Design of 240,000 orthogonal 25mer DNA barcode probes.

PubMed

Xu, Qikai; Schlabach, Michael R; Hannon, Gregory J; Elledge, Stephen J

2009-02-17

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

Design of 240,000 orthogonal 25mer DNA barcode probes

PubMed Central

Xu, Qikai; Schlabach, Michael R.; Hannon, Gregory J.; Elledge, Stephen J.

2009-01-01

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications. PMID:19171886

Wind-tunnel investigation of the thrust augmentor performance of a large-scale swept wing model. [in the Ames 40 by 80 foot wind tunnel

NASA Technical Reports Server (NTRS)

Koenig, D. G.; Falarski, M. D.

1979-01-01

Tests were made in the Ames 40- by 80-foot wind tunnel to determine the forward speed effects on wing-mounted thrust augmentors. The large-scale model was powered by the compressor output of J-85 driven viper compressors. The flap settings used were 15 deg and 30 deg with 0 deg, 15 deg, and 30 deg aileron settings. The maximum duct pressure, and wind tunnel dynamic pressure were 66 cmHg (26 in Hg) and 1190 N/sq m (25 lb/sq ft), respectively. All tests were made at zero sideslip. Test results are presented without analysis.

Improved variance estimation of classification performance via reduction of bias caused by small sample size.

PubMed

Wickenberg-Bolin, Ulrika; Göransson, Hanna; Fryknäs, Mårten; Gustafsson, Mats G; Isaksson, Anders

2006-03-13

Supervised learning for classification of cancer employs a set of design examples to learn how to discriminate between tumors. In practice it is crucial to confirm that the classifier is robust with good generalization performance to new examples, or at least that it performs better than random guessing. A suggested alternative is to obtain a confidence interval of the error rate using repeated design and test sets selected from available examples. However, it is known that even in the ideal situation of repeated designs and tests with completely novel samples in each cycle, a small test set size leads to a large bias in the estimate of the true variance between design sets. Therefore different methods for small sample performance estimation such as a recently proposed procedure called Repeated Random Sampling (RSS) is also expected to result in heavily biased estimates, which in turn translates into biased confidence intervals. Here we explore such biases and develop a refined algorithm called Repeated Independent Design and Test (RIDT). Our simulations reveal that repeated designs and tests based on resampling in a fixed bag of samples yield a biased variance estimate. We also demonstrate that it is possible to obtain an improved variance estimate by means of a procedure that explicitly models how this bias depends on the number of samples used for testing. For the special case of repeated designs and tests using new samples for each design and test, we present an exact analytical expression for how the expected value of the bias decreases with the size of the test set. We show that via modeling and subsequent reduction of the small sample bias, it is possible to obtain an improved estimate of the variance of classifier performance between design sets. However, the uncertainty of the variance estimate is large in the simulations performed indicating that the method in its present form cannot be directly applied to small data sets.

Altering Test Environments for Reducing Test Anxiety and for Improving Academic Performance.

ERIC Educational Resources Information Center

Bushnell, Don D.

To test the effects of altering situational variables in stressful examinations on high test anxious and low test anxious undergraduates, mid-terms and final examinations were administered in two environmental settings: large lecture halls and small language laboratories. Mean test scores for high test anxious students in the language labs were…

Interrater Reliability in Large-Scale Assessments--Can Teachers Score National Tests Reliably without External Controls?

ERIC Educational Resources Information Center

Pantzare, Anna Lind

2015-01-01

In most large-scale assessment systems a set of rather expensive external quality controls are implemented in order to guarantee the quality of interrater reliability. This study empirically examines if teachers' ratings of national tests in mathematics can be reliable without using monitoring, training, or other methods of external quality…

The Positive and Negative Consequences of Multiple-Choice Testing

ERIC Educational Resources Information Center

Roediger, Henry L.; Marsh, Elizabeth J.

2005-01-01

Multiple-choice tests are commonly used in educational settings but with unknown effects on students' knowledge. The authors examined the consequences of taking a multiple-choice test on a later general knowledge test in which students were warned not to guess. A large positive testing effect was obtained: Prior testing of facts aided final…

Software Manages Documentation in a Large Test Facility

NASA Technical Reports Server (NTRS)

Gurneck, Joseph M.

2001-01-01

The 3MCS computer program assists and instrumentation engineer in performing the 3 essential functions of design, documentation, and configuration management of measurement and control systems in a large test facility. Services provided by 3MCS are acceptance of input from multiple engineers and technicians working at multiple locations;standardization of drawings;automated cross-referencing; identification of errors;listing of components and resources; downloading of test settings; and provision of information to customers.

Fast structure similarity searches among protein models: efficient clustering of protein fragments

PubMed Central

2012-01-01

Background For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD) comparison is performed. Most of the time is typically spent on comparison of non-similar structures. For sets with more than, say, 10,000 models this procedure is very time-consuming and alternative faster algorithms, restricting comparisons only to most similar structures would be useful. Results We exploit the inverse triangle inequality on the RMSD between two structures given the RMSDs with a third structure. The lower bound on RMSD may be used, when restricting the search of similarity to a reasonably low RMSD threshold value, to speed up similarity searches significantly. Tests are performed on large sets of decoys which are widely used as test cases for predictive methods, with a speed-up of up to 100 times with respect to all-vs-all comparison depending on the set and parameters used. Sample applications are shown. Conclusions The algorithm presented here allows fast comparison of large data sets of structures with limited memory requirements. As an example of application we present clustering of more than 100000 fragments of length 5 from the top500H dataset into few hundred representative fragments. A more realistic scenario is provided by the search of similarity within the very large decoy sets used for the tests. Other applications regard filtering nearly-indentical conformation in selected CASP9 datasets and clustering molecular dynamics snapshots. Availability A linux executable and a Perl script with examples are given in the supplementary material (Additional file 1). The source code is available upon request from the authors. PMID:22642815

Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates.

PubMed

Schwämmle, Veit; León, Ileana Rodríguez; Jensen, Ole Nørregaard

2013-09-06

Large-scale quantitative analyses of biological systems are often performed with few replicate experiments, leading to multiple nonidentical data sets due to missing values. For example, mass spectrometry driven proteomics experiments are frequently performed with few biological or technical replicates due to sample-scarcity or due to duty-cycle or sensitivity constraints, or limited capacity of the available instrumentation, leading to incomplete results where detection of significant feature changes becomes a challenge. This problem is further exacerbated for the detection of significant changes on the peptide level, for example, in phospho-proteomics experiments. In order to assess the extent of this problem and the implications for large-scale proteome analysis, we investigated and optimized the performance of three statistical approaches by using simulated and experimental data sets with varying numbers of missing values. We applied three tools, including standard t test, moderated t test, also known as limma, and rank products for the detection of significantly changing features in simulated and experimental proteomics data sets with missing values. The rank product method was improved to work with data sets containing missing values. Extensive analysis of simulated and experimental data sets revealed that the performance of the statistical analysis tools depended on simple properties of the data sets. High-confidence results were obtained by using the limma and rank products methods for analyses of triplicate data sets that exhibited more than 1000 features and more than 50% missing values. The maximum number of differentially represented features was identified by using limma and rank products methods in a complementary manner. We therefore recommend combined usage of these methods as a novel and optimal way to detect significantly changing features in these data sets. This approach is suitable for large quantitative data sets from stable isotope labeling and mass spectrometry experiments and should be applicable to large data sets of any type. An R script that implements the improved rank products algorithm and the combined analysis is available.

Measuring CAMD technique performance. 2. How "druglike" are drugs? Implications of Random test set selection exemplified using druglikeness classification models.

PubMed

Good, Andrew C; Hermsmeier, Mark A

2007-01-01

Research into the advancement of computer-aided molecular design (CAMD) has a tendency to focus on the discipline of algorithm development. Such efforts are often wrought to the detriment of the data set selection and analysis used in said algorithm validation. Here we highlight the potential problems this can cause in the context of druglikeness classification. More rigorous efforts are applied to the selection of decoy (nondruglike) molecules from the ACD. Comparisons are made between model performance using the standard technique of random test set creation with test sets derived from explicit ontological separation by drug class. The dangers of viewing druglike space as sufficiently coherent to permit simple classification are highlighted. In addition the issues inherent in applying unfiltered data and random test set selection to (Q)SAR models utilizing large and supposedly heterogeneous databases are discussed.

Automated cognitive testing of monkeys in social groups yields results comparable to individual laboratory-based testing.

PubMed

Gazes, Regina Paxton; Brown, Emily Kathryn; Basile, Benjamin M; Hampton, Robert R

2013-05-01

Cognitive abilities likely evolved in response to specific environmental and social challenges and are therefore expected to be specialized for the life history of each species. Specialized cognitive abilities may be most readily engaged under conditions that approximate the natural environment of the species being studied. While naturalistic environments might therefore have advantages over laboratory settings for cognitive research, it is difficult to conduct certain types of cognitive tests in these settings. We implemented methods for automated cognitive testing of monkeys (Macaca mulatta) in large social groups (Field station) and compared the performance to that of laboratory-housed monkeys (Laboratory). The Field station animals shared access to four touch-screen computers in a large naturalistic social group. Each Field station subject had an RFID chip implanted in each arm for computerized identification and individualized assignment of cognitive tests. The Laboratory group was housed and tested in a typical laboratory setting, with individual access to testing computers in their home cages. Monkeys in both groups voluntarily participated at their own pace for food rewards. We evaluated performance in two visual psychophysics tests, a perceptual classification test, a transitive inference test, and a delayed matching-to-sample memory test. Despite the differences in housing, social environment, age, and sex, monkeys in the two groups performed similarly in all tests. Semi-free ranging monkeys living in complex social environments are therefore viable subjects for cognitive testing designed to take advantage of the unique affordances of naturalistic testing environments.

Automated cognitive testing of monkeys in social groups yields results comparable to individual laboratory based testing

PubMed Central

Gazes, Regina Paxton; Brown, Emily Kathryn; Basile, Benjamin M.; Hampton, Robert R.

