID:26664724
Zhang, Shen; Wu, Qi; Shan, Yichu; Zhao, Qun; Zhao, Baofeng; Weng, Yejing; Sui, Zhigang; Zhang, Lihua; Zhang, Yukui
2016-01-01
Most currently proteomic studies use data-dependent acquisition with dynamic exclusion to identify and quantify the peptides generated by the digestion of biological sample. Although dynamic exclusion permits more identifications and higher possibility to find low abundant proteins, stochastic and irreproducible precursor ion selection caused by dynamic exclusion limit the quantification capabilities, especially for MS/MS based quantification. This is because a peptide is usually triggered for fragmentation only once due to dynamic exclusion. Therefore the fragment ions used for quantification only reflect the peptide abundances at that given time point. Here, we propose a strategy of fast MS/MS acquisition without dynamic exclusion to enable precise and accurate quantification of proteome by MS/MS fragment intensity. The results showed comparable proteome identification efficiency compared to the traditional data-dependent acquisition with dynamic exclusion, better quantitative accuracy and reproducibility regardless of label-free based quantification or isobaric labeling based quantification. It provides us with new insights to fully explore the potential of modern mass spectrometers. This strategy was applied to the relative quantification of two human disease cell lines, showing great promises for quantitative proteomic applications. PMID:27198003
Rozario, T; Bereg, S; Chiu, T; Liu, H; Kearney, V; Jiang, L; Mao, W
2014-06-01
Purpose: In order to locate lung tumors on projection images without internal markers, digitally reconstructed radiograph (DRR) is created and compared with projection images. Since lung tumors always move and their locations change on projection images while they are static on DRRs, a special DRR (background DRR) is generated based on modified anatomy from which lung tumors are removed. In addition, global discrepancies exist between DRRs and projections due to their different image originations, scattering, and noises. This adversely affects comparison accuracy. A simple but efficient comparison algorithm is reported. Methods: This method divides global images into a matrix of small tiles and similarities will be evaluated by calculating normalized cross correlation (NCC) between corresponding tiles on projections and DRRs. The tile configuration (tile locations) will be automatically optimized to keep the tumor within a single tile which has bad matching with the corresponding DRR tile. A pixel based linear transformation will be determined by linear interpolations of tile transformation results obtained during tile matching. The DRR will be transformed to the projection image level and subtracted from it. The resulting subtracted image now contains only the tumor. A DRR of the tumor is registered to the subtracted image to locate the tumor. Results: This method has been successfully applied to kV fluoro images (about 1000 images) acquired on a Vero (Brainlab) for dynamic tumor tracking on phantom studies. Radiation opaque markers are implanted and used as ground truth for tumor positions. Although, other organs and bony structures introduce strong signals superimposed on tumors at some angles, this method accurately locates tumors on every projection over 12 gantry angles. The maximum error is less than 2.6 mm while the total average error is 1.0 mm. Conclusion: This algorithm is capable of detecting tumor without markers despite strong background signals.
NASA Astrophysics Data System (ADS)
Grimminck, Dennis L. A. G.; Polman, Ben J. W.; Kentgens, Arno P. M.; Leo Meerts, W.
2011-08-01
A fast and accurate fit program is presented for deconvolution of one-dimensional solid-state quadrupolar NMR spectra of powdered materials. Computational costs of the synthesis of theoretical spectra are reduced by the use of libraries containing simulated time/frequency domain data. These libraries are calculated once and with the use of second-party simulation software readily available in the NMR community, to ensure a maximum flexibility and accuracy with respect to experimental conditions. EASY-GOING deconvolution ( EGdeconv) is equipped with evolutionary algorithms that provide robust many-parameter fitting and offers efficient parallellised computing. The program supports quantification of relative chemical site abundances and (dis)order in the solid-state by incorporation of (extended) Czjzek and order parameter models. To illustrate EGdeconv's current capabilities, we provide three case studies. Given the program's simple concept it allows a straightforward extension to include other NMR interactions. The program is available as is for 64-bit Linux operating systems.
Zou, Han; Jiang, Hao; Luo, Yiwen; Zhu, Jianjie; Lu, Xiaoxuan; Xie, Lihua
2016-01-01
The location and contextual status (indoor or outdoor) is fundamental and critical information for upper-layer applications, such as activity recognition and location-based services (LBS) for individuals. In addition, optimizations of building management systems (BMS), such as the pre-cooling or heating process of the air-conditioning system according to the human traffic entering or exiting a building, can utilize the information, as well. The emerging mobile devices, which are equipped with various sensors, become a feasible and flexible platform to perform indoor-outdoor (IO) detection. However, power-hungry sensors, such as GPS and WiFi, should be used with caution due to the constrained battery storage on mobile device. We propose BlueDetect: an accurate, fast response and energy-efficient scheme for IO detection and seamless LBS running on the mobile device based on the emerging low-power iBeacon technology. By leveraging the on-broad Bluetooth module and our proposed algorithms, BlueDetect provides a precise IO detection service that can turn on/off on-board power-hungry sensors smartly and automatically, optimize their performances and reduce the power consumption of mobile devices simultaneously. Moreover, seamless positioning and navigation services can be realized by it, especially in a semi-outdoor environment, which cannot be achieved by GPS or an indoor positioning system (IPS) easily. We prototype BlueDetect on Android mobile devices and evaluate its performance comprehensively. The experimental results have validated the superiority of BlueDetect in terms of IO detection accuracy, localization accuracy and energy consumption. PMID:26907295
Zou, Han; Jiang, Hao; Luo, Yiwen; Zhu, Jianjie; Lu, Xiaoxuan; Xie, Lihua
2016-01-01
The location and contextual status (indoor or outdoor) is fundamental and critical information for upper-layer applications, such as activity recognition and location-based services (LBS) for individuals. In addition, optimizations of building management systems (BMS), such as the pre-cooling or heating process of the air-conditioning system according to the human traffic entering or exiting a building, can utilize the information, as well. The emerging mobile devices, which are equipped with various sensors, become a feasible and flexible platform to perform indoor-outdoor (IO) detection. However, power-hungry sensors, such as GPS and WiFi, should be used with caution due to the constrained battery storage on mobile device. We propose BlueDetect: an accurate, fast response and energy-efficient scheme for IO detection and seamless LBS running on the mobile device based on the emerging low-power iBeacon technology. By leveraging the on-broad Bluetooth module and our proposed algorithms, BlueDetect provides a precise IO detection service that can turn on/off on-board power-hungry sensors smartly and automatically, optimize their performances and reduce the power consumption of mobile devices simultaneously. Moreover, seamless positioning and navigation services can be realized by it, especially in a semi-outdoor environment, which cannot be achieved by GPS or an indoor positioning system (IPS) easily. We prototype BlueDetect on Android mobile devices and evaluate its performance comprehensively. The experimental results have validated the superiority of BlueDetect in terms of IO detection accuracy, localization accuracy and energy consumption. PMID:26907295
NASA Astrophysics Data System (ADS)
Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.
2009-12-01
FILMPAR is a highly efficient and portable parallel multigrid algorithm for solving a discretised form of the lubrication approximation to three-dimensional, gravity-driven, continuous thin film free-surface flow over substrates containing micro-scale topography. While generally applicable to problems involving heterogeneous and distributed features, for illustrative purposes the algorithm is benchmarked on a distributed memory IBM BlueGene/P computing platform for the case of flow over a single trench topography, enabling direct comparison with complementary experimental data and existing serial multigrid solutions. Parallel performance is assessed as a function of the number of processors employed and shown to lead to super-linear behaviour for the production of mesh-independent solutions. In addition, the approach is used to solve for the case of flow over a complex inter-connected topographical feature and a description provided of how FILMPAR could be adapted relatively simply to solve for a wider class of related thin film flow problems. Program summaryProgram title: FILMPAR Catalogue identifier: AEEL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 530 421 No. of bytes in distributed program, including test data, etc.: 1 960 313 Distribution format: tar.gz Programming language: C++ and MPI Computer: Desktop, server Operating system: Unix/Linux Mac OS X Has the code been vectorised or parallelised?: Yes. Tested with up to 128 processors RAM: 512 MBytes Classification: 12 External routines: GNU C/C++, MPI Nature of problem: Thin film flows over functional substrates containing well-defined single and complex topographical features are of enormous significance, having a wide variety of engineering
Bechet, P; Mitran, R; Munteanu, M
2013-08-01
Non-contact methods for the assessment of vital signs are of great interest for specialists due to the benefits obtained in both medical and special applications, such as those for surveillance, monitoring, and search and rescue. This paper investigates the possibility of implementing a digital processing algorithm based on the MUSIC (Multiple Signal Classification) parametric spectral estimation in order to reduce the observation time needed to accurately measure the heart rate. It demonstrates that, by proper dimensioning the signal subspace, the MUSIC algorithm can be optimized in order to accurately assess the heart rate during an 8-28 s time interval. The validation of the processing algorithm performance was achieved by minimizing the mean error of the heart rate after performing simultaneous comparative measurements on several subjects. In order to calculate the error the reference value of heart rate was measured using a classic measurement system through direct contact. PMID:24007088
NASA Astrophysics Data System (ADS)
Bechet, P.; Mitran, R.; Munteanu, M.
2013-08-01
Non-contact methods for the assessment of vital signs are of great interest for specialists due to the benefits obtained in both medical and special applications, such as those for surveillance, monitoring, and search and rescue. This paper investigates the possibility of implementing a digital processing algorithm based on the MUSIC (Multiple Signal Classification) parametric spectral estimation in order to reduce the observation time needed to accurately measure the heart rate. It demonstrates that, by proper dimensioning the signal subspace, the MUSIC algorithm can be optimized in order to accurately assess the heart rate during an 8-28 s time interval. The validation of the processing algorithm performance was achieved by minimizing the mean error of the heart rate after performing simultaneous comparative measurements on several subjects. In order to calculate the error the reference value of heart rate was measured using a classic measurement system through direct contact.
NASA Astrophysics Data System (ADS)
Gupta, Pramod; Connolly, Andrew J.; Gardner, Jeffrey P.
2014-03-01
Future astronomical surveys will produce data on ˜108 objects per night. In order to characterize and classify these sources, we will require algorithms that scale linearly with the size of the data, that can be easily parallelized and where the speedup of the parallel algorithm will be linear in the number of processing cores. In this paper, we present such an algorithm and apply it to the question of colour selection of quasars. We use non-parametric Bayesian classification and a binning algorithm implemented with hash tables (BASH tables). We show that this algorithm's run time scales linearly with the number of test set objects and is independent of the number of training set objects. We also show that it has the same classification accuracy as other algorithms. For current data set sizes, it is up to three orders of magnitude faster than commonly used naive kernel-density-estimation techniques and it is estimated to be about eight times faster than the current fastest algorithm using dual kd-trees for kernel density estimation. The BASH table algorithm scales linearly with the size of the test set data only, and so for future larger data sets, it will be even faster compared to other algorithms which all depend on the size of the test set and the size of the training set. Since it uses linear data structures, it is easier to parallelize compared to tree-based algorithms and its speedup is linear in the number of cores unlike tree-based algorithms whose speedup plateaus after a certain number of cores. Moreover, due to the use of hash tables to implement the binning, the memory usage is very small. While our analysis is for the specific problem of selection of quasars, the ideas are general and the BASH table algorithm can be applied to any density-estimation problem involving sparse high-dimensional data sets. Since sparse high-dimensional data sets are a common type of scientific data set, this method has the potential to be useful in a broad range of
NASA Technical Reports Server (NTRS)
Wehrbein, W. M.; Leovy, C. B.
1982-01-01
The circulation of the middle atmosphere of the earth (15-90 km) is driven by the unequal distribution of net radiative heating. Calculations have shown that local radiative heating is nearly balanced by radiative cooling throughout parts of the stratosphere and mesosphere. The 15 micrometer band of CO2 is the dominant component of the infrared cooling. The present investigation is concerned with an algorithm regarding the involved cooling process. The algorithm was designed for the semispectral primitive equation model of the stratosphere and mesosphere described by Holton and Wehrbein (1980). The model consists of 16 layers, each nominally 5 km thick, between the base of the stratosphere at 100 mb (approximately 16 km) and the base of the thermosphere (approximately 96 km). The considered algorithm provides a convenient means of incorporating cooling due to CO2 into dynamical models of the middle atmosphere.
Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
2016-08-01
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10-4 Ha/Bohr.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Regalia, Giulia; Coelli, Stefania; Biffi, Emilia; Ferrigno, Giancarlo; Pedrocchi, Alessandra
2016-01-01
Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting "building blocks" into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191
Pedrocchi, Alessandra
2016-01-01
Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting “building blocks” into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191
Orio, Patricio; Soudry, Daniel
2012-01-01
Background The phenomena that emerge from the interaction of the stochastic opening and closing of ion channels (channel noise) with the non-linear neural dynamics are essential to our understanding of the operation of the nervous system. The effects that channel noise can have on neural dynamics are generally studied using numerical simulations of stochastic models. Algorithms based on discrete Markov Chains (MC) seem to be the most reliable and trustworthy, but even optimized algorithms come with a non-negligible computational cost. Diffusion Approximation (DA) methods use Stochastic Differential Equations (SDE) to approximate the behavior of a number of MCs, considerably speeding up simulation times. However, model comparisons have suggested that DA methods did not lead to the same results as in MC modeling in terms of channel noise statistics and effects on excitability. Recently, it was shown that the difference arose because MCs were modeled with coupled gating particles, while the DA was modeled using uncoupled gating particles. Implementations of DA with coupled particles, in the context of a specific kinetic scheme, yielded similar results to MC. However, it remained unclear how to generalize these implementations to different kinetic schemes, or whether they were faster than MC algorithms. Additionally, a steady state approximation was used for the stochastic terms, which, as we show here, can introduce significant inaccuracies. Main Contributions We derived the SDE explicitly for any given ion channel kinetic scheme. The resulting generic equations were surprisingly simple and interpretable – allowing an easy, transparent and efficient DA implementation, avoiding unnecessary approximations. The algorithm was tested in a voltage clamp simulation and in two different current clamp simulations, yielding the same results as MC modeling. Also, the simulation efficiency of this DA method demonstrated considerable superiority over MC methods, except when
Backlund, Mikael P.; Lew, Matthew D.; Backer, Adam S.; Sahl, Steffen J.; Grover, Ginni; Agrawal, Anurag; Piestun, Rafael; Moerner, W. E.