2013-01-01

Cognitive abilities likely evolved in response to specific environmental and social challenges and are therefore expected to be specialized for the life history of each species. Specialized cognitive abilities may be most readily engaged under conditions that approximate the natural environment of the species being studied. While naturalistic environments might therefore have advantages over laboratory settings for cognitive research, it is difficult to conduct certain types of cognitive tests in these settings. We implemented methods for automated cognitive testing of monkeys (Macaca mulatta) in large social groups (Field station) and compared the performance to that of laboratory housed monkeys (Laboratory). The Field station animals shared access to four touch screen computers in a large naturalistic social group. Each Field station subject had an RFID chip implanted in each arm for computerized identification and individualized assignment of cognitive tests. The Laboratory group was housed and tested in a typical laboratory setting, with individual access to testing computers in their home cages. Monkeys in both groups voluntarily participated at their own pace for food rewards. We evaluated performance in two visual psychophysics tests, a perceptual classification test, a transitive inference test, and a delayed matching to sample memory test. Despite differences in housing, social environment, age, and sex, monkeys in the two groups performed similarly in all tests. Semi-free ranging monkeys living in complex social environments are therefore viable subjects for cognitive testing designed to take advantage of the unique affordances of naturalistic testing environments. PMID:23263675

Analyzing CMOS/SOS fabrication for LSI arrays

NASA Technical Reports Server (NTRS)

Ipri, A. C.

1978-01-01

Report discusses set of design rules that have been developed as result of work with test arrays. Set of optimum dimensions is given that would maximize process output and would correspondingly minimize costs in fabrication of large-scale integration (LSI) arrays.

Simulating Large Area, High Intensity AM0 Illumination on Earth- Representative Testing at Elevated Temperatures for the BepiColombo and SolO Missions

NASA Astrophysics Data System (ADS)

Oberhuttinger, C.; Quabis, D.; Zimmermann, C. G.

2014-08-01

During both the BepiColombo and the Solar Orbiter (SolO) mission, severe environmental conditions with sun intensities up to 10.6 solar constants (SCs) resp. 12.8 SCs will be encountered. Therefore, a special cell design was developed which can withstand these environmental loads. To verify the solar cells under representative conditions, a set of specific tests is conducted. The key qualification test for these high intensity, high temperature (HIHT) missions is a combined test, which exposes a large number of cells simultaneously to the complete AM0 spectrum at the required irradiance and temperature. Such a test was set up in the VTC1.5 chamber located at ESTEC. This paper provides an overview of the challenges in designing a setup capable of achieving this HIHT simulation. The solutions that were developed will be presented. Also the performance of the setup will be illustrated by actual test results.

Testing the statistical compatibility of independent data sets

NASA Astrophysics Data System (ADS)

Maltoni, M.; Schwetz, T.

2003-08-01

We discuss a goodness-of-fit method which tests the compatibility between statistically independent data sets. The method gives sensible results even in cases where the χ2 minima of the individual data sets are very low or when several parameters are fitted to a large number of data points. In particular, it avoids the problem that a possible disagreement between data sets becomes diluted by data points which are insensitive to the crucial parameters. A formal derivation of the probability distribution function for the proposed test statistics is given, based on standard theorems of statistics. The application of the method is illustrated on data from neutrino oscillation experiments, and its complementarity to the standard goodness-of-fit is discussed.

Effects of Active Sting Damping on Common Research Model Data Quality

NASA Technical Reports Server (NTRS)

Acheson, Michael J.; Balakrishna, S.

2011-01-01

Recent tests using the Common Research Model (CRM) at the Langley National Transonic Facility (NTF) and the Ames 11-foot Transonic Wind Tunnel (11' TWT) produced large sets of data that have been used to examine the effects of active damping on transonic tunnel aerodynamic data quality. In particular, large statistically significant sets of repeat data demonstrate that the active damping system had no apparent effect on drag, lift and pitching moment repeatability during warm testing conditions, while simultaneously enabling aerodynamic data to be obtained post stall. A small set of cryogenic (high Reynolds number) repeat data was obtained at the NTF and again showed a negligible effect on data repeatability. However, due to a degradation of control power in the active damping system cryogenically, the ability to obtain test data post-stall was not achieved during cryogenic testing. Additionally, comparisons of data repeatability between NTF and 11-ft TWT CRM data led to further (warm) testing at the NTF which demonstrated that for a modest increase in data sampling time, a 2-3 factor improvement in drag, and pitching moment repeatability was readily achieved not related with the active damping system.

Model verification of large structural systems

NASA Technical Reports Server (NTRS)

Lee, L. T.; Hasselman, T. K.

1977-01-01

A methodology was formulated, and a general computer code implemented for processing sinusoidal vibration test data to simultaneously make adjustments to a prior mathematical model of a large structural system, and resolve measured response data to obtain a set of orthogonal modes representative of the test model. The derivation of estimator equations is shown along with example problems. A method for improving the prior analytic model is included.

Evaluating the uniformity of color spaces and performance of color difference formulae

NASA Astrophysics Data System (ADS)

Lian, Yusheng; Liao, Ningfang; Wang, Jiajia; Tan, Boneng; Liu, Zilong

2010-11-01

Using small color difference data sets (Macadam ellipses dataset and RIT-DuPont suprathreshold color difference ellipses dataset), and large color difference data sets (Munsell Renovation Data and OSA Uniform Color Scales dataset), the uniformity of several color spaces and performance of color difference formulae based on these color spaces are evaluated. The color spaces used are CIELAB, DIN99d, IPT, and CIECAM02-UCS. It is found that the uniformity of lightness is better than saturation and hue. Overall, for all these color spaces, the uniformity in the blue area is inferior to the other area. The uniformity of CIECAM02-UCS is superior to the other color spaces for the whole color-difference range from small to large. The uniformity of CIELAB and IPT for the large color difference data sets is better than it for the small color difference data sets, but the DIN99d is opposite. Two common performance factors (PF/3 and STRESS) and the statistical F-test are calculated to test the performance of color difference formula. The results show that the performance of color difference formulae based on these four color spaces is consistent with the uniformity of these color spaces.

gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels.

PubMed

Larson, Nicholas B; McDonnell, Shannon; Cannon Albright, Lisa; Teerlink, Craig; Stanford, Janet; Ostrander, Elaine A; Isaacs, William B; Xu, Jianfeng; Cooney, Kathleen A; Lange, Ethan; Schleutker, Johanna; Carpten, John D; Powell, Isaac; Bailey-Wilson, Joan E; Cussenot, Olivier; Cancel-Tassin, Geraldine; Giles, Graham G; MacInnis, Robert J; Maier, Christiane; Whittemore, Alice S; Hsieh, Chih-Lin; Wiklund, Fredrik; Catalona, William J; Foulkes, William; Mandal, Diptasri; Eeles, Rosalind; Kote-Jarai, Zsofia; Ackerman, Michael J; Olson, Timothy M; Klein, Christopher J; Thibodeau, Stephen N; Schaid, Daniel J

2017-05-01

Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results. © 2017 WILEY PERIODICALS, INC.

Questionnaire-based assessment of executive functioning: Psychometrics.

PubMed

Castellanos, Irina; Kronenberger, William G; Pisoni, David B

2018-01-01

The psychometric properties of the Learning, Executive, and Attention Functioning (LEAF) scale were investigated in an outpatient clinical pediatric sample. As a part of clinical testing, the LEAF scale, which broadly measures neuropsychological abilities related to executive functioning and learning, was administered to parents of 118 children and adolescents referred for psychological testing at a pediatric psychology clinic; 85 teachers also completed LEAF scales to assess reliability across different raters and settings. Scores on neuropsychological tests of executive functioning and academic achievement were abstracted from charts. Psychometric analyses of the LEAF scale demonstrated satisfactory internal consistency, parent-teacher inter-rater reliability in the small to large effect size range, and test-retest reliability in the large effect size range, similar to values for other executive functioning checklists. Correlations between corresponding subscales on the LEAF and other behavior checklists were large, while most correlations with neuropsychological tests of executive functioning and achievement were significant but in the small to medium range. Results support the utility of the LEAF as a reliable and valid questionnaire-based assessment of delays and disturbances in executive functioning and learning. Applications and advantages of the LEAF and other questionnaire measures of executive functioning in clinical neuropsychology settings are discussed.

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

tensor, EFP calculations are basis set dependent. The smallest recommended basis set is 6- 31++G( d , p )52 The dependence of the computational cost of...and second order perturbation theory (MP2) levels with the 6-31G( d , p ) basis set. Additional SFM tests are presented for a small set of alpha...helices using the 6-31++G( d , p ) basis set. The larger 6-311++G(3df,2p) basis set is employed for creating all EFPs used for non- bonded interactions, since

A global × global test for testing associations between two large sets of variables.

PubMed

Chaturvedi, Nimisha; de Menezes, Renée X; Goeman, Jelle J

2017-01-01

In high-dimensional omics studies where multiple molecular profiles are obtained for each set of patients, there is often interest in identifying complex multivariate associations, for example, copy number regulated expression levels in a certain pathway or in a genomic region. To detect such associations, we present a novel approach to test for association between two sets of variables. Our approach generalizes the global test, which tests for association between a group of covariates and a single univariate response, to allow high-dimensional multivariate response. We apply the method to several simulated datasets as well as two publicly available datasets, where we compare the performance of multivariate global test (G2) with univariate global test. The method is implemented in R and will be available as a part of the globaltest package in R. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Large Terrain Modeling and Visualization for Planets

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan; Cameron, Jonathan; Lim, Christopher

2011-01-01

Physics-based simulations are actively used in the design, testing, and operations phases of surface and near-surface planetary space missions. One of the challenges in realtime simulations is the ability to handle large multi-resolution terrain data sets within models as well as for visualization. In this paper, we describe special techniques that we have developed for visualization, paging, and data storage for dealing with these large data sets. The visualization technique uses a real-time GPU-based continuous level-of-detail technique that delivers multiple frames a second performance even for planetary scale terrain model sizes.

Threshold Theory Tested in an Organizational Setting: The Relation between Perceived Innovativeness and Intelligence in a Large Sample of Leaders

ERIC Educational Resources Information Center

Christensen, Bo T.; Hartmann, Peter V. W.; Rasmussen, Thomas Hedegaard

2017-01-01

A large sample of leaders (N = 4257) was used to test the link between leader innovativeness and intelligence. The threshold theory of the link between creativity and intelligence assumes that below a certain IQ level (approximately IQ 120), there is some correlation between IQ and creative potential, but above this cutoff point, there is no…

A Quick Assessment of Visuospatial Abilities in Adolescents Using the Design Organization Test (DOT).

PubMed

Burggraaf, Rudolf; Frens, Maarten A; Hooge, Ignace T C; van der Geest, Jos N

2016-01-01

Tests measuring visuospatial abilities have shown that these abilities increase during adolescence. Unfortunately, the Block Design test and other such tests are complicated and time-consuming to administer, making them unsuitable for use with large groups of restless adolescents. The results of the Design Organization Test (DOT), a quick pen-and-paper test, have been shown to correlate with those of the Block Design test. A group of 198 healthy adolescents (110 male and 88 female) aged 12 to 19 years old participated in this study. A slightly modified version of the DOT has been used in which we shortened the administration time to avoid a ceiling effect in the score. Scores show a linear increase with age (on average 2.0 points per year, r = .61) independent of sex. Scores did not differ between individual setting and group setting. Thus, the DOT is a simple and effective way to assess visuospatial ability in large groups, such as in schools, and it can be easily administered year after year to follow the development of students.

ITC Guidelines on Quality Control in Scoring, Test Analysis, and Reporting of Test Scores

ERIC Educational Resources Information Center

Allalouf, Avi

2014-01-01

The Quality Control (QC) Guidelines are intended to increase the efficiency, precision, and accuracy of the scoring, analysis, and reporting process of testing. The QC Guidelines focus on large-scale testing operations where multiple forms of tests are created for use on set dates. However, they may also be used for a wide variety of other testing…

Cost-effectiveness of finding new HIV diagnoses using rapid HIV testing in community-based organizations.

PubMed

Shrestha, Ram K; Clark, Hollie A; Sansom, Stephanie L; Song, Binwei; Buckendahl, Holly; Calhoun, Cindy B; Hutchinson, Angela B; Heffelfinger, James D

2008-01-01

We assessed the cost-effectiveness of determining new human immunodeficiency virus (HIV) diagnoses using rapid HIV testing performed by community-based organizations (CBOs) in Kansas City, Missouri, and Detroit, Michigan. The CBOs performed rapid HIV testing during April 2004 through March 2006. In Kansas City, testing was performed in a clinic and in outreach settings. In Detroit, testing was performed in outreach settings only. Both CBOs used mobile testing vans. Measures of effectiveness were the number of HIV tests performed and the number of people notified of new HIV diagnoses, based on rapid tests. We retrospectively collected program costs, including those for personnel, test kits, mobile vans, and facility space. The CBO in Kansas City tested a mean of 855 people a year in its clinic and 703 people a year in outreach settings. The number of people notified of new HIV diagnoses was 19 (2.2%) in the clinic and five (0.7%) in outreach settings. The CBO in Detroit tested 976 people a year in outreach settings, and the number notified of new HIV diagnoses was 15 (1.5%). In Kansas City, the cost per person notified of a new HIV diagnosis was $3,637 in the clinic and $16,985 in outreach settings. In the Detroit outreach settings, the cost per notification was $13,448. The cost of providing a new HIV diagnosis was considerably higher in the outreach settings than in the clinic. The variation can be largely explained by differences in the number of undiagnosed infections among the people tested and by the costs of purchasing and operating a mobile van.

Cleanliness for the NIF 1ω Laser Amplifiers

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

Spaeth, M. L.; Manes, K. R.; Honig, J.

During the years before the National Ignition Facility (NIF) laser system, a set of generally accepted cleaning procedures had been developed for the large 1ω amplifiers of an inertial confinement fusion laser, and up until 1999 similar procedures were planned for NIF. Several parallel sets of test results were obtained from 1992 to 1999 for large amplifiers using these accepted cleaning procedures in the Beamlet physics test bed and in the Amplifier Module Prototype Laboratory (AMPLAB), a four-slab-high prototype large amplifier structure. Both of these showed damage to their slab surfaces that, if projected to operating conditions for NIF, wouldmore » lead to higher than acceptable slab-refurbishment rates. Finally, this study tracks the search for the smoking gun origin of this damage and describes the solution employed in NIF for avoiding flashlamp-induced aerosol damage to its 1ω amplifier slabs.« less

Cleanliness for the NIF 1ω Laser Amplifiers

DOE PAGES

Spaeth, M. L.; Manes, K. R.; Honig, J.

2017-03-23

During the years before the National Ignition Facility (NIF) laser system, a set of generally accepted cleaning procedures had been developed for the large 1ω amplifiers of an inertial confinement fusion laser, and up until 1999 similar procedures were planned for NIF. Several parallel sets of test results were obtained from 1992 to 1999 for large amplifiers using these accepted cleaning procedures in the Beamlet physics test bed and in the Amplifier Module Prototype Laboratory (AMPLAB), a four-slab-high prototype large amplifier structure. Both of these showed damage to their slab surfaces that, if projected to operating conditions for NIF, wouldmore » lead to higher than acceptable slab-refurbishment rates. Finally, this study tracks the search for the smoking gun origin of this damage and describes the solution employed in NIF for avoiding flashlamp-induced aerosol damage to its 1ω amplifier slabs.« less

Robust tracking control of a magnetically suspended rigid body

NASA Technical Reports Server (NTRS)

Lim, Kyong B.; Cox, David E.

1994-01-01

This study is an application of H-infinity and micro-synthesis for designing robust tracking controllers for the Large Angle Magnetic Suspension Test Facility. The modeling, design, analysis, simulation, and testing of a control law that guarantees tracking performance under external disturbances and model uncertainties is investigated. The type of uncertainties considered and the tracking performance metric used is discussed. This study demonstrates the tradeoff between tracking performance at low frequencies and robustness at high frequencies. Two sets of controllers were designed and tested. The first set emphasized performance over robustness, while the second set traded off performance for robustness. Comparisons of simulation and test results are also included. Current simulation and experimental results indicate that reasonably good robust tracking performance can be attained for this system using multivariable robust control approach.

Bi-Factor MIRT Observed-Score Equating for Mixed-Format Tests

ERIC Educational Resources Information Center

Lee, Guemin; Lee, Won-Chan

2016-01-01

The main purposes of this study were to develop bi-factor multidimensional item response theory (BF-MIRT) observed-score equating procedures for mixed-format tests and to investigate relative appropriateness of the proposed procedures. Using data from a large-scale testing program, three types of pseudo data sets were formulated: matched samples,…

III. FROM SMALL TO BIG: METHODS FOR INCORPORATING LARGE SCALE DATA INTO DEVELOPMENTAL SCIENCE.

PubMed

Davis-Kean, Pamela E; Jager, Justin

2017-06-01

For decades, developmental science has been based primarily on relatively small-scale data collections with children and families. Part of the reason for the dominance of this type of data collection is the complexity of collecting cognitive and social data on infants and small children. These small data sets are limited in both power to detect differences and the demographic diversity to generalize clearly and broadly. Thus, in this chapter we will discuss the value of using existing large-scale data sets to tests the complex questions of child development and how to develop future large-scale data sets that are both representative and can answer the important questions of developmental scientists. © 2017 The Society for Research in Child Development, Inc.

Building Stakeholder Partnerships for an On-Site HIV Testing Programme

PubMed Central

Woods, William J.; Erwin, Kathleen; Lazarus, Margery; Serice, Heather; Grinstead, Olga; Binson, Diane

2009-01-01

Because of the large number of individuals at risk for HIV infection who visit gay saunas and sex clubs, these venues are useful settings in which to offer HIV outreach programmes for voluntary counselling and testing (VCT). Nevertheless, establishing a successful VCT programme in such a setting can be a daunting challenge, in large part because there are many barriers to managing the various components likely to be involved. Using qualitative data from a process evaluation of a new VCT programme at a gay sauna in California, USA, we describe how the various stakeholders overcame barriers of disparate interests and responsibilities to work together to successfully facilitate a regular and frequent on-site VCT programme that was fully utilized by patrons. PMID:18432424

bigSCale: an analytical framework for big-scale single-cell data.

PubMed

Iacono, Giovanni; Mereu, Elisabetta; Guillaumet-Adkins, Amy; Corominas, Roser; Cuscó, Ivon; Rodríguez-Esteban, Gustavo; Gut, Marta; Pérez-Jurado, Luis Alberto; Gut, Ivo; Heyn, Holger

2018-06-01

Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers of cells, however, generates extremely large data sets, extending processing time and challenging computing resources. Current scRNA-seq analysis tools are not designed to interrogate large data sets and often lack sensitivity to identify marker genes. With bigSCale, we provide a scalable analytical framework to analyze millions of cells, which addresses the challenges associated with large data sets. To handle the noise and sparsity of scRNA-seq data, bigSCale uses large sample sizes to estimate an accurate numerical model of noise. The framework further includes modules for differential expression analysis, cell clustering, and marker identification. A directed convolution strategy allows processing of extremely large data sets, while preserving transcript information from individual cells. We evaluated the performance of bigSCale using both a biological model of aberrant gene expression in patient-derived neuronal progenitor cells and simulated data sets, which underlines the speed and accuracy in differential expression analysis. To test its applicability for large data sets, we applied bigSCale to assess 1.3 million cells from the mouse developing forebrain. Its directed down-sampling strategy accumulates information from single cells into index cell transcriptomes, thereby defining cellular clusters with improved resolution. Accordingly, index cell clusters identified rare populations, such as reelin ( Reln )-positive Cajal-Retzius neurons, for which we report previously unrecognized heterogeneity associated with distinct differentiation stages, spatial organization, and cellular function. Together, bigSCale presents a solution to address future challenges of large single-cell data sets. © 2018 Iacono et al.; Published by Cold Spring Harbor Laboratory Press.

Are Cognitive "g" and Academic Achievement "g" One and the Same "g"? An Exploration on the Woodcock-Johnson and Kaufman Tests

ERIC Educational Resources Information Center

Kaufman, Scott Barry; Reynolds, Matthew R.; Liu, Xin; Kaufman, Alan S.; McGrew, Kevin S.