2014-01-01
Single-molecule-based super-resolution fluorescence microscopy has recently been developed to surpass the diffraction limit by roughly an order of magnitude. These methods depend on the ability to precisely and accurately measure the position of a single-molecule emitter, typically by fitting its emission pattern to a symmetric estimator (e.g. centroid or 2D Gaussian). However, single-molecule emission patterns are not isotropic, and depend highly on the orientation of the molecule’s transition dipole moment, as well as its z-position. Failure to account for this fact can result in localization errors on the order of tens of nm for in-focus images, and ~50–200 nm for molecules at modest defocus. The latter range becomes especially important for three-dimensional (3D) single-molecule super-resolution techniques, which typically employ depths-of-field of up to ~2 μm. To address this issue we report the simultaneous measurement of precise and accurate 3D single-molecule position and 3D dipole orientation using the Double-Helix Point Spread Function (DH-PSF) microscope. We are thus able to significantly improve dipole-induced position errors, reducing standard deviations in lateral localization from ~2x worse than photon-limited precision (48 nm vs. 25 nm) to within 5 nm of photon-limited precision. Furthermore, by averaging many estimations of orientation we are able to improve from a lateral standard deviation of 116 nm (~4x worse than the precision, 28 nm) to 34 nm (within 6 nm). PMID:24817798
Clisby, Nathan
2010-02-01
We introduce a fast implementation of the pivot algorithm for self-avoiding walks, which we use to obtain large samples of walks on the cubic lattice of up to 33x10{6} steps. Consequently the critical exponent nu for three-dimensional self-avoiding walks is determined to great accuracy; the final estimate is nu=0.587 597(7). The method can be adapted to other models of polymers with short-range interactions, on the lattice or in the continuum. PMID:20366773
Hashem, Somaya; Esmat, Gamal; Elakel, Wafaa; Habashy, Shahira; Abdel Raouf, Safaa; Darweesh, Samar; Soliman, Mohamad; Elhefnawi, Mohamed; El-Adawy, Mohamed; ElHefnawi, Mahmoud
2016-01-01
Background/Aim. Respectively with the prevalence of chronic hepatitis C in the world, using noninvasive methods as an alternative method in staging chronic liver diseases for avoiding the drawbacks of biopsy is significantly increasing. The aim of this study is to combine the serum biomarkers and clinical information to develop a classification model that can predict advanced liver fibrosis. Methods. 39,567 patients with chronic hepatitis C were included and randomly divided into two separate sets. Liver fibrosis was assessed via METAVIR score; patients were categorized as mild to moderate (F0–F2) or advanced (F3-F4) fibrosis stages. Two models were developed using alternating decision tree algorithm. Model 1 uses six parameters, while model 2 uses four, which are similar to FIB-4 features except alpha-fetoprotein instead of alanine aminotransferase. Sensitivity and receiver operating characteristic curve were performed to evaluate the performance of the proposed models. Results. The best model achieved 86.2% negative predictive value and 0.78 ROC with 84.8% accuracy which is better than FIB-4. Conclusions. The risk of advanced liver fibrosis, due to chronic hepatitis C, could be predicted with high accuracy using decision tree learning algorithm that could be used to reduce the need to assess the liver biopsy. PMID:26880886
Hashem, Somaya; Esmat, Gamal; Elakel, Wafaa; Habashy, Shahira; Abdel Raouf, Safaa; Darweesh, Samar; Soliman, Mohamad; Elhefnawi, Mohamed; El-Adawy, Mohamed; ElHefnawi, Mahmoud
2016-01-01
Background/Aim. Respectively with the prevalence of chronic hepatitis C in the world, using noninvasive methods as an alternative method in staging chronic liver diseases for avoiding the drawbacks of biopsy is significantly increasing. The aim of this study is to combine the serum biomarkers and clinical information to develop a classification model that can predict advanced liver fibrosis. Methods. 39,567 patients with chronic hepatitis C were included and randomly divided into two separate sets. Liver fibrosis was assessed via METAVIR score; patients were categorized as mild to moderate (F0-F2) or advanced (F3-F4) fibrosis stages. Two models were developed using alternating decision tree algorithm. Model 1 uses six parameters, while model 2 uses four, which are similar to FIB-4 features except alpha-fetoprotein instead of alanine aminotransferase. Sensitivity and receiver operating characteristic curve were performed to evaluate the performance of the proposed models. Results. The best model achieved 86.2% negative predictive value and 0.78 ROC with 84.8% accuracy which is better than FIB-4. Conclusions. The risk of advanced liver fibrosis, due to chronic hepatitis C, could be predicted with high accuracy using decision tree learning algorithm that could be used to reduce the need to assess the liver biopsy. PMID:26880886
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-03-01
We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
NASA Astrophysics Data System (ADS)
Byun, Jaeseung; Bodony, Daniel; Pantano, Carlos
2014-11-01
Improved order-of-accuracy discretizations often require careful consideration of their numerical stability. We report on new high-order finite difference schemes using Summation-By-Parts (SBP) operators along with the Simultaneous-Approximation-Terms (SAT) boundary condition treatment for first and second-order spatial derivatives with variable coefficients. In particular, we present a highly accurate operator for SBP-SAT-based approximations of second-order derivatives with variable coefficients for Dirichlet and Neumann boundary conditions. These terms are responsible for approximating the physical dissipation of kinetic and thermal energy in a simulation, and contain grid metrics when the grid is curvilinear. Analysis using the Laplace transform method shows that strong stability is ensured with Dirichlet boundary conditions while weaker stability is obtained for Neumann boundary conditions. Furthermore, the benefits of the scheme is shown in the direct numerical simulation (DNS) of a Mach 1.5 compressible turbulent supersonic jet using curvilinear grids and skew-symmetric discretization. Particularly, we show that the improved methods allow minimization of the numerical filter often employed in these simulations and we discuss the qualities of the simulation.
Jaitly, Navdeep; Monroe, Matthew E.; Petyuk, Vladislav A.; Clauss, Therese RW; Adkins, Joshua N.; Smith, Richard D.
2006-11-01
Liquid chromatography coupled to mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS) has become a standard technique for analyzing complex peptide mixtures to determine composition and relative quantity. Several high-throughput proteomics techniques attempt to combine complementary results from multiple LC-MS and LC-MS/MS analyses to provide more comprehensive and accurate results. To effectively collate results from these techniques, variations in mass and elution time measurements between related analyses are corrected by using algorithms designed to align the various types of results: LC-MS/MS vs. LC-MS/MS, LC-MS vs. LC-MS/MS, and LC-MS vs. LC-MS. Described herein are new algorithms referred to collectively as Liquid Chromatography based Mass Spectrometric Warping and Alignment of Retention times of Peptides (LCMSWARP) which use a dynamic elution time warping approach similar to traditional algorithms that correct variation in elution time using piecewise linear functions. LCMSWARP is compared to a linear alignment algorithm that assumes a linear transformation of elution time between analyses. LCMSWARP also corrects for drift in mass measurement accuracies that are often seen in an LC-MS analysis due to factors such as analyzer drift. We also describe the alignment of LC-MS results and provide examples of alignment of analyses from different chromatographic systems to demonstrate more complex transformation functions.
Costalat, Vincent; Maldonado, Igor Lima; Strauss, Olivier; Bonafé, Alain
2011-06-15
The present study describes a new approach for aneurysm volume quantification on three-dimensional angiograms, which focuses on solving three common technical problems: the variability associated with the use of manual thresholds, the irregular morphology of some aneurysms, and the imprecision of the limits between the parent artery and the aneurysm sac. The method consists of combining an algorithm for automatic threshold determination with a spherical eraser tool that allows the user to separate the image of the aneurysm from the parent artery. The accuracy of volumetry after automatic thresholding was verified with an in vitro experiment in which 57 measurements were performed using four artificial aneurysms of known volume. The reliability of the method was compared to that obtained with the technique of ellipsoid approximation in a clinical setting of 15 real angiograms and 150 measurements performed by five different users. The mean error in the measurement of the artificial aneurysms was 7.23%. The reliability of the new approach was significantly higher than that of the ellipsoid approximation. Limits of agreement between two measurements were determined with Bland-Altman plots and ranged from -14 to 13% for complex and from -10.8 to 11.03% for simple-shaped sacs. The reproducibility was lower (>20% of variation) for small aneurysms (<70 mm³) and for those presenting a very wide neck (dome-to-neck ratio<1). The method is potentially useful in the clinical practice, since it provides relatively precise, reproducible, volume quantification. A safety coiling volume can be established in order to perform sufficient but not excessive filling of the aneurysm pouch. PMID:21540054
Buckeridge, David L; Okhmatovskaia, Anna; Tu, Samson; O'Connor, Martin; Nyulas, Csongor; Musen, Mark A
2008-01-01
Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264
Buckeridge, David L.; Okhmatovskaia, Anna; Tu, Samson; O’Connor, Martin; Nyulas, Csongor; Musen, Mark A.
2008-01-01
Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264
Yovich, John L; Alsbjerg, Birgit; Conceicao, Jason L; Hinchliffe, Peter M; Keane, Kevin N
2016-01-01
The first PIVET algorithm for individualized recombinant follicle stimulating hormone (rFSH) dosing in in vitro fertilization, reported in 2012, was based on age and antral follicle count grading with adjustments for anti-Müllerian hormone level, body mass index, day-2 FSH, and smoking history. In 2007, it was enabled by the introduction of a metered rFSH pen allowing small dosage increments of ~8.3 IU per click. In 2011, a second rFSH pen was introduced allowing more precise dosages of 12.5 IU per click, and both pens with their individual algorithms have been applied continuously at our clinic. The objective of this observational study was to validate the PIVET algorithms pertaining to the two rFSH pens with the aim of collecting ≤15 oocytes and minimizing the risk of ovarian hyperstimulation syndrome. The data set included 2,822 in vitro fertilization stimulations over a 6-year period until April 2014 applying either of the two individualized dosing algorithms and corresponding pens. The main outcome measures were mean oocytes retrieved and resultant embryos designated for transfer or cryopreservation permitted calculation of oocyte and embryo utilization rates. Ensuing pregnancies were tracked until live births, and live birth productivity rates embracing fresh and frozen transfers were calculated. Overall, the results showed that mean oocyte numbers were 10.0 for all women <40 years with 24% requiring rFSH dosages <150 IU. Applying both specific algorithms in our clinic meant that the starting dose was not altered for 79.1% of patients and for 30.1% of those receiving the very lowest rFSH dosages (≤75 IU). Only 0.3% patients were diagnosed with severe ovarian hyperstimulation syndrome, all deemed avoidable due to definable breaches from the protocols. The live birth productivity rates exceeded 50% for women <35 years and was 33.2% for the group aged 35-39 years. Routine use of both algorithms led to only 11.6% of women generating >15 oocytes
Yovich, John L; Alsbjerg, Birgit; Conceicao, Jason L; Hinchliffe, Peter M; Keane, Kevin N
2016-01-01
The first PIVET algorithm for individualized recombinant follicle stimulating hormone (rFSH) dosing in in vitro fertilization, reported in 2012, was based on age and antral follicle count grading with adjustments for anti-Müllerian hormone level, body mass index, day-2 FSH, and smoking history. In 2007, it was enabled by the introduction of a metered rFSH pen allowing small dosage increments of ~8.3 IU per click. In 2011, a second rFSH pen was introduced allowing more precise dosages of 12.5 IU per click, and both pens with their individual algorithms have been applied continuously at our clinic. The objective of this observational study was to validate the PIVET algorithms pertaining to the two rFSH pens with the aim of collecting ≤15 oocytes and minimizing the risk of ovarian hyperstimulation syndrome. The data set included 2,822 in vitro fertilization stimulations over a 6-year period until April 2014 applying either of the two individualized dosing algorithms and corresponding pens. The main outcome measures were mean oocytes retrieved and resultant embryos designated for transfer or cryopreservation permitted calculation of oocyte and embryo utilization rates. Ensuing pregnancies were tracked until live births, and live birth productivity rates embracing fresh and frozen transfers were calculated. Overall, the results showed that mean oocyte numbers were 10.0 for all women <40 years with 24% requiring rFSH dosages <150 IU. Applying both specific algorithms in our clinic meant that the starting dose was not altered for 79.1% of patients and for 30.1% of those receiving the very lowest rFSH dosages (≤75 IU). Only 0.3% patients were diagnosed with severe ovarian hyperstimulation syndrome, all deemed avoidable due to definable breaches from the protocols. The live birth productivity rates exceeded 50% for women <35 years and was 33.2% for the group aged 35–39 years. Routine use of both algorithms led to only 11.6% of women generating >15 oocytes
NASA Astrophysics Data System (ADS)
Han, Xiao; Pearson, Erik; Pelizzari, Charles; Al-Hallaq, Hania; Sidky, Emil Y.; Bian, Junguo; Pan, Xiaochuan
2015-06-01
Kilo-voltage (KV) cone-beam computed tomography (CBCT) unit mounted onto a linear accelerator treatment system, often referred to as on-board imager (OBI), plays an increasingly important role in image-guided radiation therapy. While the FDK algorithm is currently used for reconstructing images from clinical OBI data, optimization-based reconstruction has also been investigated for OBI CBCT. An optimization-based reconstruction involves numerous parameters, which can significantly impact reconstruction properties (or utility). The success of an optimization-based reconstruction for a particular class of practical applications thus relies strongly on appropriate selection of parameter values. In the work, we focus on tailoring the constrained-TV-minimization-based reconstruction, an optimization-based reconstruction previously shown of some potential for CBCT imaging conditions of practical interest, to OBI imaging through appropriate selection of parameter values. In particular, for given real data of phantoms and patient collected with OBI CBCT, we first devise utility metrics specific to OBI-quality-assurance tasks and then apply them to guiding the selection of parameter values in constrained-TV-minimization-based reconstruction. The study results show that the reconstructions are with improvement, relative to clinical FDK reconstruction, in both visualization and quantitative assessments in terms of the devised utility metrics.
Mark F. Adams; Seung-Hoe Ku; Patrick Worley; Ed D'Azevedo; Julian C. Cummings; C.S. Chang
2009-10-01
Particle-in-cell (PIC) methods have proven to be eft#11;ective in discretizing the Vlasov-Maxwell system of equations describing the core of toroidal burning plasmas for many decades. Recent physical understanding of the importance of edge physics for stability and transport in tokamaks has lead to development of the fi#12;rst fully toroidal edge PIC code - XGC1. The edge region poses special problems in meshing for PIC methods due to the lack of closed flux surfaces, which makes fi#12;eld-line following meshes and coordinate systems problematic. We present a solution to this problem with a semi-#12;field line following mesh method in a cylindrical coordinate system. Additionally, modern supercomputers require highly concurrent algorithms and implementations, with all levels of the memory hierarchy being effe#14;ciently utilized to realize optimal code performance. This paper presents a mesh and particle partitioning method, suitable to our meshing strategy, for use on highly concurrent cache-based computing platforms.
NASA Astrophysics Data System (ADS)
Harbert, W.; Hammack, R.; Veloski, G.; Hodge, G.
2011-12-01
In this study Airborne magnetic data was collected by Fugro Airborne Surveys from a helicopter platform (Figure 1) using the Midas II system over the 39 km2 NPR3 (Naval Petroleum Reserve No. 3) oilfield in east-central Wyoming. The Midas II system employs two Scintrex CS-2 cesium vapor magnetometers on opposite ends of a transversely mounted, 13.4-m long horizontal boom located amidships (Fig. 1). Each magnetic sensor had an in-flight sensitivity of 0.01 nT. Real time compensation of the magnetic data for magnetic noise induced by maneuvering of the aircraft was accomplished using two fluxgate magnetometers mounted just inboard of the cesium sensors. The total area surveyed was 40.5 km2 (NPR3) near Casper, Wyoming. The purpose of the survey was to accurately locate wells that had been drilled there during more than 90 years of continuous oilfield operation. The survey was conducted at low altitude and with closely spaced flight lines to improve the detection of wells with weak magnetic response and to increase the resolution of closely spaced wells. The survey was in preparation for a planned CO2 flood to enhance oil recovery, which requires a complete well inventory with accurate locations for all existing wells. The magnetic survey was intended to locate wells that are missing from the well database and to provide accurate locations for all wells. The well location method used combined an input dataset (for example, leveled total magnetic field reduced to the pole), combined with first and second horizontal spatial derivatives of this input dataset, which were then analyzed using focal statistics and finally combined using a fuzzy combination operation. Analytic signal and the Shi and Butt (2004) ZS attribute were also analyzed using this algorithm. A parameter could be adjusted to determine sensitivity. Depending on the input dataset 88% to 100% of the wells were located, with typical values being 95% to 99% for the NPR3 field site.
NASA Astrophysics Data System (ADS)
Theologou, I.; Patelaki, M.; Karantzalos, K.
2015-04-01
Assessing and monitoring water quality status through timely, cost effective and accurate manner is of fundamental importance for numerous environmental management and policy making purposes. Therefore, there is a current need for validated methodologies which can effectively exploit, in an unsupervised way, the enormous amount of earth observation imaging datasets from various high-resolution satellite multispectral sensors. To this end, many research efforts are based on building concrete relationships and empirical algorithms from concurrent satellite and in-situ data collection campaigns. We have experimented with Landsat 7 and Landsat 8 multi-temporal satellite data, coupled with hyperspectral data from a field spectroradiometer and in-situ ground truth data with several physico-chemical and other key monitoring indicators. All available datasets, covering a 4 years period, in our case study Lake Karla in Greece, were processed and fused under a quantitative evaluation framework. The performed comprehensive analysis posed certain questions regarding the applicability of single empirical models across multi-temporal, multi-sensor datasets towards the accurate prediction of key water quality indicators for shallow inland systems. Single linear regression models didn't establish concrete relations across multi-temporal, multi-sensor observations. Moreover, the shallower parts of the inland system followed, in accordance with the literature, different regression patterns. Landsat 7 and 8 resulted in quite promising results indicating that from the recreation of the lake and onward consistent per-sensor, per-depth prediction models can be successfully established. The highest rates were for chl-a (r2=89.80%), dissolved oxygen (r2=88.53%), conductivity (r2=88.18%), ammonium (r2=87.2%) and pH (r2=86.35%), while the total phosphorus (r2=70.55%) and nitrates (r2=55.50%) resulted in lower correlation rates.