2012-01-01

We examined the degree to which the conventional notion of g associated with IQ tests and general cognitive ability tests ("COG-g") relate to the general ability that underlies tests of reading, math, and writing achievement ("ACH-g"). Two large, nationally representative data sets and two independent individually-administered…

Probing gravity theory and cosmic acceleration using (in)consistency tests between cosmological data sets

NASA Astrophysics Data System (ADS)

Ishak-Boushaki, Mustapha B.

2018-06-01

Testing general relativity at cosmological scales and probing the cause of cosmic acceleration are among important objectives targeted by incoming and future astronomical surveys and experiments. I present our recent results on (in)consistency tests that can provide insights about the underlying gravity theory and cosmic acceleration using cosmological data sets. We use new statistical measures that can detect discordances between data sets when present. We use an algorithmic procedure based on these new measures that is able to identify in some cases whether an inconsistency is due to problems related to systematic effects in the data or to the underlying model. Some recent published tensions between data sets are also examined using our formalism, including the Hubble constant measurements, Planck and Large-Scale-Structure. (Work supported in part by NSF under Grant No. AST-1517768).

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes.

PubMed

Rohde, Palle Duun; Demontis, Ditte; Cuyabano, Beatriz Castro Dias; Børglum, Anders D; Sørensen, Peter

2016-08-01

Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case-control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and immunological responses, which previously have been implicated with schizophrenia based on experimental and observational studies. Copyright © 2016 by the Genetics Society of America.

USE OF TROUT LIVER SLICES TO ENHANCE MECHANISTIC INTERPRETATION OF ER BINDING FOR COST-EFFECTIVE PRIORITIZATION OF CHEMICALS WITHIN LARGE INVENTORIES

EPA Science Inventory

The cost of testing chemicals as reproductive toxicants precludes the possibility of evaluating large chemical inventories without a robust strategic approach for setting priorities. The use of quantitative structure-activity relationships (QSARs) in early hazard identification m...

Analyzing the test process using structural coverage

NASA Technical Reports Server (NTRS)

Ramsey, James; Basili, Victor R.

1985-01-01

A large, commercially developed FORTRAN program was modified to produce structural coverage metrics. The modified program was executed on a set of functionally generated acceptance tests and a large sample of operational usage cases. The resulting structural coverage metrics are combined with fault and error data to evaluate structural coverage. It was shown that in the software environment the functionally generated tests seem to be a good approximation of operational use. The relative proportions of the exercised statement subclasses change as the structural coverage of the program increases. A method was also proposed for evaluating if two sets of input data exercise a program in a similar manner. Evidence was provided that implies that in this environment, faults revealed in a procedure are independent of the number of times the procedure is executed and that it may be reasonable to use procedure coverage in software models that use statement coverage. Finally, the evidence suggests that it may be possible to use structural coverage to aid in the management of the acceptance test processed.

Study on kinematic and compliance test of suspension

NASA Astrophysics Data System (ADS)

Jing, Lixin; Wu, Liguang; Li, Xuepeng; Zhang, Yu

2017-09-01

Chassis performance development is a major difficulty in vehicle research and development, which is the main factor restricting the independent development of vehicles in China. These years, through a large number of studies, chassis engineers have found that the suspension K&C characteristics as a quasi-static characteristic of the suspension provides a technical route for the suspension performance R&D, and the suspension K&C test has become an important means of vehicle benchmarking, optimization and verification. However, the research on suspension K&C test is less in china, and the test conditions and setting requirements vary greatly from OEM to OEM. In this paper, the influence of different settings on the characteristics of the suspension is obtained through experiments, and the causes of the differences are analyzed; in order to fully reflect the suspension characteristics, the author recommends the appropriate test case and settings.

The Fallibility of High Stakes "11-Plus" Testing in Northern Ireland

ERIC Educational Resources Information Center

Gardner, John; Cowan, Pamela

2005-01-01

This paper sets out the findings from a large-scale analysis of the Northern Ireland Transfer Procedure Tests, used to select pupils for grammar schools. As it was not possible to get completed test scripts from government agencies, over 3000 practice scripts were completed in simulated conditions and were analysed to establish whether the tests…

Classroom Activity Connections: Demonstrating Various Flame Tests Using Common Household Materials

ERIC Educational Resources Information Center

Baldwin, Bruce W.; Hasbrouck, Scott; Smith, Jordan; Kuntzleman, Thomas S.

2010-01-01

In "JCE" Activity #67, "Flame Tests: Which Ion Causes the Color?", Michael Sanger describes how to conduct flame tests with household items. We have used this activity in outreach settings, and have extended it in a variety of ways. For example, we have demonstrated large-scale strontium (red), copper (green), and carbon (blue) flames using only…

Testing Mediation in Structural Equation Modeling: The Effectiveness of the Test of Joint Significance

ERIC Educational Resources Information Center

Leth-Steensen, Craig; Gallitto, Elena

2016-01-01

A large number of approaches have been proposed for estimating and testing the significance of indirect effects in mediation models. In this study, four sets of Monte Carlo simulations involving full latent variable structural equation models were run in order to contrast the effectiveness of the currently popular bias-corrected bootstrapping…

Executive decision-making in the domestic sheep.

PubMed

Morton, A Jennifer; Avanzo, Laura

2011-01-31

Two new large animal models of Huntington's disease (HD) have been developed recently, an old world monkey (macaque) and a sheep. Macaques, with their large brains and complex repertoire of behaviors are the 'gold-standard' laboratory animals for testing cognitive function, but there are many practical and ethical issues that must be resolved before HD macaques can be used for pre-clinical research. By contrast, despite their comparable brain size, sheep do not enjoy a reputation for intelligence, and are not used for pre-clinical cognitive testing. Given that cognitive decline is a major therapeutic target in HD, the feasibility of testing cognitive function in sheep must be explored if they are to be considered seriously as models of HD. Here we tested the ability of sheep to perform tests of executive function (discrimination learning, reversal learning and attentional set-shifting). Significantly, we found that not only could sheep perform discrimination learning and reversals, but they could also perform the intradimensional (ID) and extradimensional (ED) set-shifting tasks that are sensitive tests of cognitive dysfunction in humans. Their performance on the ID/ED shifts mirrored that seen in humans and macaques, with significantly more errors to reach criterion in the ED than the ID shift. Thus, sheep can perform 'executive' cognitive tasks that are an important part of the primate behavioral repertoire, but which have never been shown previously to exist in any other large animal. Sheep have great potential, not only for use as a large animal model of HD, but also for studying cognitive function and the evolution of complex behaviours in normal animals.

Executive Decision-Making in the Domestic Sheep

PubMed Central

Morton, A. Jennifer; Avanzo, Laura

2011-01-01

Two new large animal models of Huntington's disease (HD) have been developed recently, an old world monkey (macaque) and a sheep. Macaques, with their large brains and complex repertoire of behaviors are the ‘gold-standard’ laboratory animals for testing cognitive function, but there are many practical and ethical issues that must be resolved before HD macaques can be used for pre-clinical research. By contrast, despite their comparable brain size, sheep do not enjoy a reputation for intelligence, and are not used for pre-clinical cognitive testing. Given that cognitive decline is a major therapeutic target in HD, the feasibility of testing cognitive function in sheep must be explored if they are to be considered seriously as models of HD. Here we tested the ability of sheep to perform tests of executive function (discrimination learning, reversal learning and attentional set-shifting). Significantly, we found that not only could sheep perform discrimination learning and reversals, but they could also perform the intradimensional (ID) and extradimensional (ED) set-shifting tasks that are sensitive tests of cognitive dysfunction in humans. Their performance on the ID/ED shifts mirrored that seen in humans and macaques, with significantly more errors to reach criterion in the ED than the ID shift. Thus, sheep can perform ‘executive’ cognitive tasks that are an important part of the primate behavioral repertoire, but which have never been shown previously to exist in any other large animal. Sheep have great potential, not only for use as a large animal model of HD, but also for studying cognitive function and the evolution of complex behaviours in normal animals. PMID:21305061

Test method research on weakening interface strength of steel - concrete under cyclic loading

NASA Astrophysics Data System (ADS)

Liu, Ming-wei; Zhang, Fang-hua; Su, Guang-quan

2018-02-01

The mechanical properties of steel - concrete interface under cyclic loading are the key factors affecting the rule of horizontal load transfer, the calculation of bearing capacity and cumulative horizontal deformation. Cyclic shear test is an effective method to study the strength reduction of steel - concrete interface. A test system composed of large repeated direct shear test instrument, hydraulic servo system, data acquisition system, test control software system and so on is independently designed, and a set of test method, including the specimen preparation, the instrument preparation, the loading method and so on, is put forward. By listing a set of test results, the validity of the test method is verified. The test system and the test method based on it provide a reference for the experimental study on mechanical properties of steel - concrete interface.

Xenon monitoring and the Comprehensive Nuclear-Test-Ban Treaty

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

Bowyer, Theodore W.

How do you monitor (verify) a CTBT? It is a difficult challenge to monitor the entire world for nuclear tests, regardless of size. Nuclear tests 'normally' occur underground, above ground or underwater. Setting aside very small tests (let's limit our thinking to 1 kiloton or more), nuclear tests shake the ground, emit large amounts of radioactivity, and make loud noises if in the atmosphere (or hydroacoustic waves if underwater)

A new test set for validating predictions of protein-ligand interaction.

PubMed

Nissink, J Willem M; Murray, Chris; Hartshorn, Mike; Verdonk, Marcel L; Cole, Jason C; Taylor, Robin

2002-12-01

We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk). Copyright 2002 Wiley-Liss, Inc.

A semiparametric graphical modelling approach for large-scale equity selection.

PubMed

Liu, Han; Mulvey, John; Zhao, Tianqi

2016-01-01

We propose a new stock selection strategy that exploits rebalancing returns and improves portfolio performance. To effectively harvest rebalancing gains, we apply ideas from elliptical-copula graphical modelling and stability inference to select stocks that are as independent as possible. The proposed elliptical-copula graphical model has a latent Gaussian representation; its structure can be effectively inferred using the regularized rank-based estimators. The resulting algorithm is computationally efficient and scales to large data-sets. To show the efficacy of the proposed method, we apply it to conduct equity selection based on a 16-year health care stock data-set and a large 34-year stock data-set. Empirical tests show that the proposed method is superior to alternative strategies including a principal component analysis-based approach and the classical Markowitz strategy based on the traditional buy-and-hold assumption.

Of Small Beauties and Large Beasts: The Quality of Distractors on Multiple-Choice Tests Is More Important than Their Quantity

ERIC Educational Resources Information Center

Papenberg, Martin; Musch, Jochen

2017-01-01

In multiple-choice tests, the quality of distractors may be more important than their number. We therefore examined the joint influence of distractor quality and quantity on test functioning by providing a sample of 5,793 participants with five parallel test sets consisting of items that differed in the number and quality of distractors.…

Scale out databases for CERN use cases

NASA Astrophysics Data System (ADS)

Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Lanza Garcia, Daniel; Surdy, Kacper

2015-12-01

Data generation rates are expected to grow very fast for some database workloads going into LHC run 2 and beyond. In particular this is expected for data coming from controls, logging and monitoring systems. Storing, administering and accessing big data sets in a relational database system can quickly become a very hard technical challenge, as the size of the active data set and the number of concurrent users increase. Scale-out database technologies are a rapidly developing set of solutions for deploying and managing very large data warehouses on commodity hardware and with open source software. In this paper we will describe the architecture and tests on database systems based on Hadoop and the Cloudera Impala engine. We will discuss the results of our tests, including tests of data loading and integration with existing data sources and in particular with relational databases. We will report on query performance tests done with various data sets of interest at CERN, notably data from the accelerator log database.

Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function

PubMed Central

Raychaudhuri, Soumya; Korn, Joshua M.; McCarroll, Steven A.; Altshuler, David; Sklar, Pamela; Purcell, Shaun; Daly, Mark J.

2010-01-01

Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied “pathway” analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package. PMID:20838587

Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers

PubMed Central

Wang, Jun; Luo, Ray

2009-01-01

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. PMID:20063271

The NASA/industry Design Analysis Methods for Vibrations (DAMVIBS) program: McDonnell-Douglas Helicopter Company achievements

NASA Technical Reports Server (NTRS)

Toossi, Mostafa; Weisenburger, Richard; Hashemi-Kia, Mostafa

1993-01-01

This paper presents a summary of some of the work performed by McDonnell Douglas Helicopter Company under NASA Langley-sponsored rotorcraft structural dynamics program known as DAMVIBS (Design Analysis Methods for VIBrationS). A set of guidelines which is applicable to dynamic modeling, analysis, testing, and correlation of both helicopter airframes and a large variety of structural finite element models is presented. Utilization of these guidelines and the key features of their applications to vibration modeling of helicopter airframes are discussed. Correlation studies with the test data, together with the development and applications of a set of efficient finite element model checkout procedures, are demonstrated on a large helicopter airframe finite element model. Finally, the lessons learned and the benefits resulting from this program are summarized.

Rapid and Accurate Machine Learning Recognition of High Performing Metal Organic Frameworks for CO2 Capture.

PubMed

Fernandez, Michael; Boyd, Peter G; Daff, Thomas D; Aghaji, Mohammad Zein; Woo, Tom K

2014-09-04

In this work, we have developed quantitative structure-property relationship (QSPR) models using advanced machine learning algorithms that can rapidly and accurately recognize high-performing metal organic framework (MOF) materials for CO2 capture. More specifically, QSPR classifiers have been developed that can, in a fraction of a section, identify candidate MOFs with enhanced CO2 adsorption capacity (>1 mmol/g at 0.15 bar and >4 mmol/g at 1 bar). The models were tested on a large set of 292 050 MOFs that were not part of the training set. The QSPR classifier could recover 945 of the top 1000 MOFs in the test set while flagging only 10% of the whole library for compute intensive screening. Thus, using the machine learning classifiers as part of a high-throughput screening protocol would result in an order of magnitude reduction in compute time and allow intractably large structure libraries and search spaces to be screened.

Building an Evaluation Scale using Item Response Theory.

PubMed

Lalor, John P; Wu, Hao; Yu, Hong

2016-11-01

Evaluation of NLP methods requires testing against a previously vetted gold-standard test set and reporting standard metrics (accuracy/precision/recall/F1). The current assumption is that all items in a given test set are equal with regards to difficulty and discriminating power. We propose Item Response Theory (IRT) from psychometrics as an alternative means for gold-standard test-set generation and NLP system evaluation. IRT is able to describe characteristics of individual items - their difficulty and discriminating power - and can account for these characteristics in its estimation of human intelligence or ability for an NLP task. In this paper, we demonstrate IRT by generating a gold-standard test set for Recognizing Textual Entailment. By collecting a large number of human responses and fitting our IRT model, we show that our IRT model compares NLP systems with the performance in a human population and is able to provide more insight into system performance than standard evaluation metrics. We show that a high accuracy score does not always imply a high IRT score, which depends on the item characteristics and the response pattern.

Building an Evaluation Scale using Item Response Theory

PubMed Central

Lalor, John P.; Wu, Hao; Yu, Hong

2016-01-01

Evaluation of NLP methods requires testing against a previously vetted gold-standard test set and reporting standard metrics (accuracy/precision/recall/F1). The current assumption is that all items in a given test set are equal with regards to difficulty and discriminating power. We propose Item Response Theory (IRT) from psychometrics as an alternative means for gold-standard test-set generation and NLP system evaluation. IRT is able to describe characteristics of individual items - their difficulty and discriminating power - and can account for these characteristics in its estimation of human intelligence or ability for an NLP task. In this paper, we demonstrate IRT by generating a gold-standard test set for Recognizing Textual Entailment. By collecting a large number of human responses and fitting our IRT model, we show that our IRT model compares NLP systems with the performance in a human population and is able to provide more insight into system performance than standard evaluation metrics. We show that a high accuracy score does not always imply a high IRT score, which depends on the item characteristics and the response pattern.1 PMID:28004039

Cognitive Sex Differences in Reasoning Tasks: Evidence from Brazilian Samples of Educational Settings

ERIC Educational Resources Information Center

Flores-Mendoza, Carmen; Widaman, Keith F.; Rindermann, Heiner; Primi, Ricardo; Mansur-Alves, Marcela; Pena, Carla Couto

2013-01-01

Sex differences on the Attention Test (AC), the Raven's Standard Progressive Matrices (SPM), and the Brazilian Cognitive Battery (BPR5), were investigated using four large samples (total N=6780), residing in the states of Minas Gerais and Sao Paulo. The majority of samples used, which were obtained from educational settings, could be considered a…

Benefits and costs of HIV testing.

PubMed

Bloom, D E; Glied, S

1991-06-28

The benefits and costs of human immunodeficiency virus (HIV) testing in employment settings are examined from two points of view: that of private employers whose profitability may be affected by their testing policies and that of public policy-makers who may affect social welfare through their design of regulations related to HIV testing. The results reveal that HIV testing is clearly not cost-beneficial for most firms, although the benefits of HIV testing may outweigh the costs for some large firms that offer generous fringe-benefit packages and that recruit workers from populations in which the prevalence of HIV infection is high. The analysis also indicates that the testing decisions of unregulated employers are not likely to yield socially optimal economic outcomes and that existing state and federal legislation related to HIV testing in employment settings has been motivated primarily by concerns over social equity.

Considering the Use of General and Modified Assessment Items in Computerized Adaptive Testing

ERIC Educational Resources Information Center

Wyse, Adam E.; Albano, Anthony D.

2015-01-01

This article used several data sets from a large-scale state testing program to examine the feasibility of combining general and modified assessment items in computerized adaptive testing (CAT) for different groups of students. Results suggested that several of the assumptions made when employing this type of mixed-item CAT may not be met for…

Dynamic Bayesian Networks as a Probabilistic Metamodel for Combat Simulations

DTIC Science & Technology

2014-09-18

test is commonly used for large data sets and is the method of comparison presented in Section 5.5. 4.3.3 Kullback - Leibler Divergence Goodness of Fit ...methods exist that might improve the results. A goodness of fit test using the Kullback - Leibler Divergence was proposed in the first paper, but still... Kullback - Leibler Divergence Goodness of Fit Test . . .

Efficiency of parallel direct optimization

NASA Technical Reports Server (NTRS)

Janies, D. A.; Wheeler, W. C.

2001-01-01

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

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

Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

2016-07-28

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

Implementation and Operational Research: Effectiveness and Patient Acceptability of a Sexually Transmitted Infection Self-Testing Program in an HIV Care Setting.

PubMed

Barbee, Lindley A; Tat, Susana; Dhanireddy, Shireesha; Marrazzo, Jeanne M

2016-06-01

Rates of screening for bacterial sexually transmitted infections (STI) among men who have sex with men in HIV care settings remain low despite high prevalence of these infections. STI self-testing may help increase screening rates in clinical settings. We implemented an STI self-testing program at a large, urban HIV care clinic and evaluated its effectiveness and acceptability. We compared measures obtained during the first year of the STI self-testing program (Intervention Year, April 1, 2013-March 31, 2014) to Baseline Year (January 1, 2012-December 31, 2012) to determine: (1) overall clinic change in STI testing coverage and diagnostic yield and; (2) program-specific outcomes including appropriate anatomic site screening and patient-reported acceptability. Overall, testing for gonorrhea and chlamydia increased significantly between Baseline and Intervention Year, and 50% more gonococcal and 47% more chlamydial infections were detected. Syphilis testing coverage remained unchanged. Nearly 95% of 350 men who participated in the STI self-testing program completed site-specific testing appropriately based on self-reported exposures, and 92% rated their self-testing experience as "good" or "very good." STI self-testing in HIV care settings significantly increases testing coverage and detection of gonorrhea and chlamydia, and the program is acceptable to patients. Additional interventions to increase syphilis screening rates are needed.