McDonnell, Mark D.; Tissera, Migel D.; Vladusich, Tony; van Schaik, André; Tapson, Jonathan
2015-01-01
Recent advances in training deep (multi-layer) architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the ‘Extreme Learning Machine’ (ELM) approach, which also enables a very rapid training time (∼ 10 minutes). Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random ‘receptive field’ sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems. PMID:26262687
NASA Astrophysics Data System (ADS)
Wang, Li-yong; Li, Le; Zhang, Zhi-hua
2016-07-01
Hot compression tests of Ti-6Al-4V alloy in a wide temperature range of 1023-1323 K and strain rate range of 0.01-10 s-1 were conducted by a servo-hydraulic and computer-controlled Gleeble-3500 machine. In order to accurately and effectively characterize the highly nonlinear flow behaviors, support vector regression (SVR) which is a machine learning method was combined with genetic algorithm (GA) for characterizing the flow behaviors, namely, the GA-SVR. The prominent character of GA-SVR is that it with identical training parameters will keep training accuracy and prediction accuracy at a stable level in different attempts for a certain dataset. The learning abilities, generalization abilities, and modeling efficiencies of the mathematical regression model, ANN, and GA-SVR for Ti-6Al-4V alloy were detailedly compared. Comparison results show that the learning ability of the GA-SVR is stronger than the mathematical regression model. The generalization abilities and modeling efficiencies of these models were shown as follows in ascending order: the mathematical regression model < ANN < GA-SVR. The stress-strain data outside experimental conditions were predicted by the well-trained GA-SVR, which improved simulation accuracy of the load-stroke curve and can further improve the related research fields where stress-strain data play important roles, such as speculating work hardening and dynamic recovery, characterizing dynamic recrystallization evolution, and improving processing maps.
Guo, Hengkai; Wang, Guijin; Huang, Lingyun; Hu, Yuxin; Yuan, Chun; Li, Rui; Zhao, Xihai
2016-01-01
Atherosclerosis is among the leading causes of death and disability. Combining information from multi-modal vascular images is an effective and efficient way to diagnose and monitor atherosclerosis, in which image registration is a key technique. In this paper a feature-based registration algorithm, Two-step Auto-labeling Conditional Iterative Closed Points (TACICP) algorithm, is proposed to align three-dimensional carotid image datasets from ultrasound (US) and magnetic resonance (MR). Based on 2D segmented contours, a coarse-to-fine strategy is employed with two steps: rigid initialization step and non-rigid refinement step. Conditional Iterative Closest Points (CICP) algorithm is given in rigid initialization step to obtain the robust rigid transformation and label configurations. Then the labels and CICP algorithm with non-rigid thin-plate-spline (TPS) transformation model is introduced to solve non-rigid carotid deformation between different body positions. The results demonstrate that proposed TACICP algorithm has achieved an average registration error of less than 0.2mm with no failure case, which is superior to the state-of-the-art feature-based methods. PMID:26881433
NASA Technical Reports Server (NTRS)
Wang, Lui; Bayer, Steven E.
1991-01-01
Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.
Ekberg, Peter; Su, Rong; Chang, Ernest W.; Yun, Seok Hyun; Mattsson, Lars
2014-01-01
Optical coherence tomography (OCT) is useful for materials defect analysis and inspection with the additional possibility of quantitative dimensional metrology. Here, we present an automated image-processing algorithm for OCT analysis of roll-to-roll multilayers in 3D manufacturing of advanced ceramics. It has the advantage of avoiding filtering and preset modeling, and will, thus, introduce a simplification. The algorithm is validated for its capability of measuring the thickness of ceramic layers, extracting the boundaries of embedded features with irregular shapes, and detecting the geometric deformations. The accuracy of the algorithm is very high, and the reliability is better than 1 µm when evaluating with the OCT images using the same gauge block step height reference. The method may be suitable for industrial applications to the rapid inspection of manufactured samples with high accuracy and robustness. PMID:24562018
Boursier, J; Ducancelle, A; Vergniol, J; Veillon, P; Moal, V; Dufour, C; Bronowicki, J-P; Larrey, D; Hézode, C; Zoulim, F; Fontaine, H; Canva, V; Poynard, T; Allam, S; De Lédinghen, V
2015-12-01
Triple therapy using boceprevir or telaprevir remains the reference treatment for genotype 1 chronic hepatitis C in countries where new interferon-free regimens have not yet become available. Antiviral treatment is highly required in cirrhotic patients, but they represent a difficult-to-treat population. We aimed to develop a simple algorithm for the prediction of sustained viral response (SVR) in cirrhotic patients treated with triple therapy. A total of 484 cirrhotic patients from the ANRS CO20 CUPIC cohort treated with triple therapy were randomly distributed into derivation and validation sets. A total of 52.1% of patients achieved SVR. In the derivation set, a D0 score for the prediction of SVR before treatment initiation included the following independent predictors collected at day 0: prior treatment response, gamma-GT, platelets, telaprevir treatment, viral load. To refine the prediction at the early phase of the treatment, a W4 score included as additional parameter the viral load collected at week 4. The D0 and W4 scores were combined in the CUPIC algorithm defining three subgroups: 'no treatment initiation or early stop at week 4', 'undetermined' and 'SVR highly probable'. In the validation set, the rates of SVR in these three subgroups were, respectively, 11.1%, 50.0% and 82.2% (P < 0.001). By replacing the variable 'prior treatment response' with 'IL28B genotype', another algorithm was derived for treatment-naïve patients with similar results. The CUPIC algorithm is an easy-to-use tool that helps physicians weigh their decision between immediately treating cirrhotic patients using boceprevir/telaprevir triple therapy or waiting for new drugs to become available in their country. PMID:26216230
Accurate monotone cubic interpolation
NASA Technical Reports Server (NTRS)
Huynh, Hung T.
1991-01-01
Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.
Gott, Jonatha M.; Parimi, Neeta; Bundschuh, Ralf
2005-01-01
Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for sites of nucleotide insertion; this feature is particularly useful when designing primers for sequencing edited RNAs. Applying this algorithm, we successfully identified the nad2, nad4L, nad6 and atp8 genes within the mitochondrial genome of Physarum polycephalum, which had gone undetected by existing programs. Characterization of their mRNA products led to the unanticipated discovery of nucleotide deletion editing in Physarum. The deletion event, which results in the removal of three adjacent A residues, was confirmed by primer extension sequencing of total RNA. This finding is remarkable in that it comprises the first known instance of nucleotide deletion in this organelle, to be contrasted with nearly 500 sites of single and dinucleotide addition in characterized mitochondrial RNAs. Statistical analysis of this larger pool of editing sites indicates that there are significant biases in the 2 nt immediately upstream of editing sites, including a reduced incidence of nucleotide repeats, in addition to the previously identified purine-U bias. PMID:16147990
A caGRID-ENABLED, LEARNING BASED IMAGE SEGMENTATION METHOD FOR HISTOPATHOLOGY SPECIMENS
Foran, David J.; Yang, Lin; Tuzel, Oncel; Chen, Wenjin; Hu, Jun; Kurc, Tahsin M.; Ferreira, Renato; Saltz, Joel H.
2009-01-01
Accurate segmentation of tissue microarrays is a challenging topic because of some of the similarities exhibited by normal tissue and tumor regions. Processing speed is another consideration when dealing with imaged tissue microarrays as each microscopic slide may contain hundreds of digitized tissue discs. In this paper, a fast and accurate image segmentation algorithm is presented. Both a whole disc delineation algorithm and a learning based tumor region segmentation approach which utilizes multiple scale texton histograms are introduced. The algorithm is completely automatic and computationally efficient. The mean pixel-wise segmentation accuracy is about 90%. It requires about 1 second for whole disc (1024×1024 pixels) segmentation and less than 5 seconds for segmenting tumor regions. In order to enable remote access to the algorithm and collaborative studies, an analytical service is implemented using the caGrid infrastructure. This service wraps the algorithm and provides interfaces for remote clients to submit images for analysis and retrieve analysis results. PMID:19936299
Apparatus enables accurate determination of alkali oxides in alkali metals
NASA Technical Reports Server (NTRS)
Dupraw, W. A.; Gahn, R. F.; Graab, J. W.; Maple, W. E.; Rosenblum, L.
1966-01-01
Evacuated apparatus determines the alkali oxide content of an alkali metal by separating the metal from the oxide by amalgamation with mercury. The apparatus prevents oxygen and moisture from inadvertently entering the system during the sampling and analytical procedure.
D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data.
Perrone, Daniele; Jeurissen, Ben; Aelterman, Jan; Roine, Timo; Sijbers, Jan; Pizurica, Aleksandra; Leemans, Alexander; Philips, Wilfried
2016-01-01
Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well. PMID:26930054
D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data
Perrone, Daniele; Jeurissen, Ben; Aelterman, Jan; Roine, Timo; Sijbers, Jan; Pizurica, Aleksandra; Leemans, Alexander; Philips, Wilfried
2016-01-01
Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well. PMID:26930054
Nakhleh, Luay
2014-03-12
I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.
Advancements to the planogram frequency–distance rebinning algorithm
Champley, Kyle M; Raylman, Raymond R; Kinahan, Paul E
2010-01-01
In this paper we consider the task of image reconstruction in positron emission tomography (PET) with the planogram frequency–distance rebinning (PFDR) algorithm. The PFDR algorithm is a rebinning algorithm for PET systems with panel detectors. The algorithm is derived in the planogram coordinate system which is a native data format for PET systems with panel detectors. A rebinning algorithm averages over the redundant four-dimensional set of PET data to produce a three-dimensional set of data. Images can be reconstructed from this rebinned three-dimensional set of data. This process enables one to reconstruct PET images more quickly than reconstructing directly from the four-dimensional PET data. The PFDR algorithm is an approximate rebinning algorithm. We show that implementing the PFDR algorithm followed by the (ramp) filtered backprojection (FBP) algorithm in linogram coordinates from multiple views reconstructs a filtered version of our image. We develop an explicit formula for this filter which can be used to achieve exact reconstruction by means of a modified FBP algorithm applied to the stack of rebinned linograms and can also be used to quantify the errors introduced by the PFDR algorithm. This filter is similar to the filter in the planogram filtered backprojection algorithm derived by Brasse et al. The planogram filtered backprojection and exact reconstruction with the PFDR algorithm require complete projections which can be completed with a reprojection algorithm. The PFDR algorithm is similar to the rebinning algorithm developed by Kao et al. By expressing the PFDR algorithm in detector coordinates, we provide a comparative analysis between the two algorithms. Numerical experiments using both simulated data and measured data from a positron emission mammography/tomography (PEM/PET) system are performed. Images are reconstructed by PFDR+FBP (PFDR followed by 2D FBP reconstruction), PFDRX (PFDR followed by the modified FBP algorithm for exact
Algorithms and Algorithmic Languages.
ERIC Educational Resources Information Center
Veselov, V. M.; Koprov, V. M.
This paper is intended as an introduction to a number of problems connected with the description of algorithms and algorithmic languages, particularly the syntaxes and semantics of algorithmic languages. The terms "letter, word, alphabet" are defined and described. The concept of the algorithm is defined and the relation between the algorithm and…
A fast and efficient algorithm for Slater determinant updates in quantum Monte Carlo simulations
Nukala, Phani K. V. V.; Kent, P. R. C.
2009-05-28
We present an efficient low-rank updating algorithm for updating the trial wave functions used in quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is O(kN) during the kth step compared to traditional algorithms that require O(N{sup 2}) computations, where N is the system size. For single determinant trial wave functions the new algorithm is faster than the traditional O(N{sup 2}) Sherman-Morrison algorithm for up to O(N) updates. For multideterminant configuration-interaction-type trial wave functions of M+1 determinants, the new algorithm is significantly more efficient, saving both O(MN{sup 2}) work and O(MN{sup 2}) storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration-interaction-type wave functions.
A fast and efficient algorithm for Slater determinant updates in quantum Monte Carlo simulations
NASA Astrophysics Data System (ADS)
Nukala, Phani K. V. V.; Kent, P. R. C.
2009-05-01
We present an efficient low-rank updating algorithm for updating the trial wave functions used in quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is O(kN) during the kth step compared to traditional algorithms that require O(N2) computations, where N is the system size. For single determinant trial wave functions the new algorithm is faster than the traditional O(N2) Sherman-Morrison algorithm for up to O(N ) updates. For multideterminant configuration-interaction-type trial wave functions of M +1 determinants, the new algorithm is significantly more efficient, saving both O(MN2) work and O(MN2) storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration-interaction-type wave functions.
A fast and efficient algorithm for Slater determinant updates in quantum Monte Carlo simulations.
Nukala, Phani K V V; Kent, P R C
2009-05-28
We present an efficient low-rank updating algorithm for updating the trial wave functions used in quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is O(kN) during the kth step compared to traditional algorithms that require O(N(2)) computations, where N is the system size. For single determinant trial wave functions the new algorithm is faster than the traditional O(N(2)) Sherman-Morrison algorithm for up to O(N) updates. For multideterminant configuration-interaction-type trial wave functions of M+1 determinants, the new algorithm is significantly more efficient, saving both O(MN(2)) work and O(MN(2)) storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration-interaction-type wave functions. PMID:19485435
A Fast and efficient Algorithm for Slater Determinant Updates in Quantum Monte Carlo Simulations
Nukala, Phani K; Kent, Paul R
2009-01-01
We present an efficient low-rank updating algorithm for updating the trial wavefunctions used in Quantum Monte Carlo (QMC) simulations. The algorithm is based on low-rank updating of the Slater determinants. In particular, the computational complexity of the algorithm is $\\mathcal{O}(k N)$ during the $k$-th step compared with traditional algorithms that require $\\mathcal{O}(N^2)$ computations, where $N$ is the system size. For single determinant trial wavefunctions the new algorithm is faster than the traditional $\\mathcal{O}(N^2)$ Sherman-Morrison algorithm for up to $\\mathcal{O}(N)$ updates. For multideterminant configuration-interaction type trial wavefunctions of $M+1$ determinants, the new algorithm is significantly more efficient, saving both $\\mathcal{O}(MN^2)$ work and $\\mathcal{O}(MN^2)$ storage. The algorithm enables more accurate and significantly more efficient QMC calculations using configuration interaction type wavefunctions.
Mayampurath, Anoop M.; Jaitly, Navdeep; Purvine, Samuel O.; Monroe, Matthew E.; Auberry, Kenneth J.; Adkins, Joshua N.; Smith, Richard D.
2008-04-01
We present a new software tool for tandem MS analyses that: • accurately calculates the monoisotopic mass and charge of high–resolution parent ions • accurately operates regardless of the mass selected for fragmentation • performs independent of instrument settings • enables optimal selection of search mass tolerance for high mass accuracy experiments • is open source and thus can be tailored to individual needs • incorporates a SVM-based charge detection algorithm for analyzing low resolution tandem MS spectra • creates multiple output data formats (.dta, .MGF) • handles .RAW files and .mzXML formats • compatible with SEQUEST, MASCOT, X!Tandem
Accurate and consistent automatic seismocardiogram annotation without concurrent ECG.
Laurin, A; Khosrow-Khavar, F; Blaber, A P; Tavakolian, Kouhyar
2016-09-01
Seismocardiography (SCG) is the measurement of vibrations in the sternum caused by the beating of the heart. Precise cardiac mechanical timings that are easily obtained from SCG are critically dependent on accurate identification of fiducial points. So far, SCG annotation has relied on concurrent ECG measurements. An algorithm capable of annotating SCG without the use any other concurrent measurement was designed. We subjected 18 participants to graded lower body negative pressure. We collected ECG and SCG, obtained R peaks from the former, and annotated the latter by hand, using these identified peaks. We also annotated the SCG automatically. We compared the isovolumic moment timings obtained by hand to those obtained using our algorithm. Mean ± confidence interval of the percentage of accurately annotated cardiac cycles were [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] for levels of negative pressure 0, -20, -30, -40, and -50 mmHg. LF/HF ratios, the relative power of low-frequency variations to high-frequency variations in heart beat intervals, obtained from isovolumic moments were also compared to those obtained from R peaks. The mean differences ± confidence interval were [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] for increasing levels of negative pressure. The accuracy and consistency of the algorithm enables the use of SCG as a stand-alone heart monitoring tool in healthy individuals at rest, and could serve as a basis for an eventual application in pathological cases. PMID:27510446
Crespo, Cristina; Fernández, José R; Aboy, Mateo; Mojón, Artemio
2013-03-01
This paper reports the results of a study designed to determine whether there are statistically significant differences between the values of ambulatory blood pressure monitoring (ABPM) parameters obtained using different methods-fixed schedule, diary, and automatic algorithm based on actigraphy-of defining the main activity and rest periods, and to determine the clinical relevance of such differences. We studied 233 patients (98 men/135 women), 61.29 ± .83 yrs of age (mean ± SD). Statistical methods were used to measure agreement in the diagnosis and classification of subjects within the context of ABPM and cardiovascular disease risk assessment. The results show that there are statistically significant differences both at the group and individual levels. Those at the individual level have clinically significant implications, as they can result in a different classification, and, therefore, different diagnosis and treatment for individual subjects. The use of an automatic algorithm based on actigraphy can lead to better individual treatment by correcting the accuracy problems associated with the fixed schedule on patients whose actual activity/rest routine differs from the fixed schedule assumed, and it also overcomes the limitations and reliability issues associated with the use of diaries. PMID:23130607
Hu, Wei; Zhao, Zhangyan; Wang, Yunfeng; Zhang, Haiying; Lin, Fujiang
2014-03-01
The designed sensor enables accurate reconstruction of chest-wall movement caused by cardiopulmonary activities, and the algorithm enables estimation of respiration, heartbeat rate, and some indicators of heart rate variability (HRV). In particular, quadrature receiver and arctangent demodulation with calibration are introduced for high linearity representation of chest displacement; 24-bit ADCs with oversampling are adopted for radar baseband acquisition to achieve a high signal resolution; continuous-wavelet filter and ensemble empirical mode decomposition (EEMD) based algorithm are applied for cardio/pulmonary signal recovery and separation so that accurate beat-to-beat interval can be acquired in time domain for HRV analysis. In addition, the wireless sensor is realized and integrated on a printed circuit board compactly. The developed sensor system is successfully tested on both simulated target and human subjects. In simulated target experiments, the baseband signal-to-noise ratio (SNR) is 73.27 dB, high enough for heartbeat detection. The demodulated signal has 0.35% mean squared error, indicating high demodulation linearity. In human subject experiments, the relative error of extracted beat-to-beat intervals ranges from 2.53% to 4.83% compared with electrocardiography (ECG) R-R peak intervals. The sensor provides an accurate analysis for heart rate with the accuracy of 100% for p = 2% and higher than 97% for p = 1%. PMID:24235293
Accurate ab Initio Spin Densities
2012-01-01
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921
ERIC Educational Resources Information Center
Rom, Mark Carl
2011-01-01
Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…
Puckett, Elbridge Gerry; Miller, Gregory Hale
2012-10-14
Much of the work conducted under the auspices of DE-FG02-03ER25579 was characterized by an exceptionally close collaboration with researchers at the Lawrence Berkeley National Laboratory (LBNL). For example, Andy Nonaka, one of Professor Miller's graduate students in the Department of Applied Science at U. C. Davis (UCD) wrote his PhD thesis in an area of interest to researchers in the Applied Numerical Algorithms Group (ANAG), which is a part of the National Energy Research Supercomputer Center (NERSC) at LBNL. Dr. Nonaka collaborated closely with these researchers and subsequently published the results of this collaboration jointly with them, one article in a peer reviewed journal article and one paper in the proceedings of a conference. Dr. Nonaka is now a research scientist in the Center for Computational Sciences and Engineering (CCSE), which is also part of the National Energy Research Supercomputer Center (NERSC) at LBNL. This collaboration with researchers at LBNL also included having one of Professor Puckett's graduate students in the Graduate Group in Applied Mathematics (GGAM) at UCD, Sarah Williams, spend the summer working with Dr. Ann Almgren, who is a staff scientist in CCSE. As a result of this visit Sarah decided work on a problem suggested by the head of CCSE, Dr. John Bell, for her PhD thesis. Having finished all of the coursework and examinations required for a PhD, Sarah stayed at LBNL to work on her thesis under the guidance of Dr. Bell. Sarah finished her PhD thesis in June of 2007. Writing a PhD thesis while working at one of the University of California (UC) managed DOE laboratories is long established tradition at UC and Professor Puckett has always encouraged his students to consider doing this. Another one of Professor Puckett's graduate students in the GGAM at UCD, Christopher Algieri, was partially supported with funds from DE-FG02-03ER25579 while he wrote his MS thesis in which he analyzed and extended work originally published by Dr
Technology Enabled Learning. Symposium.
ERIC Educational Resources Information Center
2002
This document contains three papers on technology-enabled learning and human resource development. Among results found in "Current State of Technology-enabled Learning Programs in Select Federal Government Organizations: a Case Study of Ten Organizations" (Letitia A. Combs) are the following: the dominant delivery method is traditional…
Accurate thickness measurement of graphene
NASA Astrophysics Data System (ADS)
Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.
2016-03-01
Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.
NASA Astrophysics Data System (ADS)
Itano, Wayne M.; Ramsey, Norman F.
1993-07-01
The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.
Accurate quantum chemical calculations
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.
Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham
2015-01-01
Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943
NASA Technical Reports Server (NTRS)
Hilton, Kevin; Karl, Chad; Litherland, Mark; Ritchie, David; Sun, Nancy
1992-01-01
The dust control group designed a system to restrict dust that is disturbed by the Enabler during its operation from interfering with astronaut or camera visibility. This design also considers the many different wheel positions made possible through the use of artinuation joints that provide the steering and wheel pitching for the Enabler. The system uses a combination of brushes and fenders to restrict the dust when the vehicle is moving in either direction and in a turn. This design also allows for each of maintenance as well as accessibility of the remainder of the vehicle.
NASA Technical Reports Server (NTRS)
Hilton, Kevin; Karl, Chad; Litherland, Mark; Ritchie, David; Sun, Nancy
1992-01-01
The dust control group designed a system to restrict dust that is disturbed by the Enabler during its operation from interfering with astronaut or camera visibility. This design also considers the many different wheel positions made possible through the use of artinuation joints that provide the steering and wheel pitching for the Enabler. The system uses a combination of brushes and fenders to restrict the dust when the vehicle is moving in either direction and in a turn. This design also allows for ease of maintenance as well as accessibility of the remainder of the vehicle.
Microsystems Enabled Photovoltaics
Gupta, Vipin; Nielson, Greg; Okandan, Murat, Granata, Jennifer; Nelson, Jeff; Haney, Mike; Cruz-Campa, Jose Luiz
2014-06-23
Sandia's microsystems enabled photovoltaic advances combine mature technology and tools currently used in microsystem production with groundbreaking advances in photovoltaics cell design, decreasing production and system costs while improving energy conversion efficiency. The technology has potential applications in buildings, houses, clothing, portable electronics, vehicles, and other contoured structures.
Microsystems Enabled Photovoltaics
Gupta, Vipin; Nielson, Greg; Okandan, Murat, Granata, Jennifer; Nelson, Jeff; Haney, Mike; Cruz-Campa, Jose Luiz
2012-07-02
Sandia's microsystems enabled photovoltaic advances combine mature technology and tools currently used in microsystem production with groundbreaking advances in photovoltaics cell design, decreasing production and system costs while improving energy conversion efficiency. The technology has potential applications in buildings, houses, clothing, portable electronics, vehicles, and other contoured structures.
An Accurate Scalable Template-based Alignment Algorithm.
Gardner, David P; Xu, Weijia; Miranker, Daniel P; Ozer, Stuart; Cannone, Jamie J; Gutell, Robin R
2012-12-31
The rapid determination of nucleic acid sequences is increasing the number of sequences that are available. Inherent in a template or seed alignment is the culmination of structural and functional constraints that are selecting those mutations that are viable during the evolution of the RNA. While we might not understand these structural and functional, template-based alignment programs utilize the patterns of sequence conservation to encapsulate the characteristics of viable RNA sequences that are aligned properly. We have developed a program that utilizes the different dimensions of information in rCAD, a large RNA informatics resource, to establish a profile for each position in an alignment. The most significant include sequence identity and column composition in different phylogenetic taxa. We have compared our methods with a maximum of eight alternative alignment methods on different sets of 16S and 23S rRNA sequences with sequence percent identities ranging from 50% to 100%. The results showed that CRWAlign outperformed the other alignment methods in both speed and accuracy. A web-based alignment server is available at http://www.rna.ccbb.utexas.edu/SAE/2F/CRWAlign. PMID:24772376
A Complete and Accurate Ab Initio Repeat Finding Algorithm.
Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua
2016-03-01
It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474
Tang, Shi-Yang; Khoshmanesh, Khashayar; Sivan, Vijay; Petersen, Phred; O’Mullane, Anthony P.; Abbott, Derek; Mitchell, Arnan; Kalantar-zadeh, Kourosh
2014-01-01
Small-scale pumps will be the heartbeat of many future micro/nanoscale platforms. However, the integration of small-scale pumps is presently hampered by limited flow rate with respect to the input power, and their rather complicated fabrication processes. These issues arise as many conventional pumping effects require intricate moving elements. Here, we demonstrate a system that we call the liquid metal enabled pump, for driving a range of liquids without mechanical moving parts, upon the application of modest electric field. This pump incorporates a droplet of liquid metal, which induces liquid flow at high flow rates, yet with exceptionally low power consumption by electrowetting/deelectrowetting at the metal surface. We present theory explaining this pumping mechanism and show that the operation is fundamentally different from other existing pumps. The presented liquid metal enabled pump is both efficient and simple, and thus has the potential to fundamentally advance the field of microfluidics. PMID:24550485
Fast and accurate propagation of coherent light
Lewis, R. D.; Beylkin, G.; Monzón, L.
2013-01-01
We describe a fast algorithm to propagate, for any user-specified accuracy, a time-harmonic electromagnetic field between two parallel planes separated by a linear, isotropic and homogeneous medium. The analytical formulation of this problem (ca 1897) requires the evaluation of the so-called Rayleigh–Sommerfeld integral. If the distance between the planes is small, this integral can be accurately evaluated in the Fourier domain; if the distance is very large, it can be accurately approximated by asymptotic methods. In the large intermediate region of practical interest, where the oscillatory Rayleigh–Sommerfeld kernel must be applied directly, current numerical methods can be highly inaccurate without indicating this fact to the user. In our approach, for any user-specified accuracy ϵ>0, we approximate the kernel by a short sum of Gaussians with complex-valued exponents, and then efficiently apply the result to the input data using the unequally spaced fast Fourier transform. The resulting algorithm has computational complexity , where we evaluate the solution on an N×N grid of output points given an M×M grid of input samples. Our algorithm maintains its accuracy throughout the computational domain. PMID:24204184
Enabling Wind Power Nationwide
Jose, Zayas; Michael, Derby; Patrick, Gilman; Ananthan, Shreyas; Lantz, Eric; Cotrell, Jason; Beck, Fredic; Tusing, Richard
2015-05-01
Leveraging this experience, the U.S. Department of Energy’s (DOE’s) Wind and Water Power Technologies Office has evaluated the potential for wind power to generate electricity in all 50 states. This report analyzes and quantifies the geographic expansion that could be enabled by accessing higher above ground heights for wind turbines and considers the means by which this new potential could be responsibly developed.
Bedrails: restraints or enablers?
Mullette, Betty; Zulkowski, Karen
2004-08-01
Bedrails presently are used as both mobility restraints and enablers in long-term care facilities. As enablers, bedrails facilitate movement and may reduce the risk of pressure ulcer development. As restraints, they impede movement and may increase risk of ulcer development. Omnibus Budget Reconciliation Act regulations on restraint use have led to confusion for state Medicare surveyors and facilities regarding the definition of appropriate bedrail use and need for supportive documentation. Consequently, some facilities receive deficiency citations for inappropriate use or documentation while others do not. The purpose of this survey was to compare responses of Directors of Nursing in long-term care facilities and Medicare state surveyors to determine how each interprets the Omnibus Budget Reconciliation Act bedrail language for use and documentation. Questionnaires on bedrail use and documentation were sent to state surveyors and Directors of Nursing. One hundred, three (103) Directors of Nursing in 45 states and 65 surveyors from 39 states participated in the survey (response rate 61%). Study results demonstrated general acceptance of bedrail use as an enabler but not as a restraint by both Directors of Nursing and state surveyors. Four percent (4%) of Directors of Nursing reported receiving a citation for bedrail use and 59% of surveyors reported issuing citations for bedrail use. Significant differences were noted between the two groups regarding appropriate bedrail use and necessary documentation. The intent of Medicare guidelines and the Centers for Medicare and Medicaid Services is to standardize care for nursing home residents in the United States; yet, current regulations are open to individual interpretation by state surveyors and confusion exists between the intent of the Omnibus Budget Reconciliation Act and the daily operations of nursing homes. Educating clinicians about the risks and benefits of bedrail use, either as restraint or enabler, and
High-performance combinatorial algorithms
Pinar, Ali
2003-10-31
Combinatorial algorithms have long played an important role in many applications of scientific computing such as sparse matrix computations and parallel computing. The growing importance of combinatorial algorithms in emerging applications like computational biology and scientific data mining calls for development of a high performance library for combinatorial algorithms. Building such a library requires a new structure for combinatorial algorithms research that enables fast implementation of new algorithms. We propose a structure for combinatorial algorithms research that mimics the research structure of numerical algorithms. Numerical algorithms research is nicely complemented with high performance libraries, and this can be attributed to the fact that there are only a small number of fundamental problems that underlie numerical solvers. Furthermore there are only a handful of kernels that enable implementation of algorithms for these fundamental problems. Building a similar structure for combinatorial algorithms will enable efficient implementations for existing algorithms and fast implementation of new algorithms. Our results will promote utilization of combinatorial techniques and will impact research in many scientific computing applications, some of which are listed.
Accurate, Automated Detection of Atrial Fibrillation in Ambulatory Recordings.
Linker, David T
2016-06-01
A highly accurate, automated algorithm would facilitate cost-effective screening for asymptomatic atrial fibrillation. This study analyzed a new algorithm and compared it to existing techniques. The incremental benefit of each step in refinement of the algorithm was measured, and the algorithm was compared to other methods using the Physionet atrial fibrillation and normal sinus rhythm databases. When analyzing segments of 21 RR intervals or less, the algorithm had a significantly higher area under the receiver operating characteristic curve (AUC) than the other algorithms tested. At analysis segment sizes of up to 101 RR intervals, the algorithm continued to have a higher AUC than any of the other methods tested, although the difference from the second best other algorithm was no longer significant, with an AUC of 0.9992 with a 95% confidence interval (CI) of 0.9986-0.9998, vs. 0.9986 (CI 0.9978-0.9994). With identical per-subject sensitivity, per-subject specificity of the current algorithm was superior to the other tested algorithms even at 101 RR intervals, with no false positives (CI 0.0-0.8%) vs. 5.3% false positives for the second best algorithm (CI 3.4-7.9%). The described algorithm shows great promise for automated screening for atrial fibrillation by reducing false positives requiring manual review, while maintaining high sensitivity. PMID:26850411
Algorithms and Sensors for Small Robot Path Following
NASA Technical Reports Server (NTRS)
Hogg, Robert W.; Rankin, Arturo L.; Roumeliotis, Stergios I.; McHenry, Michael C.; Helmick, Daniel M.; Bergh, Charles F.; Matthies, Larry
2002-01-01
Tracked mobile robots in the 20 kg size class are under development for applications in urban reconnaissance. For efficient deployment, it is desirable for teams of robots to be able to automatically execute path following behaviors, with one or more followers tracking the path taken by a leader. The key challenges to enabling such a capability are (l) to develop sensor packages for such small robots that can accurately determine the path of the leader and (2) to develop path following algorithms for the subsequent robots. To date, we have integrated gyros, accelerometers, compass/inclinometers, odometry, and differential GPS into an effective sensing package. This paper describes the sensor package, sensor processing algorithm, and path tracking algorithm we have developed for the leader/follower problem in small robots and shows the result of performance characterization of the system. We also document pragmatic lessons learned about design, construction, and electromagnetic interference issues particular to the performance of state sensors on small robots.
Fast and Provably Accurate Bilateral Filtering
NASA Astrophysics Data System (ADS)
Chaudhury, Kunal N.; Dabhade, Swapnil D.
2016-06-01
The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires $O(S)$ operations per pixel, where $S$ is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to $O(1)$ per pixel for any arbitrary $S$. The algorithm has a simple implementation involving $N+1$ spatial filterings, where $N$ is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to to estimate the order $N$ required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with state-of-the-art methods in terms of speed and accuracy.
Fast and Provably Accurate Bilateral Filtering.