A semiparametric graphical modelling approach for large-scale equity selection

PubMed Central

Liu, Han; Mulvey, John; Zhao, Tianqi

2016-01-01

We propose a new stock selection strategy that exploits rebalancing returns and improves portfolio performance. To effectively harvest rebalancing gains, we apply ideas from elliptical-copula graphical modelling and stability inference to select stocks that are as independent as possible. The proposed elliptical-copula graphical model has a latent Gaussian representation; its structure can be effectively inferred using the regularized rank-based estimators. The resulting algorithm is computationally efficient and scales to large data-sets. To show the efficacy of the proposed method, we apply it to conduct equity selection based on a 16-year health care stock data-set and a large 34-year stock data-set. Empirical tests show that the proposed method is superior to alternative strategies including a principal component analysis-based approach and the classical Markowitz strategy based on the traditional buy-and-hold assumption. PMID:28316507

A powerful and efficient set test for genetic markers that handles confounders

PubMed Central

Listgarten, Jennifer; Lippert, Christoph; Kang, Eun Yong; Xiang, Jing; Kadie, Carl M.; Heckerman, David

2013-01-01

Motivation: Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger datasets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects—one to capture the set association signal and one to capture confounders. We also introduce a computational speedup for two random-effects models that makes this approach feasible even for extremely large cohorts. Using this model with both the likelihood ratio test and score test, we find that the former yields more power while controlling type I error. Application of our approach to richly structured Genetic Analysis Workshop 14 data demonstrates that our method successfully corrects for population structure and family relatedness, whereas application of our method to a 15 000 individual Crohn’s disease case–control cohort demonstrates that it additionally recovers genes not recoverable by univariate analysis. Availability: A Python-based library implementing our approach is available at http://mscompbio.codeplex.com. Contact: jennl@microsoft.com or lippert@microsoft.com or heckerma@microsoft.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23599503

Requirements for a mobile communications satellite system. Volume 3: Large space structures measurements study

NASA Technical Reports Server (NTRS)

Akle, W.

1983-01-01

This study report defines a set of tests and measurements required to characterize the performance of a Large Space System (LSS), and to scale this data to other LSS satellites. Requirements from the Mobile Communication Satellite (MSAT) configurations derived in the parent study were used. MSAT utilizes a large, mesh deployable antenna, and encompasses a significant range of LSS technology issues in the areas of structural/dynamics, control, and performance predictability. In this study, performance requirements were developed for the antenna. Special emphasis was placed on antenna surface accuracy, and pointing stability. Instrumentation and measurement systems, applicable to LSS, were selected from existing or on-going technology developments. Laser ranging and angulation systems, presently in breadboard status, form the backbone of the measurements. Following this, a set of ground, STS, and GEO-operational were investigated. A third scale (15 meter) antenna system as selected for ground characterization followed by STS flight technology development. This selection ensures analytical scaling from ground-to-orbit, and size scaling. Other benefits are cost and ability to perform reasonable ground tests. Detail costing of the various tests and measurement systems were derived and are included in the report.

Modeling Alaska boreal forests with a controlled trend surface approach

Treesearch

Mo Zhou; Jingjing Liang

2012-01-01

An approach of Controlled Trend Surface was proposed to simultaneously take into consideration large-scale spatial trends and nonspatial effects. A geospatial model of the Alaska boreal forest was developed from 446 permanent sample plots, which addressed large-scale spatial trends in recruitment, diameter growth, and mortality. The model was tested on two sets of...

Using Collaborative Two-Stage Examinations to Address Test Anxiety in a Large Enrollment Gateway Course

ERIC Educational Resources Information Center

Fournier, Kimberly A.; Couret, Jannelle; Ramsay, Jason B.; Caulkins, Joshua L.

2017-01-01

Large enrollment foundational courses are perceived as "high stakes" because of their potential to act as barriers for progression to the next course or admittance to a program. The nature of gateway courses makes them ideal settings to explore the relationship between anxiety, pedagogical interventions, and student performance. Here,…

Bitter or not? BitterPredict, a tool for predicting taste from chemical structure.

PubMed

Dagan-Wiener, Ayana; Nissim, Ido; Ben Abu, Natalie; Borgonovo, Gigliola; Bassoli, Angela; Niv, Masha Y

2017-09-21

Bitter taste is an innately aversive taste modality that is considered to protect animals from consuming toxic compounds. Yet, bitterness is not always noxious and some bitter compounds have beneficial effects on health. Hundreds of bitter compounds were reported (and are accessible via the BitterDB http://bitterdb.agri.huji.ac.il/dbbitter.php ), but numerous additional bitter molecules are still unknown. The dramatic chemical diversity of bitterants makes bitterness prediction a difficult task. Here we present a machine learning classifier, BitterPredict, which predicts whether a compound is bitter or not, based on its chemical structure. BitterDB was used as the positive set, and non-bitter molecules were gathered from literature to create the negative set. Adaptive Boosting (AdaBoost), based on decision trees machine-learning algorithm was applied to molecules that were represented using physicochemical and ADME/Tox descriptors. BitterPredict correctly classifies over 80% of the compounds in the hold-out test set, and 70-90% of the compounds in three independent external sets and in sensory test validation, providing a quick and reliable tool for classifying large sets of compounds into bitter and non-bitter groups. BitterPredict suggests that about 40% of random molecules, and a large portion (66%) of clinical and experimental drugs, and of natural products (77%) are bitter.

Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

ERIC Educational Resources Information Center

Li, Spencer D.

2011-01-01

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

Are All Ames Strains in the OECD Mutagenicity Test Guideline 471 Useful and Necessary? An Analysis of Large Mutagenicity Data Sets for the IWGT

EPA Science Inventory

The International Workshop on Genetic Toxicology (IWGT) meets every four years with an objective to reach consensus recommendations on difficult or conflicting approaches to genotoxicity testing based upon practical experience and newly available data and data analysis techniques...

Signature extension studies

NASA Technical Reports Server (NTRS)

Vincent, R. K.; Thomas, G. S.; Nalepka, R. F.

1974-01-01

The importance of specific spectral regions to signature extension is explored. In the recent past, the signature extension task was focused on the development of new techniques. Tested techniques are now used to investigate this spectral aspect of the large area survey. Sets of channels were sought which, for a given technique, were the least affected by several sources of variation over four data sets and yet provided good object class separation on each individual data set. Using sets of channels determined as part of this study, signature extension was accomplished between data sets collected over a six-day period and over a range of about 400 kilometers.

Serial and parallel attentive visual searches: evidence from cumulative distribution functions of response times.

PubMed

Sung, Kyongje

2008-12-01

Participants searched a visual display for a target among distractors. Each of 3 experiments tested a condition proposed to require attention and for which certain models propose a serial search. Serial versus parallel processing was tested by examining effects on response time means and cumulative distribution functions. In 2 conditions, the results suggested parallel rather than serial processing, even though the tasks produced significant set-size effects. Serial processing was produced only in a condition with a difficult discrimination and a very large set-size effect. The results support C. Bundesen's (1990) claim that an extreme set-size effect leads to serial processing. Implications for parallel models of visual selection are discussed.

Transfer Learning with Convolutional Neural Networks for Classification of Abdominal Ultrasound Images.

PubMed

Cheng, Phillip M; Malhi, Harshawn S

2017-04-01

The purpose of this study is to evaluate transfer learning with deep convolutional neural networks for the classification of abdominal ultrasound images. Grayscale images from 185 consecutive clinical abdominal ultrasound studies were categorized into 11 categories based on the text annotation specified by the technologist for the image. Cropped images were rescaled to 256 × 256 resolution and randomized, with 4094 images from 136 studies constituting the training set, and 1423 images from 49 studies constituting the test set. The fully connected layers of two convolutional neural networks based on CaffeNet and VGGNet, previously trained on the 2012 Large Scale Visual Recognition Challenge data set, were retrained on the training set. Weights in the convolutional layers of each network were frozen to serve as fixed feature extractors. Accuracy on the test set was evaluated for each network. A radiologist experienced in abdominal ultrasound also independently classified the images in the test set into the same 11 categories. The CaffeNet network classified 77.3% of the test set images accurately (1100/1423 images), with a top-2 accuracy of 90.4% (1287/1423 images). The larger VGGNet network classified 77.9% of the test set accurately (1109/1423 images), with a top-2 accuracy of VGGNet was 89.7% (1276/1423 images). The radiologist classified 71.7% of the test set images correctly (1020/1423 images). The differences in classification accuracies between both neural networks and the radiologist were statistically significant (p < 0.001). The results demonstrate that transfer learning with convolutional neural networks may be used to construct effective classifiers for abdominal ultrasound images.

Large aluminium convex mirror for the cryo-optical test of the Planck primary reflector

NASA Astrophysics Data System (ADS)

Gloesener, P.; Flébus, C.; Cola, M.; Roose, S.; Stockman, Y.; de Chambure, D.

2017-11-01

In the frame of the PLANCK mission telescope development, it is requested to measure the reflector changes of the surface figure error (SFE) with respect to the best ellipsoid, between 293 K and 50 K, with 1 μm RMS accuracy. To achieve this, Infra Red interferometry has been selected and a dedicated thermo mechanical set-up has been constructed. In order to realise the test set-up for this reflector, a large aluminium convex mirror with radius of 19500 mm has been manufactured. The mirror has to operate in a cryogenic environment lower than 30 K, and has a contribution to the RMS WFE with less than 1 μm between room temperature and cryogenic temperature. This paper summarises the design, manufacturing and characterisation of this mirror, showing it has fulfilled its requirements.

Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes.

PubMed

Risthaus, Tobias; Grimme, Stefan

2013-03-12

A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

Numerical experiments on short-term meteorological effects on solar variability

NASA Technical Reports Server (NTRS)

Somerville, R. C. J.; Hansen, J. E.; Stone, P. H.; Quirk, W. J.; Lacis, A. A.

1975-01-01

A set of numerical experiments was conducted to test the short-range sensitivity of a large atmospheric general circulation model to changes in solar constant and ozone amount. On the basis of the results of 12-day sets of integrations with very large variations in these parameters, it is concluded that realistic variations would produce insignificant meteorological effects. Any causal relationships between solar variability and weather, for time scales of two weeks or less, rely upon changes in parameters other than solar constant or ozone amounts, or upon mechanisms not yet incorporated in the model.

Choosing the Most Effective Pattern Classification Model under Learning-Time Constraint.

PubMed

Saito, Priscila T M; Nakamura, Rodrigo Y M; Amorim, Willian P; Papa, João P; de Rezende, Pedro J; Falcão, Alexandre X

2015-01-01

Nowadays, large datasets are common and demand faster and more effective pattern analysis techniques. However, methodologies to compare classifiers usually do not take into account the learning-time constraints required by applications. This work presents a methodology to compare classifiers with respect to their ability to learn from classification errors on a large learning set, within a given time limit. Faster techniques may acquire more training samples, but only when they are more effective will they achieve higher performance on unseen testing sets. We demonstrate this result using several techniques, multiple datasets, and typical learning-time limits required by applications.

Butyl rubber O-ring seals: Revision of test procedures for stockpile materials

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

Domeier, L.A.; Wagter, K.R.

1996-12-01

Extensive testing showed little correlation between test slab and O-ring performance. New procedures, comparable to those used with the traditional test slabs, were defined for hardness, compression set, and tensile property testing on sacrificial O-ring specimens. Changes in target performance values were made as needed and were, in one case, tightened to reflect the O-ring performance data. An additional study was carried out on O-ring and slab performance vs cure cycle and showed little sensitivity of material performance to large changes in curing time. Aging and spectra of certain materials indicated that two sets of test slabs from current vendormore » were accidently made from EPDM rather than butyl rubber. Random testing found no O-rings made from EPDM. As a result, and additional spectroscope test will be added to the product acceptance procedures to verify the type of rubber compound used.« less

Dtest Testing Software

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Cameron, Jonathan M.; Myint, Steven

2013-01-01

This software runs a suite of arbitrary software tests spanning various software languages and types of tests (unit level, system level, or file comparison tests). The dtest utility can be set to automate periodic testing of large suites of software, as well as running individual tests. It supports distributing multiple tests over multiple CPU cores, if available. The dtest tool is a utility program (written in Python) that scans through a directory (and its subdirectories) and finds all directories that match a certain pattern and then executes any tests in that directory as described in simple configuration files.

Dividing the Force Concept Inventory into two equivalent half-length tests

NASA Astrophysics Data System (ADS)

Han, Jing; Bao, Lei; Chen, Li; Cai, Tianfang; Pi, Yuan; Zhou, Shaona; Tu, Yan; Koenig, Kathleen

2015-06-01

The Force Concept Inventory (FCI) is a 30-question multiple-choice assessment that has been a building block for much of the physics education research done today. In practice, there are often concerns regarding the length of the test and possible test-retest effects. Since many studies in the literature use the mean score of the FCI as the primary variable, it would be useful then to have different shorter tests that can produce FCI-equivalent scores while providing the benefits of being quicker to administer and overcoming the test-retest effects. In this study, we divide the 1995 version of the FCI into two half-length tests; each contains a different subset of the original FCI questions. The two new tests are shorter, still cover the same set of concepts, and produce mean scores equivalent to those of the FCI. Using a large quantitative data set collected at a large midwestern university, we statistically compare the assessment features of the two half-length tests and the full-length FCI. The results show that the mean error of equivalent scores between any two of the three tests is within 3%. Scores from all tests are well correlated. Based on the analysis, it appears that the two half-length tests can be a viable option for score based assessment that need to administer tests quickly or need to measure short-term gains where using identical pre- and post-test questions is a concern.

SkData: data sets and algorithm evaluation protocols in Python

NASA Astrophysics Data System (ADS)

Bergstra, James; Pinto, Nicolas; Cox, David D.

2015-01-01

Machine learning benchmark data sets come in all shapes and sizes, whereas classification algorithms assume sanitized input, such as (x, y) pairs with vector-valued input x and integer class label y. Researchers and practitioners know all too well how tedious it can be to get from the URL of a new data set to a NumPy ndarray suitable for e.g. pandas or sklearn. The SkData library handles that work for a growing number of benchmark data sets (small and large) so that one-off in-house scripts for downloading and parsing data sets can be replaced with library code that is reliable, community-tested, and documented. The SkData library also introduces an open-ended formalization of training and testing protocols that facilitates direct comparison with published research. This paper describes the usage and architecture of the SkData library.

Experimental instrumentation system for the Phased Array Mirror Extendible Large Aperture (PAMELA) test program

NASA Technical Reports Server (NTRS)

Boykin, William H., Jr.

1993-01-01

Adaptive optics are used in telescopes for both viewing objects with minimum distortion and for transmitting laser beams with minimum beam divergence and dance. In order to test concepts on a smaller scale, NASA MSFC is in the process of setting up an adaptive optics test facility with precision (fraction of wavelengths) measurement equipment. The initial system under test is the adaptive optical telescope called PAMELA (Phased Array Mirror Extendible Large Aperture). Goals of this test are: assessment of test hardware specifications for PAMELA application and the determination of the sensitivities of instruments for measuring PAMELA (and other adaptive optical telescopes) imperfections; evaluation of the PAMELA system integration effort and test progress and recommended actions to enhance these activities; and development of concepts and prototypes of experimental apparatuses for PAMELA.

U.S. Food Safety and Inspection Service testing for Salmonella in selected raw meat and poultry products in the United States, 1998 through 2003: analysis of set results.

PubMed

Naugle, Alecia Larew; Barlow, Kristina E; Eblen, Denise R; Teter, Vanessa; Umholtz, Robert

2006-11-01

The U.S. Food Safety and Inspection Service (FSIS) tests sets of samples of selected raw meat and poultry products for Salmonella to ensure that federally inspected establishments meet performance standards defined in the pathogen reduction-hazard analysis and critical control point system (PR-HACCP) final rule. In the present report, sample set results are described and associations between set failure and set and establishment characteristics are identified for 4,607 sample sets collected from 1998 through 2003. Sample sets were obtained from seven product classes: broiler chicken carcasses (n = 1,010), cow and bull carcasses (n = 240), market hog carcasses (n = 560), steer and heifer carcasses (n = 123), ground beef (n = 2,527), ground chicken (n = 31), and ground turkey (n = 116). Of these 4,607 sample sets, 92% (4,255) were collected as part of random testing efforts (A sets), and 93% (4,166) passed. However, the percentage of positive samples relative to the maximum number of positive results allowable in a set increased over time for broilers but decreased or stayed the same for the other product classes. Three factors associated with set failure were identified: establishment size, product class, and year. Set failures were more likely early in the testing program (relative to 2003). Small and very small establishments were more likely to fail than large ones. Set failure was less likely in ground beef than in other product classes. Despite an overall decline in set failures through 2003, these results highlight the need for continued vigilance to reduce Salmonella contamination in broiler chicken and continued implementation of programs designed to assist small and very small establishments with PR-HACCP compliance issues.

A depth-first search algorithm to compute elementary flux modes by linear programming.

PubMed

Quek, Lake-Ee; Nielsen, Lars K

2014-07-30

The decomposition of complex metabolic networks into elementary flux modes (EFMs) provides a useful framework for exploring reaction interactions systematically. Generating a complete set of EFMs for large-scale models, however, is near impossible. Even for moderately-sized models (<400 reactions), existing approaches based on the Double Description method must iterate through a large number of combinatorial candidates, thus imposing an immense processor and memory demand. Based on an alternative elementarity test, we developed a depth-first search algorithm using linear programming (LP) to enumerate EFMs in an exhaustive fashion. Constraints can be introduced to directly generate a subset of EFMs satisfying the set of constraints. The depth-first search algorithm has a constant memory overhead. Using flux constraints, a large LP problem can be massively divided and parallelized into independent sub-jobs for deployment into computing clusters. Since the sub-jobs do not overlap, the approach scales to utilize all available computing nodes with minimal coordination overhead or memory limitations. The speed of the algorithm was comparable to efmtool, a mainstream Double Description method, when enumerating all EFMs; the attrition power gained from performing flux feasibility tests offsets the increased computational demand of running an LP solver. Unlike the Double Description method, the algorithm enables accelerated enumeration of all EFMs satisfying a set of constraints.

Wind-Tunnel Tests on a Series of Wing Models Through a Large Angle of Attack Range. Part I : Force Tests

NASA Technical Reports Server (NTRS)

Knight, Montgomery; Wenzinger, Carl J

1930-01-01

This investigation covers force tests through a large range of angle of attack on a series of monoplane and biplane wing models. The tests were conducted in the atmospheric wind tunnel of the National Advisory Committee for Aeronautics. The models were arranged in such a manner as to make possible a determination of the effects of variations in tip shape, aspect ratio, flap setting, stagger, gap, decalage, sweep back, and airfoil profile. The arrangements represented most of the types of wing systems in use on modern airplanes. The effect of each variable is illustrated by means of groups of curves. In addition, there are included approximate autorotational characteristics in the form of calculated ranges of "rotary instability." a correction for blocking in this tunnel which applies to monoplanes at large angles of attack has been developed, and is given in an appendix. (author)

Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMI.

PubMed

Vimaleswaran, Karani S; Tachmazidou, Ioanna; Zhao, Jing Hua; Hirschhorn, Joel N; Dudbridge, Frank; Loos, Ruth J F

2012-10-15

Before the advent of genome-wide association studies (GWASs), hundreds of candidate genes for obesity-susceptibility had been identified through a variety of approaches. We examined whether those obesity candidate genes are enriched for associations with body mass index (BMI) compared with non-candidate genes by using data from a large-scale GWAS. A thorough literature search identified 547 candidate genes for obesity-susceptibility based on evidence from animal studies, Mendelian syndromes, linkage studies, genetic association studies and expression studies. Genomic regions were defined to include the genes ±10 kb of flanking sequence around candidate and non-candidate genes. We used summary statistics publicly available from the discovery stage of the genome-wide meta-analysis for BMI performed by the genetic investigation of anthropometric traits consortium in 123 564 individuals. Hypergeometric, rank tail-strength and gene-set enrichment analysis tests were used to test for the enrichment of association in candidate compared with non-candidate genes. The hypergeometric test of enrichment was not significant at the 5% P-value quantile (P = 0.35), but was nominally significant at the 25% quantile (P = 0.015). The rank tail-strength and gene-set enrichment tests were nominally significant for the full set of genes and borderline significant for the subset without SNPs at P < 10(-7). Taken together, the observed evidence for enrichment suggests that the candidate gene approach retains some value. However, the degree of enrichment is small despite the extensive number of candidate genes and the large sample size. Studies that focus on candidate genes have only slightly increased chances of detecting associations, and are likely to miss many true effects in non-candidate genes, at least for obesity-related traits.

Walking to transit.