Chaudhury, Kunal N; Dabhade, Swapnil D
2016-06-01
The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy. PMID:27093722
Fast and Accurate Detection of Multiple Quantitative Trait Loci
Nettelblad, Carl; Holmgren, Sverker
2013-01-01
Abstract We present a new computational scheme that enables efficient and reliable quantitative trait loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving more than two loci to be performed in practice, at least if permutation testing is used to determine significance. Some more elaborate global optimization approaches, for example, DIRECT have been adopted earlier to QTL search problems. Dramatic speedups have been reported for high-dimensional scans. However, since a heuristic termination criterion must be used in these types of algorithms, the accuracy of the optimization process cannot be guaranteed. Indeed, earlier results show that a small bias in the significance thresholds is sometimes introduced. Our new optimization scheme, PruneDIRECT, is based on an analysis leading to a computable (Lipschitz) bound on the slope of a transformed objective function. The bound is derived for both infinite- and finite-size populations. Introducing a Lipschitz bound in DIRECT leads to an algorithm related to classical Lipschitz optimization. Regions in the search space can be permanently excluded (pruned) during the optimization process. Heuristic termination criteria can thus be avoided. Hence, PruneDIRECT has a well-defined error bound and can in practice be guaranteed to be equivalent to a corresponding exhaustive search. We present simulation results that show that for simultaneous mapping of three QTLS using permutation testing, PruneDIRECT is typically more than 50 times faster than exhaustive search. The speedup is higher for stronger QTL. This could be used to quickly detect strong candidate eQTL networks. PMID:23919387
None, None
2014-10-15
The combined team of GE Global Research, Federal Express, National Renewable Energy Laboratory, and Consolidated Edison has successfully achieved the established goals contained within the Department of Energy’s Smart Grid Capable Electric Vehicle Supply Equipment funding opportunity. The final program product, shown charging two vehicles in Figure 1, reduces by nearly 50% the total installed system cost of the electric vehicle supply equipment (EVSE) as well as enabling a host of new Smart Grid enabled features. These include bi-directional communications, load control, utility message exchange and transaction management information. Using the new charging system, Utilities or energy service providers will now be able to monitor transportation related electrical loads on their distribution networks, send load control commands or preferences to individual systems, and then see measured responses. Installation owners will be able to authorize usage of the stations, monitor operations, and optimally control their electricity consumption. These features and cost reductions have been developed through a total system design solution.
Saan, Hans; Wise, Marilyn
2011-12-01
The authors of the Ottawa Charter selected the words enable, mediate and advocate to describe the core activities in what was, in 1986, the new Public Health. This article considers these concepts and the values and ideas upon which they were based. We discuss their relevance in the current context within which health promotion is being conducted, and discuss the implications of changes in the health agenda, media and globalization for practice. We consider developments within health promotion since 1986: its central role in policy rhetoric, the increasing understanding of complexities and the interlinkage with many other societal processes. So the three core activities are reviewed: they still fit well with the main health promotion challenges, but should be refreshed by new ideas and values. As the role of health promotion in the political arena has grown we have become part of the policy establishment and that is a mixed blessing. Making way for community advocates is now our challenge. Enabling requires greater sensitivity to power relations involved and an understanding of the role of health literacy. Mediating keeps its central role as it bridges vital interests of parties. We conclude that these core concepts in the Ottawa Charter need no serious revision. There are, however, lessons from the last 25 years that point to ways to address present and future challenges with greater sensitivity and effectiveness. We invite the next generation to avoid canonizing this text: as is true of every heritage, the heirs must decide on its use. PMID:22080073
Enabling Computational Technologies for Terascale Scientific Simulations
Ashby, S.F.
2000-08-24
We develop scalable algorithms and object-oriented code frameworks for terascale scientific simulations on massively parallel processors (MPPs). Our research in multigrid-based linear solvers and adaptive mesh refinement enables Laboratory programs to use MPPs to explore important physical phenomena. For example, our research aids stockpile stewardship by making practical detailed 3D simulations of radiation transport. The need to solve large linear systems arises in many applications, including radiation transport, structural dynamics, combustion, and flow in porous media. These systems result from discretizations of partial differential equations on computational meshes. Our first research objective is to develop multigrid preconditioned iterative methods for such problems and to demonstrate their scalability on MPPs. Scalability describes how total computational work grows with problem size; it measures how effectively additional resources can help solve increasingly larger problems. Many factors contribute to scalability: computer architecture, parallel implementation, and choice of algorithm. Scalable algorithms have been shown to decrease simulation times by several orders of magnitude.
NPOESS Tools for Rapid Algorithm Updates
NASA Astrophysics Data System (ADS)
Route, G.; Grant, K. D.; Hughes, B.; Reed, B.
2009-12-01
The National Oceanic and Atmospheric Administration (NOAA), Department of Defense (DoD), and National Aeronautics and Space Administration (NASA) are jointly acquiring the next-generation weather and environmental satellite system; the National Polar-orbiting Operational Environmental Satellite System (NPOESS). NPOESS replaces the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA and the Defense Meteorological Satellite Program (DMSP) managed by the DoD. The NPOESS satellites carry a suite of sensors that collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The ground data processing segment for NPOESS is the Interface Data Processing Segment (IDPS), developed by Raytheon Intelligence and Information Systems. The IDPS processes both NPP and NPOESS satellite data to provide environmental data products to NOAA and DoD processing centers operated by the United States government. Northrop Grumman Aerospace Systems Algorithms and Data Products (A&DP) organization is responsible for the algorithms that produce the EDRs, including their quality aspects. As the Calibration and Validation activities move forward following both the NPP launch and subsequent NPOESS launches, rapid algorithm updates may be required. Raytheon and Northrop Grumman have developed tools and processes to enable changes to be evaluated, tested, and moved into the operational baseline in a rapid and efficient manner. This presentation will provide an overview of the tools available to the Cal/Val teams to ensure rapid and accurate assessment of algorithm changes, along with the processes in place to ensure baseline integrity.
Accurate mask model for advanced nodes
NASA Astrophysics Data System (ADS)
Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle
2014-07-01
Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.
Procrustes algorithm for multisensor track fusion
NASA Astrophysics Data System (ADS)
Fernandez, Manuel F.; Aridgides, Tom; Evans, John S., Jr.
1990-10-01
The association or "fusion" of multiple-sensor reports allows the generation of a highly accurate description of the environment by enabling efficient compression and processing of otherwise unwieldy quantities of data. Assuming that the observations from each sensor are aligned in feature space and in time, this association procedure may be executed on the basis of how well each sensor's vectors of observations match previously fused tracks. Unfortunately, distance-based algorithms alone do not suffice in those situations where match-assignments are not of an obvious nature (e.g., high target density or high false alarm rate scenarios). Our proposed approach is based on recognizing that, together, the sensors' observations and the fused tracks span a vector subspace whose dimensionality and singularity characteristics can be used to determine the total number of targets appearing across sensors. A properly constrained transformation can then be found which aligns the subspaces spanned individually by the observations and by the fused tracks, yielding the relationship existing between both sets of vectors ("Procrustes Problem"). The global nature of this approach thus enables fusing closely-spaced targets by treating them--in a manner analogous to PDA/JPDA algorithms - as clusters across sensors. Since our particular version of the Procrustes Problem consists basically of a minimization in the Total Least Squares sense, the resulting transformations associate both observations-to-tracks and tracks-to--observations. This means that the number of tracks being updated will increase or decrease depending on the number of targets present, automatically initiating or deleting "fused" tracks as required, without the need of ancillary procedures. In addition, it is implicitly assumed that both the tracker filters' target trajectory models and the sensors' observations are "noisy", yielding an algorithm robust even against maneuvering targets. Finally, owing to the fact
Enabling graphene nanoelectronics.
Pan, Wei; Ohta, Taisuke; Biedermann, Laura Butler; Gutierrez, Carlos; Nolen, C. M.; Howell, Stephen Wayne; Beechem Iii, Thomas Edwin; McCarty, Kevin F.; Ross, Anthony Joseph, III
2011-09-01
Recent work has shown that graphene, a 2D electronic material amenable to the planar semiconductor fabrication processing, possesses tunable electronic material properties potentially far superior to metals and other standard semiconductors. Despite its phenomenal electronic properties, focused research is still required to develop techniques for depositing and synthesizing graphene over large areas, thereby enabling the reproducible mass-fabrication of graphene-based devices. To address these issues, we combined an array of growth approaches and characterization resources to investigate several innovative and synergistic approaches for the synthesis of high quality graphene films on technologically relevant substrate (SiC and metals). Our work focused on developing the fundamental scientific understanding necessary to generate large-area graphene films that exhibit highly uniform electronic properties and record carrier mobility, as well as developing techniques to transfer graphene onto other substrates.
Algorithm To Design Finite-Field Normal-Basis Multipliers
NASA Technical Reports Server (NTRS)
Wang, Charles C.
1988-01-01
Way found to exploit Massey-Omura multiplication algorithm. Generalized algorithm locates normal basis in Galois filed GF(2m) and enables development of another algorithm to construct product function.
Low resource processing algorithms for laser Doppler blood flow imaging.
Nguyen, Hoang C; Hayes-Gill, Barrie R; Zhu, Yiqun; Crowe, John A; He, Diwei; Morgan, Stephen P
2011-07-01
The emergence of full field laser Doppler blood flow imaging systems based on CMOS camera technology means that a large amount of data from each pixel in the image needs to be processed rapidly and system resources need to be used efficiently. Conventional processing algorithms that are utilized in single point or scanning systems are therefore not an ideal solution as they will consume too much system resource. Two processing algorithms that address this problem are described and efficiently implemented in a field programmable gate array. The algorithms are simple enough to use low system resource but effective enough to produce accurate flow measurements. This enables the processing unit to be integrated entirely in an embedded system, such as in an application-specific integrated circuit. The first algorithm uses a short Fourier transformation length (typically 8) but averages the output multiple times (typically 128). The second method utilizes an infinite impulse response filter with a low number of filter coefficients that operates in the time domain and has a frequency-weighted response. The algorithms compare favorably with the reference standard 1024 point fast Fourier transform in terms of both resource usage and accuracy. The number of data words per pixel that need to be stored for the algorithms is 1024 for the reference standard, 8 for the short length Fourier transform algorithm and 5 for the algorithm based on the infinite impulse response filter. Compared to the reference standard the error in the flow calculation is 1.3% for the short length Fourier transform algorithm and 0.7% for the algorithm based on the infinite impulse response filter. PMID:21316289
Energy Science and Technology Software Center (ESTSC)
2005-03-30
The Robotic Follow Algorithm enables allows any robotic vehicle to follow a moving target while reactively choosing a route around nearby obstacles. The robotic follow behavior can be used with different camera systems and can be used with thermal or visual tracking as well as other tracking methods such as radio frequency tags.
Pelletier, Mathew G; Viera, Joseph A; Wanjura, John; Holt, Greg
2010-01-01
The use of microwave imaging is becoming more prevalent for detection of interior hidden defects in manufactured and packaged materials. In applications for detection of hidden moisture, microwave tomography can be used to image the material and then perform an inverse calculation to derive an estimate of the variability of the hidden material, such internal moisture, thereby alerting personnel to damaging levels of the hidden moisture before material degradation occurs. One impediment to this type of imaging occurs with nearby objects create strong reflections that create destructive and constructive interference, at the receiver, as the material is conveyed past the imaging antenna array. In an effort to remove the influence of the reflectors, such as metal bale ties, research was conducted to develop an algorithm for removal of the influence of the local proximity reflectors from the microwave images. This research effort produced a technique, based upon the use of ultra-wideband signals, for the removal of spurious reflections created by local proximity reflectors. This improvement enables accurate microwave measurements of moisture in such products as cotton bales, as well as other physical properties such as density or material composition. The proposed algorithm was shown to reduce errors by a 4:1 ratio and is an enabling technology for imaging applications in the presence of metal bale ties. PMID:22163668
Pelletier, Mathew G.; Viera, Joseph A.; Wanjura, John; Holt, Greg
2010-01-01
The use of microwave imaging is becoming more prevalent for detection of interior hidden defects in manufactured and packaged materials. In applications for detection of hidden moisture, microwave tomography can be used to image the material and then perform an inverse calculation to derive an estimate of the variability of the hidden material, such internal moisture, thereby alerting personnel to damaging levels of the hidden moisture before material degradation occurs. One impediment to this type of imaging occurs with nearby objects create strong reflections that create destructive and constructive interference, at the receiver, as the material is conveyed past the imaging antenna array. In an effort to remove the influence of the reflectors, such as metal bale ties, research was conducted to develop an algorithm for removal of the influence of the local proximity reflectors from the microwave images. This research effort produced a technique, based upon the use of ultra-wideband signals, for the removal of spurious reflections created by local proximity reflectors. This improvement enables accurate microwave measurements of moisture in such products as cotton bales, as well as other physical properties such as density or material composition. The proposed algorithm was shown to reduce errors by a 4:1 ratio and is an enabling technology for imaging applications in the presence of metal bale ties. PMID:22163668
Enabling distributed petascale science.
Baranovski, A.; Bharathi, S.; Bresnahan, J.; chervenak, A.; Foster, I.; Fraser, D.; Freeman, T.; Gunter, D.; Jackson, K.; Keahey, K.; Kesselman, C.; Konerding, D. E.; Leroy, N.; Link, M.; Livny, M.; Miller, N.; Miller, R.; Oleynik, G.; Pearlman, L.; Schopf, J. M.; Schuler, R.; Tierney, B.; Mathematics and Computer Science; FNL; Univ. of Southern California; Univ. of Chicago; LBNL; Univ. of Wisconsin
2007-01-01
Petascale science is an end-to-end endeavour, involving not only the creation of massive datasets at supercomputers or experimental facilities, but the subsequent analysis of that data by a user community that may be distributed across many laboratories and universities. The new SciDAC Center for Enabling Distributed Petascale Science (CEDPS) is developing tools to support this end-to-end process. These tools include data placement services for the reliable, high-performance, secure, and policy-driven placement of data within a distributed science environment; tools and techniques for the construction, operation, and provisioning of scalable science services; and tools for the detection and diagnosis of failures in end-to-end data placement and distributed application hosting configurations. In each area, we build on a strong base of existing technology and have made useful progress in the first year of the project. For example, we have recently achieved order-of-magnitude improvements in transfer times (for lots of small files) and implemented asynchronous data staging capabilities; demonstrated dynamic deployment of complex application stacks for the STAR experiment; and designed and deployed end-to-end troubleshooting services. We look forward to working with SciDAC application and technology projects to realize the promise of petascale science.
Enabling immersive simulation.
McCoy, Josh; Mateas, Michael; Hart, Derek H.; Whetzel, Jonathan; Basilico, Justin Derrick; Glickman, Matthew R.; Abbott, Robert G.
2009-02-01
The object of the 'Enabling Immersive Simulation for Complex Systems Analysis and Training' LDRD has been to research, design, and engineer a capability to develop simulations which (1) provide a rich, immersive interface for participation by real humans (exploiting existing high-performance game-engine technology wherever possible), and (2) can leverage Sandia's substantial investment in high-fidelity physical and cognitive models implemented in the Umbra simulation framework. We report here on these efforts. First, we describe the integration of Sandia's Umbra modular simulation framework with the open-source Delta3D game engine. Next, we report on Umbra's integration with Sandia's Cognitive Foundry, specifically to provide for learning behaviors for 'virtual teammates' directly from observed human behavior. Finally, we describe the integration of Delta3D with the ABL behavior engine, and report on research into establishing the theoretical framework that will be required to make use of tools like ABL to scale up to increasingly rich and realistic virtual characters.
Moser, Richard P.; Hesse, Bradford W.; Shaikh, Abdul R.; Courtney, Paul; Morgan, Glen; Augustson, Erik; Kobrin, Sarah; Levin, Kerry; Helba, Cynthia; Garner, David; Dunn, Marsha; Coa, Kisha
2011-01-01
Scientists are taking advantage of the Internet and collaborative web technology to accelerate discovery in a massively connected, participative environment —a phenomenon referred to by some as Science 2.0. As a new way of doing science, this phenomenon has the potential to push science forward in a more efficient manner than was previously possible. The Grid-Enabled Measures (GEM) database has been conceptualized as an instantiation of Science 2.0 principles by the National Cancer Institute with two overarching goals: (1) Promote the use of standardized measures, which are tied to theoretically based constructs; and (2) Facilitate the ability to share harmonized data resulting from the use of standardized measures. This is done by creating an online venue connected to the Cancer Biomedical Informatics Grid (caBIG®) where a virtual community of researchers can collaborate together and come to consensus on measures by rating, commenting and viewing meta-data about the measures and associated constructs. This paper will describe the web 2.0 principles on which the GEM database is based, describe its functionality, and discuss some of the important issues involved with creating the GEM database, such as the role of mutually agreed-on ontologies (i.e., knowledge categories and the relationships among these categories— for data sharing). PMID:21521586
The accurate assessment of small-angle X-ray scattering data
Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.
2015-01-01
A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality. Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.
The accurate assessment of small-angle X-ray scattering data
Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.
2015-01-23
Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less
The accurate assessment of small-angle X-ray scattering data
Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.
2015-01-23
Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.
The accurate assessment of small-angle X-ray scattering data
Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; Matsui, Tsutomu; Weiss, Thomas M.; Martel, Anne; Snell, Edward H.
2015-01-01
Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality. PMID:25615859
NASA Astrophysics Data System (ADS)
Bucci, Ovidio M.; Gennarelli, Claudio; Savarese, Catello
1991-01-01
An optimal sampling interpolation algorithm which allows the accurate recovery of plane-rectangular near-field samples from the knowledge of the plane-polar ones is developed. This enables the standard near field-far field (NF-FF) transformation, which takes full advantage of the FFT algorithm, to be applied to plane-polar scanning. The maximum allowable sample spacing is also rigorously derived, and it is shown that it can be significantly greater than lambda/2 as the measurement place moves away from the source. This allows a remarkable reduction of both measurement time and memory storage requirements. The sampling approach is compared with that based on the bivariate Lagrange interpolation (BLI) method. The sampling reconstruction agrees with the exact results significantly better than the BLI, in spite of the significantly lower number of required measurements.
Sreeskandarajan, Sutharzan; Flowers, Michelle M.; Karro, John E.; Liang, Chun
2014-01-01
Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA–protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs. Availability and implementation: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php) Contact: liangc@miamioh.edu or karroje@miamioh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24215021
Volume-preserving algorithm for secular relativistic dynamics of charged particles
Zhang, Ruili; Liu, Jian; Wang, Yulei; He, Yang; Qin, Hong; Sun, Yajuan
2015-04-15
Secular dynamics of relativistic charged particles has theoretical significance and a wide range of applications. However, conventional algorithms are not applicable to this problem due to the coherent accumulation of numerical errors. To overcome this difficulty, we develop a volume-preserving algorithm (VPA) with long-term accuracy and conservativeness via a systematic splitting method. Applied to the simulation of runaway electrons with a time-span over 10 magnitudes, the VPA generates accurate results and enables the discovery of new physics for secular runaway dynamics.
Enabling cleanup technology transfer.
Ditmars, J. D.
2002-08-12
Technology transfer in the environmental restoration, or cleanup, area has been challenging. While there is little doubt that innovative technologies are needed to reduce the times, risks, and costs associated with the cleanup of federal sites, particularly those of the Departments of Energy (DOE) and Defense, the use of such technologies in actual cleanups has been relatively limited. There are, of course, many reasons why technologies do not reach the implementation phase or do not get transferred from developing entities to the user community. For example, many past cleanup contracts provided few incentives for performance that would compel a contractor to seek improvement via technology applications. While performance-based contracts are becoming more common, they alone will not drive increased technology applications. This paper focuses on some applications of cleanup methodologies and technologies that have been successful and are illustrative of a more general principle. The principle is at once obvious and not widely practiced. It is that, with few exceptions, innovative cleanup technologies are rarely implemented successfully alone but rather are implemented in the context of enabling processes and methodologies. And, since cleanup is conducted in a regulatory environment, the stage is better set for technology transfer when the context includes substantive interactions with the relevant stakeholders. Examples of this principle are drawn from Argonne National Laboratory's experiences in Adaptive Sampling and Analysis Programs (ASAPs), Precise Excavation, and the DOE Technology Connection (TechCon) Program. The lessons learned may be applicable to the continuing challenges posed by the cleanup and long-term stewardship of radioactive contaminants and unexploded ordnance (UXO) at federal sites.
NNLOPS accurate associated HW production
NASA Astrophysics Data System (ADS)
Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia
2016-06-01
We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.
Visell, Yon
2015-04-01
This paper proposes a fast, physically accurate method for synthesizing multimodal, acoustic and haptic, signatures of distributed fracture in quasi-brittle heterogeneous materials, such as wood, granular media, or other fiber composites. Fracture processes in these materials are challenging to simulate with existing methods, due to the prevalence of large numbers of disordered, quasi-random spatial degrees of freedom, representing the complex physical state of a sample over the geometric volume of interest. Here, I develop an algorithm for simulating such processes, building on a class of statistical lattice models of fracture that have been widely investigated in the physics literature. This algorithm is enabled through a recently published mathematical construction based on the inverse transform method of random number sampling. It yields a purely time domain stochastic jump process representing stress fluctuations in the medium. The latter can be readily extended by a mean field approximation that captures the averaged constitutive (stress-strain) behavior of the material. Numerical simulations and interactive examples demonstrate the ability of these algorithms to generate physically plausible acoustic and haptic signatures of fracture in complex, natural materials interactively at audio sampling rates. PMID:26357094
Accurate 3-D finite difference computation of traveltimes in strongly heterogeneous media
NASA Astrophysics Data System (ADS)
Noble, M.; Gesret, A.; Belayouni, N.
2014-12-01
Seismic traveltimes and their spatial derivatives are the basis of many imaging methods such as pre-stack depth migration and tomography. A common approach to compute these quantities is to solve the eikonal equation with a finite-difference scheme. If many recently published algorithms for resolving the eikonal equation do now yield fairly accurate traveltimes for most applications, the spatial derivatives of traveltimes remain very approximate. To address this accuracy issue, we develop a new hybrid eikonal solver that combines a spherical approximation when close to the source and a plane wave approximation when far away. This algorithm reproduces properly the spherical behaviour of wave fronts in the vicinity of the source. We implement a combination of 16 local operators that enables us to handle velocity models with sharp vertical and horizontal velocity contrasts. We associate to these local operators a global fast sweeping method to take into account all possible directions of wave propagation. Our formulation allows us to introduce a variable grid spacing in all three directions of space. We demonstrate the efficiency of this algorithm in terms of computational time and the gain in accuracy of the computed traveltimes and their derivatives on several numerical examples.
FOILFEST :community enabled security.
Moore, Judy Hennessey; Johnson, Curtis Martin; Whitley, John B.; Drayer, Darryl Donald; Cummings, John C., Jr.
2005-09-01
The Advanced Concepts Group of Sandia National Laboratories hosted a workshop, ''FOILFest: Community Enabled Security'', on July 18-21, 2005, in Albuquerque, NM. This was a far-reaching look into the future of physical protection consisting of a series of structured brainstorming sessions focused on preventing and foiling attacks on public places and soft targets such as airports, shopping malls, hotels, and public events. These facilities are difficult to protect using traditional security devices since they could easily be pushed out of business through the addition of arduous and expensive security measures. The idea behind this Fest was to explore how the public, which is vital to the function of these institutions, can be leveraged as part of a physical protection system. The workshop considered procedures, space design, and approaches for building community through technology. The workshop explored ways to make the ''good guys'' in public places feel safe and be vigilant while making potential perpetrators of harm feel exposed and convinced that they will not succeed. Participants in the Fest included operators of public places, social scientists, technology experts, representatives of government agencies including DHS and the intelligence community, writers and media experts. Many innovative ideas were explored during the fest with most of the time spent on airports, including consideration of the local airport, the Albuquerque Sunport. Some provocative ideas included: (1) sniffers installed in passage areas like revolving door, escalators, (2) a ''jumbotron'' showing current camera shots in the public space, (3) transparent portal screeners allowing viewing of the screening, (4) a layered open/funnel/open/funnel design where open spaces are used to encourage a sense of ''communitas'' and take advantage of citizen ''sensing'' and funnels are technological tunnels of sensors (the tunnels of truth), (5) curved benches with blast proof walls or backs, (6
Blind Alley Aware ACO Routing Algorithm
NASA Astrophysics Data System (ADS)
Yoshikawa, Masaya; Otani, Kazuo
2010-10-01
The routing problem is applied to various engineering fields. Many researchers study this problem. In this paper, we propose a new routing algorithm which is based on Ant Colony Optimization. The proposed algorithm introduces the tabu search mechanism to escape the blind alley. Thus, the proposed algorithm enables to find the shortest route, even if the map data contains the blind alley. Experiments using map data prove the effectiveness in comparison with Dijkstra algorithm which is the most popular conventional routing algorithm.
Accurate phase-shift velocimetry in rock.
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139
Accurate phase-shift velocimetry in rock
NASA Astrophysics Data System (ADS)
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.
How to accurately bypass damage
Broyde, Suse; Patel, Dinshaw J.
2016-01-01
Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203
Ultra-accurate collaborative information filtering via directed user similarity
NASA Astrophysics Data System (ADS)
Guo, Q.; Song, W.-J.; Liu, J.-G.
2014-07-01
A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones in opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random walks proposed by Liu et al. (Int. J. Mod. Phys. C, 20 (2009) 285) the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3% and 19.1% for MovieLens and Netflix, respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.
Accurate Evaluation of Quantum Integrals
NASA Technical Reports Server (NTRS)
Galant, David C.; Goorvitch, D.
1994-01-01
Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.
Enabling R&D for accurate simulation of non-ideal explosives.
Aidun, John Bahram; Thompson, Aidan Patrick; Schmitt, Robert Gerard
2010-09-01
We implemented two numerical simulation capabilities essential to reliably predicting the effect of non-ideal explosives (NXs). To begin to be able to treat the multiple, competing, multi-step reaction paths and slower kinetics of NXs, Sandia's CTH shock physics code was extended to include the TIGER thermochemical equilibrium solver as an in-line routine. To facilitate efficient exploration of reaction pathways that need to be identified for the CTH simulations, we implemented in Sandia's LAMMPS molecular dynamics code the MSST method, which is a reactive molecular dynamics technique for simulating steady shock wave response. Our preliminary demonstrations of these two capabilities serve several purposes: (i) they demonstrate proof-of-principle for our approach; (ii) they provide illustration of the applicability of the new functionality; and (iii) they begin to characterize the use of the new functionality and identify where improvements will be needed for the ultimate capability to meet national security needs. Next steps are discussed.
Enabling accurate photodiode detection of multiple optical traps by spatial filtering
NASA Astrophysics Data System (ADS)
Ott, Dino; Reihani, S. Nader S.; Oddershede, Lene B.
2014-09-01
Dual and multiple beam optical tweezers allow for advanced trapping geometries beyond single traps, however, these increased manipulation capabilities, usually complicate the detection of position and force. The accuracy of position and force measurements is often compromised by crosstalk between the detected signals, this crosstalk leading to a systematic error on the measured forces and distances. In dual-beam optical trapping setups, the two traps are typically orthogonal polarized and crosstalk can be minimized by inserting polarization optics in front of the detector, however, this method is not perfect because of the de-polarization of the trapping beam introduced by the required high numerical aperture optics. Moreover, the restriction to two orthogonal polarisation states limits the number of detectable traps to two. Here, we present an easy-to-implement simple method to efficiently eliminate cross-talk in dual beam setups.1 The technique is based on spatial filtering and is highly compatible with standard back-focal-plane photodiode based detection. The reported method significantly improves the accuracy of force-distance measurements, e.g., of single molecules, hence providing much more scientific value for the experimental efforts. Furthermore, it opens the possibility for fast and simultaneous photodiode based detection of multiple holographically generated optical traps.
Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method
Sinha, Debalina; Pavanello, Michele
2015-08-28
The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.
Efficient and accurate computation of generalized singular-value decompositions
NASA Astrophysics Data System (ADS)
Drmac, Zlatko
2001-11-01
We present a new family of algorithms for accurate floating--point computation of the singular value decomposition (SVD) of various forms of products (quotients) of two or three matrices. The main goal of such an algorithm is to compute all singular values to high relative accuracy. This means that we are seeking guaranteed number of accurate digits even in the smallest singular values. We also want to achieve computational efficiency, while maintaining high accuracy. To illustrate, consider the SVD of the product A=BTSC. The new algorithm uses certain preconditioning (based on diagonal scalings, the LU and QR factorizations) to replace A with A'=(B')TS'C', where A and A' have the same singular values and the matrix A' is computed explicitly. Theoretical analysis and numerical evidence show that, in the case of full rank B, C, S, the accuracy of the new algorithm is unaffected by replacing B, S, C with, respectively, D1B, D2SD3, D4C, where Di, i=1,...,4 are arbitrary diagonal matrices. As an application, the paper proposes new accurate algorithms for computing the (H,K)-SVD and (H1,K)-SVD of S.
Camera-enabled techniques for organic synthesis
Ingham, Richard J; O’Brien, Matthew; Browne, Duncan L
2013-01-01
Summary A great deal of time is spent within synthetic chemistry laboratories on non-value-adding activities such as sample preparation and work-up operations, and labour intensive activities such as extended periods of continued data collection. Using digital cameras connected to computer vision algorithms, camera-enabled apparatus can perform some of these processes in an automated fashion, allowing skilled chemists to spend their time more productively. In this review we describe recent advances in this field of chemical synthesis and discuss how they will lead to advanced synthesis laboratories of the future. PMID:23766820
Practical aspects of spatially high accurate methods
NASA Technical Reports Server (NTRS)
Godfrey, Andrew G.; Mitchell, Curtis R.; Walters, Robert W.
1992-01-01
The computational qualities of high order spatially accurate methods for the finite volume solution of the Euler equations are presented. Two dimensional essentially non-oscillatory (ENO), k-exact, and 'dimension by dimension' ENO reconstruction operators are discussed and compared in terms of reconstruction and solution accuracy, computational cost and oscillatory behavior in supersonic flows with shocks. Inherent steady state convergence difficulties are demonstrated for adaptive stencil algorithms. An exact solution to the heat equation is used to determine reconstruction error, and the computational intensity is reflected in operation counts. Standard MUSCL differencing is included for comparison. Numerical experiments presented include the Ringleb flow for numerical accuracy and a shock reflection problem. A vortex-shock interaction demonstrates the ability of the ENO scheme to excel in simulating unsteady high-frequency flow physics.
Solar Occultation Retrieval Algorithm Development
NASA Technical Reports Server (NTRS)
Lumpe, Jerry D.
2004-01-01
This effort addresses the comparison and validation of currently operational solar occultation retrieval algorithms, and the development of generalized algorithms for future application to multiple platforms. initial development of generalized forward model algorithms capable of simulating transmission data from of the POAM II/III and SAGE II/III instruments. Work in the 2" quarter will focus on: completion of forward model algorithms, including accurate spectral characteristics for all instruments, and comparison of simulated transmission data with actual level 1 instrument data for specific occultation events.
Robust, accurate and fast automatic segmentation of the spinal cord.
De Leener, Benjamin; Kadoury, Samuel; Cohen-Adad, Julien
2014-09-01
Spinal cord segmentation provides measures of atrophy and facilitates group analysis via inter-subject correspondence. Automatizing this procedure enables studies with large throughput and minimizes user bias. Although several automatic segmentation methods exist, they are often restricted in terms of image contrast and field-of-view. This paper presents a new automatic segmentation method (PropSeg) optimized for robustness, accuracy and speed. The algorithm is based on the propagation of a deformable model and is divided into three parts: firstly, an initialization step detects the spinal cord position and orientation using a circular Hough transform on multiple axial slices rostral and caudal to the starting plane and builds an initial elliptical tubular mesh. Secondly, a low-resolution deformable model is propagated along the spinal cord. To deal with highly variable contrast levels between the spinal cord and the cerebrospinal fluid, the deformation is coupled with a local contrast-to-noise adaptation at each iteration. Thirdly, a refinement process and a global deformation are applied on the propagated mesh to provide an accurate segmentation of the spinal cord. Validation was performed in 15 healthy subjects and two patients with spinal cord injury, using T1- and T2-weighted images of the entire spinal cord and on multiecho T2*-weighted images. Our method was compared against manual segmentation and against an active surface method. Results show high precision for all the MR sequences. Dice coefficients were 0.9 for the T1- and T2-weighted cohorts and 0.86 for the T2*-weighted images. The proposed method runs in less than 1min on a normal computer and can be used to quantify morphological features such as cross-sectional area along the whole spinal cord. PMID:24780696
Method and system for enabling real-time speckle processing using hardware platforms
NASA Technical Reports Server (NTRS)
Ortiz, Fernando E. (Inventor); Kelmelis, Eric (Inventor); Durbano, James P. (Inventor); Curt, Peterson F. (Inventor)
2012-01-01
An accelerator for the speckle atmospheric compensation algorithm may enable real-time speckle processing of video feeds that may enable the speckle algorithm to be applied in numerous real-time applications. The accelerator may be implemented in various forms, including hardware, software, and/or machine-readable media.
Accurate Thermal Stresses for Beams: Normal Stress
NASA Technical Reports Server (NTRS)
Johnson, Theodore F.; Pilkey, Walter D.
2003-01-01
Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.
Accurate Thermal Stresses for Beams: Normal Stress
NASA Technical Reports Server (NTRS)
Johnson, Theodore F.; Pilkey, Walter D.
2002-01-01
Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.
Toward Accurate and Quantitative Comparative Metagenomics.
Nayfach, Stephen; Pollard, Katherine S
2016-08-25
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341
Accurate Prediction of Docked Protein Structure Similarity.
Akbal-Delibas, Bahar; Pomplun, Marc; Haspel, Nurit
2015-09-01
One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin. PMID:26335807
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
Accurate radiative transfer calculations for layered media.
Selden, Adrian C
2016-07-01
Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700
Power spectral estimation algorithms
NASA Technical Reports Server (NTRS)
Bhatia, Manjit S.
1989-01-01
Algorithms to estimate the power spectrum using Maximum Entropy Methods were developed. These algorithms were coded in FORTRAN 77 and were implemented on the VAX 780. The important considerations in this analysis are: (1) resolution, i.e., how close in frequency two spectral components can be spaced and still be identified; (2) dynamic range, i.e., how small a spectral peak can be, relative to the largest, and still be observed in the spectra; and (3) variance, i.e., how accurate the estimate of the spectra is to the actual spectra. The application of the algorithms based on Maximum Entropy Methods to a variety of data shows that these criteria are met quite well. Additional work in this direction would help confirm the findings. All of the software developed was turned over to the technical monitor. A copy of a typical program is included. Some of the actual data and graphs used on this data are also included.
Algorithms and Requirements for Measuring Network Bandwidth
Jin, Guojun
2002-12-08
This report unveils new algorithms for actively measuring (not estimating) available bandwidths with very low intrusion, computing cross traffic, thus estimating the physical bandwidth, provides mathematical proof that the algorithms are accurate, and addresses conditions, requirements, and limitations for new and existing algorithms for measuring network bandwidths. The paper also discusses a number of important terminologies and issues for network bandwidth measurement, and introduces a fundamental parameter -Maximum Burst Size that is critical for implementing algorithms based on multiple packets.
Toward genome-enabled mycology.
Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W
2013-01-01
Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data. PMID:23928422
The Superior Lambert Algorithm
NASA Astrophysics Data System (ADS)
der, G.
2011-09-01
Lambert algorithms are used extensively for initial orbit determination, mission planning, space debris correlation, and missile targeting, just to name a few applications. Due to the significance of the Lambert problem in Astrodynamics, Gauss, Battin, Godal, Lancaster, Gooding, Sun and many others (References 1 to 15) have provided numerous formulations leading to various analytic solutions and iterative methods. Most Lambert algorithms and their computer programs can only work within one revolution, break down or converge slowly when the transfer angle is near zero or 180 degrees, and their multi-revolution limitations are either ignored or barely addressed. Despite claims of robustness, many Lambert algorithms fail without notice, and the users seldom have a clue why. The DerAstrodynamics lambert2 algorithm, which is based on the analytic solution formulated by Sun, works for any number of revolutions and converges rapidly at any transfer angle. It provides significant capability enhancements over every other Lambert algorithm in use today. These include improved speed, accuracy, robustness, and multirevolution capabilities as well as implementation simplicity. Additionally, the lambert2 algorithm provides a powerful tool for solving the angles-only problem without artificial singularities (pointed out by Gooding in Reference 16), which involves 3 lines of sight captured by optical sensors, or systems such as the Air Force Space Surveillance System (AFSSS). The analytic solution is derived from the extended Godal’s time equation by Sun, while the iterative method of solution is that of Laguerre, modified for robustness. The Keplerian solution of a Lambert algorithm can be extended to include the non-Keplerian terms of the Vinti algorithm via a simple targeting technique (References 17 to 19). Accurate analytic non-Keplerian trajectories can be predicted for satellites and ballistic missiles, while performing at least 100 times faster in speed than most
Technology Enabling the First 100 Exoplanets
NASA Astrophysics Data System (ADS)
Marcy, Geoffrey W.
2014-01-01
The discoveries of the first 100 exoplanets by precise radial velocities in the late 1990's at Lick Observatory and Observatoire de Haute-Provence were enabled by several technological advances and a cultural one. A key ingredient was a cross-dispersed echelle spectrometer at a stable, coude focus, with a CCD detector, offering high spectral resolution, large wavelength coverage, and a linear response to photons. A second ingredient was a computer capable of storing the megabyte images from such spectrometers and analyzing them for Doppler shifts. Both Lick and OHP depended on these advents. A third ingredient was a stable wavelength calibration. Here, two technologies emerged independently, with iodine gas employed by Marcy's group (used first by solar physicists doing helioseismology) and simultaneous thorium-argon spectra (enabled by fiber optics) used by Mayor's group. A final ingredient was a new culture emerging in the 1990's of forward-modeling of spectra on computers, enabled by the well-behaved photon noise of CCDs, giving Poisson errors amenable to rigorous statistical algorithms for measuring millipixel Doppler shifts. The prospect of detecting the 12 meter/sec reflex velocity (1/100 pixel) of a Jupiter-like planet was considered impossible, except to a few who asked, "What actually limits Doppler precision?". Inspired insights were provided by Robert Howard, Paul Schechter, Bruce Campbell, and Gordon Walker, leading to the first 100 exoplanets.
An algorithm to discover gene signatures with predictive potential
2010-01-01
Background The advent of global gene expression profiling has generated unprecedented insight into our molecular understanding of cancer, including breast cancer. For example, human breast cancer patients display significant diversity in terms of their survival, recurrence, metastasis as well as response to treatment. These patient outcomes can be predicted by the transcriptional programs of their individual breast tumors. Predictive gene signatures allow us to correctly classify human breast tumors into various risk groups as well as to more accurately target therapy to ensure more durable cancer treatment. Results Here we present a novel algorithm to generate gene signatures with predictive potential. The method first classifies the expression intensity for each gene as determined by global gene expression profiling as low, average or high. The matrix containing the classified data for each gene is then used to score the expression of each gene based its individual ability to predict the patient characteristic of interest. Finally, all examined genes are ranked based on their predictive ability and the most highly ranked genes are included in the master gene signature, which is then ready for use as a predictor. This method was used to accurately predict the survival outcomes in a cohort of human breast cancer patients. Conclusions We confirmed the capacity of our algorithm to generate gene signatures with bona fide predictive ability. The simplicity of our algorithm will enable biological researchers to quickly generate valuable gene signatures without specialized software or extensive bioinformatics training. PMID:20813028
NASA Astrophysics Data System (ADS)
Tang, Jie; Nett, Brian E.; Chen, Guang-Hong
2009-10-01
Of all available reconstruction methods, statistical iterative reconstruction algorithms appear particularly promising since they enable accurate physical noise modeling. The newly developed compressive sampling/compressed sensing (CS) algorithm has shown the potential to accurately reconstruct images from highly undersampled data. The CS algorithm can be implemented in the statistical reconstruction framework as well. In this study, we compared the performance of two standard statistical reconstruction algorithms (penalized weighted least squares and q-GGMRF) to the CS algorithm. In assessing the image quality using these iterative reconstructions, it is critical to utilize realistic background anatomy as the reconstruction results are object dependent. A cadaver head was scanned on a Varian Trilogy system at different dose levels. Several figures of merit including the relative root mean square error and a quality factor which accounts for the noise performance and the spatial resolution were introduced to objectively evaluate reconstruction performance. A comparison is presented between the three algorithms for a constant undersampling factor comparing different algorithms at several dose levels. To facilitate this comparison, the original CS method was formulated in the framework of the statistical image reconstruction algorithms. Important conclusions of the measurements from our studies are that (1) for realistic neuro-anatomy, over 100 projections are required to avoid streak artifacts in the reconstructed images even with CS reconstruction, (2) regardless of the algorithm employed, it is beneficial to distribute the total dose to more views as long as each view remains quantum noise limited and (3) the total variation-based CS method is not appropriate for very low dose levels because while it can mitigate streaking artifacts, the images exhibit patchy behavior, which is potentially harmful for medical diagnosis.
A fast and accurate decoder for underwater acoustic telemetry
NASA Astrophysics Data System (ADS)
Ingraham, J. M.; Deng, Z. D.; Li, X.; Fu, T.; McMichael, G. A.; Trumbo, B. A.
2014-07-01
The Juvenile Salmon Acoustic Telemetry System, developed by the U.S. Army Corps of Engineers, Portland District, has been used to monitor the survival of juvenile salmonids passing through hydroelectric facilities in the Federal Columbia River Power System. Cabled hydrophone arrays deployed at dams receive coded transmissions sent from acoustic transmitters implanted in fish. The signals' time of arrival on different hydrophones is used to track fish in 3D. In this article, a new algorithm that decodes the received transmissions is described and the results are compared to results for the previous decoding algorithm. In a laboratory environment, the new decoder was able to decode signals with lower signal strength than the previous decoder, effectively increasing decoding efficiency and range. In field testing, the new algorithm decoded significantly more signals than the previous decoder and three-dimensional tracking experiments showed that the new decoder's time-of-arrival estimates were accurate. At multiple distances from hydrophones, the new algorithm tracked more points more accurately than the previous decoder. The new algorithm was also more than 10 times faster, which is critical for real-time applications on an embedded system.
A fast and accurate decoder for underwater acoustic telemetry.
Ingraham, J M; Deng, Z D; Li, X; Fu, T; McMichael, G A; Trumbo, B A
2014-07-01
The Juvenile Salmon Acoustic Telemetry System, developed by the U.S. Army Corps of Engineers, Portland District, has been used to monitor the survival of juvenile salmonids passing through hydroelectric facilities in the Federal Columbia River Power System. Cabled hydrophone arrays deployed at dams receive coded transmissions sent from acoustic transmitters implanted in fish. The signals' time of arrival on different hydrophones is used to track fish in 3D. In this article, a new algorithm that decodes the received transmissions is described and the results are compared to results for the previous decoding algorithm. In a laboratory environment, the new decoder was able to decode signals with lower signal strength than the previous decoder, effectively increasing decoding efficiency and range. In field testing, the new algorithm decoded significantly more signals than the previous decoder and three-dimensional tracking experiments showed that the new decoder's time-of-arrival estimates were accurate. At multiple distances from hydrophones, the new algorithm tracked more points more accurately than the previous decoder. The new algorithm was also more than 10 times faster, which is critical for real-time applications on an embedded system. PMID:25085162
JPSS CGS Tools For Rapid Algorithm Updates
NASA Astrophysics Data System (ADS)
Smith, D. C.; Grant, K. D.
2011-12-01
Northrop Grumman have developed tools and processes to enable changes to be evaluated, tested, and moved into the operational baseline in a rapid and efficient manner. This presentation will provide an overview of the tools available to the Cal/Val teams to ensure rapid and accurate assessment of algorithm changes, along with the processes in place to ensure baseline integrity. [1] K. Grant and G. Route, "JPSS CGS Tools for Rapid Algorithm Updates," NOAA 2011 Satellite Direct Readout Conference, Miami FL, Poster, Apr 2011. [2] K. Grant, G. Route and B. Reed, "JPSS CGS Tools for Rapid Algorithm Updates," AMS 91st Annual Meeting, Seattle WA, Poster, Jan 2011. [3] K. Grant, G. Route and B. Reed, "JPSS CGS Tools for Rapid Algorithm Updates," AGU 2010 Fall Meeting, San Francisco CA, Oral Presentation, Dec 2010.
PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
Livne, Oren E.; Han, Lide; Alkorta-Aranburu, Gorka; Wentworth-Sheilds, William; Abney, Mark; Ober, Carole; Nicolae, Dan L.
2015-01-01
Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm), a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD) segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs), from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost. PMID:25735005
Development of an Interval Management Algorithm Using Ground Speed Feedback for Delayed Traffic
NASA Technical Reports Server (NTRS)
Barmore, Bryan E.; Swieringa, Kurt A.; Underwood, Matthew C.; Abbott, Terence; Leonard, Robert D.
2016-01-01
One of the goals of NextGen is to enable frequent use of Optimized Profile Descents (OPD) for aircraft, even during periods of peak traffic demand. NASA is currently testing three new technologies that enable air traffic controllers to use speed adjustments to space aircraft during arrival and approach operations. This will allow an aircraft to remain close to their OPD. During the integration of these technologies, it was discovered that, due to a lack of accurate trajectory information for the leading aircraft, Interval Management aircraft were exhibiting poor behavior. NASA's Interval Management algorithm was modified to address the impact of inaccurate trajectory information and a series of studies were performed to assess the impact of this modification. These studies show that the modification provided some improvement when the Interval Management system lacked accurate trajectory information for the leading aircraft.
Accurate mask registration on tilted lines for 6F2 DRAM manufacturing
NASA Astrophysics Data System (ADS)
Roeth, K. D.; Choi, W.; Lee, Y.; Kim, S.; Yim, D.; Laske, F.; Ferber, M.; Daneshpanah, M.; Kwon, E.
2015-10-01
193nm immersion lithography is the mainstream production technology for the 22nm half pitch (HP) DRAM manufacturing. Considering multi-patterning as the technology to solve the very low k1 situation in the resolution equation puts extreme pressure on the intra-field overlay, to which mask registration error may be a significant error contributor [3]. The International Technology Roadmap for Semiconductors (ITRS [1]) requests a registration error below 4 nm for each mask of a multi-patterning set forming one layer on the wafer. For mask metrology at the 22nm HP node, maintaining a precision-to-tolerance (P/T) ratio below 0.25 will be very challenging. Mask registration error impacts intra-field wafer overlay directly and has a major impact on wafer yield. DRAM makers moved several years ago to 6F2 (figure 1, [2]) cell design and thus printing tilted lines at 15 or 30 degree. Overlay of contact layer over buried line has to be well controlled. However, measuring mask registration performance accurately on tilted lines was a challenge. KLA Tencor applied the model-based algorithm to enable the accurate registration measurement of tilted lines on the Poly layer as well as the mask-to-mask overlay to the adjacent contact layers. The metrology solution is discussed and measurement results are provided.
NASA Astrophysics Data System (ADS)
Wohlfeil, J.; Hirschmüller, H.; Piltz, B.; Börner, A.; Suppa, M.
2012-07-01
Modern pixel-wise image matching algorithms like Semi-Global Matching (SGM) are able to compute high resolution digital surface models from airborne and spaceborne stereo imagery. Although image matching itself can be performed automatically, there are prerequisites, like high geometric accuracy, which are essential for ensuring the high quality of resulting surface models. Especially for line cameras, these prerequisites currently require laborious manual interaction using standard tools, which is a growing problem due to continually increasing demand for such surface models. The tedious work includes partly or fully manual selection of tie- and/or ground control points for ensuring the required accuracy of the relative orientation of images for stereo matching. It also includes masking of large water areas that seriously reduce the quality of the results. Furthermore, a good estimate of the depth range is required, since accurate estimates can seriously reduce the processing time for stereo matching. In this paper an approach is presented that allows performing all these steps fully automated. It includes very robust and precise tie point selection, enabling the accurate calculation of the images' relative orientation via bundle adjustment. It is also shown how water masking and elevation range estimation can be performed automatically on the base of freely available SRTM data. Extensive tests with a large number of different satellite images from QuickBird and WorldView are presented as proof of the robustness and reliability of the proposed method.
Algorithms Could Automate Cancer Diagnosis
NASA Technical Reports Server (NTRS)
Baky, A. A.; Winkler, D. G.
1982-01-01
Five new algorithms are a complete statistical procedure for quantifying cell abnormalities from digitized images. Procedure could be basis for automated detection and diagnosis of cancer. Objective of procedure is to assign each cell an atypia status index (ASI), which quantifies level of abnormality. It is possible that ASI values will be accurate and economical enough to allow diagnoses to be made quickly and accurately by computer processing of laboratory specimens extracted from patients.
NASA Astrophysics Data System (ADS)
Abrams, Daniel S.
This thesis describes several new quantum algorithms. These include a polynomial time algorithm that uses a quantum fast Fourier transform to find eigenvalues and eigenvectors of a Hamiltonian operator, and that can be applied in cases (commonly found in ab initio physics and chemistry problems) for which all known classical algorithms require exponential time. Fast algorithms for simulating many body Fermi systems are also provided in both first and second quantized descriptions. An efficient quantum algorithm for anti-symmetrization is given as well as a detailed discussion of a simulation of the Hubbard model. In addition, quantum algorithms that calculate numerical integrals and various characteristics of stochastic processes are described. Two techniques are given, both of which obtain an exponential speed increase in comparison to the fastest known classical deterministic algorithms and a quadratic speed increase in comparison to classical Monte Carlo (probabilistic) methods. I derive a simpler and slightly faster version of Grover's mean algorithm, show how to apply quantum counting to the problem, develop some variations of these algorithms, and show how both (apparently distinct) approaches can be understood from the same unified framework. Finally, the relationship between physics and computation is explored in some more depth, and it is shown that computational complexity theory depends very sensitively on physical laws. In particular, it is shown that nonlinear quantum mechanics allows for the polynomial time solution of NP-complete and #P oracle problems. Using the Weinberg model as a simple example, the explicit construction of the necessary gates is derived from the underlying physics. Nonlinear quantum algorithms are also presented using Polchinski type nonlinearities which do not allow for superluminal communication. (Copies available exclusively from MIT Libraries, Rm. 14- 0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Computer Security Systems Enable Access.
ERIC Educational Resources Information Center
Riggen, Gary
1989-01-01
A good security system enables access and protects information from damage or tampering, but the most important aspects of a security system aren't technical. A security procedures manual addresses the human element of computer security. (MLW)
Enabling Space Science and Exploration
NASA Technical Reports Server (NTRS)
Weber, William J.
2006-01-01
This viewgraph presentation on enabling space science and exploration covers the following topics: 1) Today s Deep Space Network; 2) Next Generation Deep Space Network; 3) Needed technologies; 4) Mission IT and networking; and 5) Multi-mission operations.
NASA Astrophysics Data System (ADS)
Chen, Peng; Quarteroni, Alfio
2015-10-01
In this work we develop an adaptive and reduced computational algorithm based on dimension-adaptive sparse grid approximation and reduced basis methods for solving high-dimensional uncertainty quantification (UQ) problems. In order to tackle the computational challenge of "curse of dimensionality" commonly faced by these problems, we employ a dimension-adaptive tensor-product algorithm [16] and propose a verified version to enable effective removal of the stagnation phenomenon besides automatically detecting the importance and interaction of different dimensions. To reduce the heavy computational cost of UQ problems modelled by partial differential equations (PDE), we adopt a weighted reduced basis method [7] and develop an adaptive greedy algorithm in combination with the previous verified algorithm for efficient construction of an accurate reduced basis approximation. The efficiency and accuracy of the proposed algorithm are demonstrated by several numerical experiments.
Towards Accurate Application Characterization for Exascale (APEX)
Hammond, Simon David
2015-09-01
Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns. Primarily the research was to intended to focus on generating accurate and reproducible low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.
Note-accurate audio segmentation based on MPEG-7
NASA Astrophysics Data System (ADS)
Wellhausen, Jens
2003-12-01
Segmenting audio data into the smallest musical components is the basis for many further meta data extraction algorithms. For example, an automatic music transcription system needs to know where the exact boundaries of each tone are. In this paper a note accurate audio segmentation algorithm based on MPEG-7 low level descriptors is introduced. For a reliable detection of different notes, both features in the time and the frequency domain are used. Because of this, polyphonic instrument mixes and even melodies characterized by human voices can be examined with this alogrithm. For testing and verification of the note accurate segmentation, a simple music transcription system was implemented. The dominant frequency within each segment is used to build a MIDI file representing the processed audio data.
NASA Astrophysics Data System (ADS)
Saenz, Daniel L.; Kim, Hojin; Chen, Josephine; Stathakis, Sotirios; Kirby, Neil
2016-09-01
The primary purpose of the study was to determine how detailed deformable image registration (DIR) phantoms need to adequately simulate human anatomy and accurately assess the quality of DIR algorithms. In particular, how many distinct tissues are required in a phantom to simulate complex human anatomy? Pelvis and head-and-neck patient CT images were used for this study as virtual phantoms. Two data sets from each site were analyzed. The virtual phantoms were warped to create two pairs consisting of undeformed and deformed images. Otsu’s method was employed to create additional segmented image pairs of n distinct soft tissue CT number ranges (fat, muscle, etc). A realistic noise image was added to each image. Deformations were applied in MIM Software (MIM) and Velocity deformable multi-pass (DMP) and compared with the known warping. Images with more simulated tissue levels exhibit more contrast, enabling more accurate results. Deformation error (magnitude of the vector difference between known and predicted deformation) was used as a metric to evaluate how many CT number gray levels are needed for a phantom to serve as a realistic patient proxy. Stabilization of the mean deformation error was reached by three soft tissue levels for Velocity DMP and MIM, though MIM exhibited a persisting difference in accuracy between the discrete images and the unprocessed image pair. A minimum detail of three levels allows a realistic patient proxy for use with Velocity and MIM deformation algorithms.
Saenz, Daniel L; Kim, Hojin; Chen, Josephine; Stathakis, Sotirios; Kirby, Neil
2016-09-01
The primary purpose of the study was to determine how detailed deformable image registration (DIR) phantoms need to adequately simulate human anatomy and accurately assess the quality of DIR algorithms. In particular, how many distinct tissues are required in a phantom to simulate complex human anatomy? Pelvis and head-and-neck patient CT images were used for this study as virtual phantoms. Two data sets from each site were analyzed. The virtual phantoms were warped to create two pairs consisting of undeformed and deformed images. Otsu's method was employed to create additional segmented image pairs of n distinct soft tissue CT number ranges (fat, muscle, etc). A realistic noise image was added to each image. Deformations were applied in MIM Software (MIM) and Velocity deformable multi-pass (DMP) and compared with the known warping. Images with more simulated tissue levels exhibit more contrast, enabling more accurate results. Deformation error (magnitude of the vector difference between known and predicted deformation) was used as a metric to evaluate how many CT number gray levels are needed for a phantom to serve as a realistic patient proxy. Stabilization of the mean deformation error was reached by three soft tissue levels for Velocity DMP and MIM, though MIM exhibited a persisting difference in accuracy between the discrete images and the unprocessed image pair. A minimum detail of three levels allows a realistic patient proxy for use with Velocity and MIM deformation algorithms. PMID:27494827
Comparison of Fully Numerical Predictor-Corrector and Apollo Skip Entry Guidance Algorithms
NASA Astrophysics Data System (ADS)
Brunner, Christopher W.; Lu, Ping
2012-09-01
The dramatic increase in computational power since the Apollo program has enabled the development of numerical predictor-corrector (NPC) entry guidance algorithms that allow on-board accurate determination of a vehicle's trajectory. These algorithms are sufficiently mature to be flown. They are highly adaptive, especially in the face of extreme dispersion and off-nominal situations compared with reference-trajectory following algorithms. The performance and reliability of entry guidance are critical to mission success. This paper compares the performance of a recently developed fully numerical predictor-corrector entry guidance (FNPEG) algorithm with that of the Apollo skip entry guidance. Through extensive dispersion testing, it is clearly demonstrated that the Apollo skip entry guidance algorithm would be inadequate in meeting the landing precision requirement for missions with medium (4000-7000 km) and long (>7000 km) downrange capability requirements under moderate dispersions chiefly due to poor modeling of atmospheric drag. In the presence of large dispersions, a significant number of failures occur even for short-range missions due to the deviation from planned reference trajectories. The FNPEG algorithm, on the other hand, is able to ensure high landing precision in all cases tested. All factors considered, a strong case is made for adopting fully numerical algorithms for future skip entry missions.
Accurate biopsy-needle depth estimation in limited-angle tomography using multi-view geometry
NASA Astrophysics Data System (ADS)
van der Sommen, Fons; Zinger, Sveta; de With, Peter H. N.
2016-03-01
Recently, compressed-sensing based algorithms have enabled volume reconstruction from projection images acquired over a relatively small angle (θ < 20°). These methods enable accurate depth estimation of surgical tools with respect to anatomical structures. However, they are computationally expensive and time consuming, rendering them unattractive for image-guided interventions. We propose an alternative approach for depth estimation of biopsy needles during image-guided interventions, in which we split the problem into two parts and solve them independently: needle-depth estimation and volume reconstruction. The complete proposed system consists of the previous two steps, preceded by needle extraction. First, we detect the biopsy needle in the projection images and remove it by interpolation. Next, we exploit epipolar geometry to find point-to-point correspondences in the projection images to triangulate the 3D position of the needle in the volume. Finally, we use the interpolated projection images to reconstruct the local anatomical structures and indicate the position of the needle within this volume. For validation of the algorithm, we have recorded a full CT scan of a phantom with an inserted biopsy needle. The performance of our approach ranges from a median error of 2.94 mm for an distributed viewing angle of 1° down to an error of 0.30 mm for an angle larger than 10°. Based on the results of this initial phantom study, we conclude that multi-view geometry offers an attractive alternative to time-consuming iterative methods for the depth estimation of surgical tools during C-arm-based image-guided interventions.
Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits
Ljungberg, Kajsa; Mishchenko, Kateryna; Holmgren, Sverker
2010-01-01
We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called quantitative trait loci (QTL), and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. We also improve the evaluation of the QTL mapping objective function to enable exploitation of the smoothness properties of the optimization landscape. Our best two-phase method is demonstrated to be accurate in at least six dimensions and up to ten times faster than currently used QTL mapping algorithms. PMID:21918629
Olivares, Alberto; Ruiz-Garcia, Gonzalo; Olivares, Gonzalo; Górriz, Juan Manuel; Ramirez, Javier
2013-01-01
Ellipsoid fitting algorithms are widely used to calibrate Magnetic Angular Rate and Gravity (MARG) sensors. These algorithms are based on the minimization of an error function that optimizes the parameters of a mathematical sensor model that is subsequently applied to calibrate the raw data. The convergence of this kind of algorithms to a correct solution is very sensitive to input data. Input calibration datasets must be properly distributed in space so data can be accurately fitted to the theoretical ellipsoid model. Gathering a well distributed set is not an easy task as it is difficult for the operator carrying out the maneuvers to keep a visual record of all the positions that have already been covered, as well as the remaining ones. It would be then desirable to have a system that gives feedback to the operator when the dataset is ready, or to enable the calibration process in auto-calibrated systems. In this work, we propose two different algorithms that analyze the goodness of the distributions by computing four different indicators. The first approach is based on a thresholding algorithm that uses only one indicator as its input and the second one is based on a Fuzzy Logic System (FLS) that estimates the calibration error for a given calibration set using a weighted combination of two indicators. Very accurate classification between valid and invalid datasets is achieved with average Area Under Curve (AUC) of up to 0.98. PMID:24013490
Predicting polymeric crystal structures by evolutionary algorithms
NASA Astrophysics Data System (ADS)
Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy
2014-10-01
The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.
Sobel, E.; Lange, K.; O`Connell, J.R.
1996-12-31
Haplotyping is the logical process of inferring gene flow in a pedigree based on phenotyping results at a small number of genetic loci. This paper formalizes the haplotyping problem and suggests four algorithms for haplotype reconstruction. These algorithms range from exhaustive enumeration of all haplotype vectors to combinatorial optimization by simulated annealing. Application of the algorithms to published genetic analyses shows that manual haplotyping is often erroneous. Haplotyping is employed in screening pedigrees for phenotyping errors and in positional cloning of disease genes from conserved haplotypes in population isolates. 26 refs., 6 figs., 3 tabs.
Enabling a New Planning and Scheduling Paradigm
NASA Technical Reports Server (NTRS)
Jaap, John; Davis, Elizabeth
2004-01-01
The Flight Projects Directorate at NASA's Marshall Space Flight Center is developing a new planning and scheduling environment and a new scheduling algorithm to enable a paradigm shift in planning and scheduling concepts. Over the past 33 years Marshall has developed and evolved a paradigm for generating payload timelines for Skylab, Spacelab, various other Shuttle payloads, and the International Space Station. The current paradigm starts by collecting the requirements, called "tasks models," from the scientists and technologists for the tasks that they want to be done. Because of shortcomings in the current modeling schema, some requirements are entered as notes. Next a cadre with knowledge of vehicle and hardware modifies these models to encompass and be compatible with the hardware model; again, notes are added when the modeling schema does not provide a better way to represent the requirements. Finally, another cadre further modifies the models to be compatible with the scheduling engine. This last cadre also submits the models to the scheduling engine or builds the timeline manually to accommodate requirements that are expressed in notes. A future paradigm would provide a scheduling engine that accepts separate science models and hardware models. The modeling schema would have the capability to represent all the requirements without resorting to notes. Furthermore, the scheduling engine would not require that the models be modified to account for the capabilities (limitations) of the scheduling engine. The enabling technology under development at Marshall has three major components. (1) A new modeling schema allows expressing all the requirements of the tasks without resorting to notes or awkward contrivances. The chosen modeling schema is both maximally expressive and easy to use. It utilizes graphics methods to show hierarchies of task constraints and networks of temporal relationships. (2) A new scheduling algorithm automatically schedules the models
Predict amine solution properties accurately
Cheng, S.; Meisen, A.; Chakma, A.
1996-02-01
Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.
Evaluating super resolution algorithms
NASA Astrophysics Data System (ADS)
Kim, Youn Jin; Park, Jong Hyun; Shin, Gun Shik; Lee, Hyun-Seung; Kim, Dong-Hyun; Park, Se Hyeok; Kim, Jaehyun
2011-01-01
This study intends to establish a sound testing and evaluation methodology based upon the human visual characteristics for appreciating the image restoration accuracy; in addition to comparing the subjective results with predictions by some objective evaluation methods. In total, six different super resolution (SR) algorithms - such as iterative back-projection (IBP), robust SR, maximum a posteriori (MAP), projections onto convex sets (POCS), a non-uniform interpolation, and frequency domain approach - were selected. The performance comparison between the SR algorithms in terms of their restoration accuracy was carried out through both subjectively and objectively. The former methodology relies upon the paired comparison method that involves the simultaneous scaling of two stimuli with respect to image restoration accuracy. For the latter, both conventional image quality metrics and color difference methods are implemented. Consequently, POCS and a non-uniform interpolation outperformed the others for an ideal situation, while restoration based methods appear more accurate to the HR image in a real world case where any prior information about the blur kernel is remained unknown. However, the noise-added-image could not be restored successfully by any of those methods. The latest International Commission on Illumination (CIE) standard color difference equation CIEDE2000 was found to predict the subjective results accurately and outperformed conventional methods for evaluating the restoration accuracy of those SR algorithms.
Probability tree algorithm for general diffusion processes
NASA Astrophysics Data System (ADS)
Ingber, Lester; Chen, Colleen; Mondescu, Radu Paul; Muzzall, David; Renedo, Marco
2001-11-01
Motivated by path-integral numerical solutions of diffusion processes, PATHINT, we present a tree algorithm, PATHTREE, which permits extremely fast accurate computation of probability distributions of a large class of general nonlinear diffusion processes.
Health-Enabled Smart Sensor Fusion Technology
NASA Technical Reports Server (NTRS)
Wang, Ray
2012-01-01
A process was designed to fuse data from multiple sensors in order to make a more accurate estimation of the environment and overall health in an intelligent rocket test facility (IRTF), to provide reliable, high-confidence measurements for a variety of propulsion test articles. The object of the technology is to provide sensor fusion based on a distributed architecture. Specifically, the fusion technology is intended to succeed in providing health condition monitoring capability at the intelligent transceiver, such as RF signal strength, battery reading, computing resource monitoring, and sensor data reading. The technology also provides analytic and diagnostic intelligence at the intelligent transceiver, enhancing the IEEE 1451.x-based standard for sensor data management and distributions, as well as providing appropriate communications protocols to enable complex interactions to support timely and high-quality flow of information among the system elements.
The network-enabled optimization system server
Mesnier, M.P.
1995-08-01
Mathematical optimization is a technology under constant change and advancement, drawing upon the most efficient and accurate numerical methods to date. Further, these methods can be tailored for a specific application or generalized to accommodate a wider range of problems. This perpetual change creates an ever growing field, one that is often difficult to stay abreast of. Hence, the impetus behind the Network-Enabled Optimization System (NEOS) server, which aims to provide users, both novice and expert, with a guided tour through the expanding world of optimization. The NEOS server is responsible for bridging the gap between users and the optimization software they seek. More specifically, the NEOS server will accept optimization problems over the Internet and return a solution to the user either interactively or by e-mail. This paper discusses the current implementation of the server.
Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately
NASA Technical Reports Server (NTRS)
Bednarcyk, Brett A.; Arnold, Steven M.
2001-01-01
A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.