DOT National Transportation Integrated Search

2011-12-01

Using a real-life setting, WalkBostons project focused on developing and testing techniques to broaden the scope and range of public participation in transportation planning in a large neighborhood in Boston. The team explored methods of seeking o...

Solution for testing large high-power laser lenses having long focal length (Conference Presentation)

NASA Astrophysics Data System (ADS)

Fappani, Denis; IDE, Monique

2017-05-01

Many high power laser facilities are in operation all around the world and include various tight optical components such as large focussing lenses. Such lenses exhibit generally long focal lengths which induces some issues for their optical testing during manufacturing and inspection. Indeed, their transmitted wave fronts need to be very accurate and interferometric testing is the baseline to achieve that. But, it is always a problem to manage simultaneously long testing distances and fine accuracies in such interferometry testing. Taking example of the large focusing lenses produced for the Orion experimentation at AWE (UK), the presentation will describe which kind of testing method has been developed to demonstrate simultaneously good performances with sufficiently good repeatability and absolute accuracy. Special emphasis will be made onto the optical manufacturing issues and interferometric testing solutions. Some ZEMAX results presenting the test set-up and the calibration method will be presented as well. The presentation will conclude with a brief overview of the existing "state of the art" at Thales SESO for these technologies.

IRIS thermal balance test within ESTEC LSS

NASA Technical Reports Server (NTRS)

Messidoro, Piero; Ballesio, Marino; Vessaz, J. P.

1988-01-01

The Italian Research Interim Stage (IRIS) thermal balance test was successfully performed in the ESTEC Large Space Simulator (LSS) to qualify the thermal design and to validate the thermal mathematical model. Characteristics of the test were the complexity of the set-up required to simulate the Shuttle cargo bay and allowing IRIS mechanism actioning and operation for the first time in the new LSS facility. Details of the test are presented, and test results for IRIS and the LSS facility are described.

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

Papajak, Ewa; Truhlar, Donald G.

We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”,more » “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.« less

Bias-Free Chemically Diverse Test Sets from Machine Learning.

PubMed

Swann, Ellen T; Fernandez, Michael; Coote, Michelle L; Barnard, Amanda S

2017-08-14

Current benchmarking methods in quantum chemistry rely on databases that are built using a chemist's intuition. It is not fully understood how diverse or representative these databases truly are. Multivariate statistical techniques like archetypal analysis and K-means clustering have previously been used to summarize large sets of nanoparticles however molecules are more diverse and not as easily characterized by descriptors. In this work, we compare three sets of descriptors based on the one-, two-, and three-dimensional structure of a molecule. Using data from the NIST Computational Chemistry Comparison and Benchmark Database and machine learning techniques, we demonstrate the functional relationship between these structural descriptors and the electronic energy of molecules. Archetypes and prototypes found with topological or Coulomb matrix descriptors can be used to identify smaller, statistically significant test sets that better capture the diversity of chemical space. We apply this same method to find a diverse subset of organic molecules to demonstrate how the methods can easily be reapplied to individual research projects. Finally, we use our bias-free test sets to assess the performance of density functional theory and quantum Monte Carlo methods.

"Familias: Preparando La Nueva Generación": A Randomized Control Trial Testing the Effects on Positive Parenting Practices

ERIC Educational Resources Information Center

Marsiglia, Flavio F.; Williams, Lela Rankin; Ayers, Stephanie L.; Booth, Jaime M.

2014-01-01

Objectives: This article reports the effects of a culturally grounded parenting intervention to strengthen positive parenting practices. Method: The intervention was designed and tested with primarily Mexican origin parents in a large urban setting of the southwestern United States using an ecodevelopmental approach. Parents (N = 393) were…

Modeling the College Application Decision Process in a Land-Grant Institution.

ERIC Educational Resources Information Center

DesJardins, Stephen L.; And Others

This study used a logistic probability model to investigate the effects of variables relating student characteristics and institutional factors on the decision to apply to a large land-grant research university. The study used the entire data set from American College Testing (ACT) program test-takers in the fall of 1995 and institutional data on…

Accounting for multiple stressors in regional stream ecosystem analysis: A demonstration with riparian invasive plants

EPA Science Inventory

Background/Questions/Methods: Large cross-sectional data sets allow testing of hypotheses about how one part of an ecosystem relates to other parts. Tests such as these are of interest for many reasons, one of which is to gain insight into the role of stressors, such as land co...

Testing the Predictors of Boredom at School: Development and Validation of the Precursors to Boredom Scales

ERIC Educational Resources Information Center

Daschmann, Elena C.; Goetz, Thomas; Stupnisky, Robert H.

2011-01-01

Background: Boredom has been found to be an important emotion for students' learning processes and achievement outcomes; however, the precursors of this emotion remain largely unexplored. Aim: In the current study, scales assessing the precursors to boredom in academic achievement settings were developed and tested. Sample: Participants were 1,380…

Complexity as a Factor of Quality and Cost in Large Scale Software Development.

DTIC Science & Technology

1979-12-01

allocating testing resources." [69 69I V. THE ROLE OF COMPLEXITY IN RESOURCE ESTIMATION AND ALLOCATION A. GENERAL It can be argued that blame for the...and allocation of testing resource by - identifying independent substructures and - identifying heavily used logic paths. 2. Setting a Design Threshold... RESOURCE ESTIMATION -------- 70 1. New Dynamic Field ------------------------- 70 2. Quality and Testing ----------------------- 71 3. Programming Units of

Hypothesis test of mediation effect in causal mediation model with high-dimensional continuous mediators.

PubMed

Huang, Yen-Tsung; Pan, Wen-Chi

2016-06-01

Causal mediation modeling has become a popular approach for studying the effect of an exposure on an outcome through a mediator. However, current methods are not applicable to the setting with a large number of mediators. We propose a testing procedure for mediation effects of high-dimensional continuous mediators. We characterize the marginal mediation effect, the multivariate component-wise mediation effects, and the L2 norm of the component-wise effects, and develop a Monte-Carlo procedure for evaluating their statistical significance. To accommodate the setting with a large number of mediators and a small sample size, we further propose a transformation model using the spectral decomposition. Under the transformation model, mediation effects can be estimated using a series of regression models with a univariate transformed mediator, and examined by our proposed testing procedure. Extensive simulation studies are conducted to assess the performance of our methods for continuous and dichotomous outcomes. We apply the methods to analyze genomic data investigating the effect of microRNA miR-223 on a dichotomous survival status of patients with glioblastoma multiforme (GBM). We identify nine gene ontology sets with expression values that significantly mediate the effect of miR-223 on GBM survival. © 2015, The International Biometric Society.

Access to diagnostic tests and essential medicines for cardiovascular diseases and diabetes care: cost, availability and affordability in the West Region of Cameroon.

PubMed

Jingi, Ahmadou M; Noubiap, Jean Jacques N; Ewane Onana, Arnold; Nansseu, Jobert Richie N; Wang, Binhuan; Kingue, Samuel; Kengne, André Pascal

2014-01-01

To assess the availability and affordability of medicines and routine tests for cardiovascular disease (CVD) and diabetes in the West region of Cameroon, a low-income setting. A survey was conducted on the availability and cost of twelve routine tests and twenty medicines for CVD and diabetes in eight health districts (four urban and four rural) covering over 60% of the population of the region (1.8 million). We analyzed the percentage of tests and medicines available, the median price against the international reference price (median price ratio) for the medicines, and affordability in terms of the number of days' wages it would cost the lowest-paid unskilled government worker for initial investigation tests and procurement for one month of treatment. The availability of tests varied between 10% for the ECG to 100% for the fasting blood sugar. The average cost for the initial investigation using the minimum tests cost 29.76 days' wages. The availability of medicines varied from 36.4% to 59.1% in urban and from 9.1% to 50% in rural settings. Only metformin and benzathine-benzylpenicilline had a median price ratio of ≤ 1.5, with statins being largely unaffordable (at least 30.51 days' wages). One month of combination treatment for coronary heart disease costs at least 40.87 days' wages. The investigation and management of patients with medium-to-high cardiovascular risk remains largely unavailable and unaffordable in this setting. An effective non-communicable disease program should lay emphasis on primary prevention, and improve affordable access to essential medicines in public outlets.

Electronic Detection of Delayed Test Result Follow-Up in Patients with Hypothyroidism.

PubMed

Meyer, Ashley N D; Murphy, Daniel R; Al-Mutairi, Aymer; Sittig, Dean F; Wei, Li; Russo, Elise; Singh, Hardeep

2017-07-01

Delays in following up abnormal test results are a common problem in outpatient settings. Surveillance systems that use trigger tools to identify delayed follow-up can help reduce missed opportunities in care. To develop and test an electronic health record (EHR)-based trigger algorithm to identify instances of delayed follow-up of abnormal thyroid-stimulating hormone (TSH) results in patients being treated for hypothyroidism. We developed an algorithm using structured EHR data to identify patients with hypothyroidism who had delayed follow-up (>60 days) after an abnormal TSH. We then retrospectively applied the algorithm to a large EHR data warehouse within the Department of Veterans Affairs (VA), on patient records from two large VA networks for the period from January 1, 2011, to December 31, 2011. Identified records were reviewed to confirm the presence of delays in follow-up. During the study period, 645,555 patients were seen in the outpatient setting within the two networks. Of 293,554 patients with at least one TSH test result, the trigger identified 1250 patients on treatment for hypothyroidism with elevated TSH. Of these patients, 271 were flagged as potentially having delayed follow-up of their test result. Chart reviews confirmed delays in 163 of the 271 flagged patients (PPV = 60.1%). An automated trigger algorithm applied to records in a large EHR data warehouse identified patients with hypothyroidism with potential delays in thyroid function test results follow-up. Future prospective application of the TSH trigger algorithm can be used by clinical teams as a surveillance and quality improvement technique to monitor and improve follow-up.

A support vector machine based test for incongruence between sets of trees in tree space

PubMed Central

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license. PMID:22909268

Integrated Energy Solutions | NREL

Science.gov Websites

Transitions A man and woman standing in front of a large, color 3D visualization screen that spans the height a woman and a man testing a scaled model of a microgrid controller in a laboratory setting

Large strain dynamic compression for soft materials using a direct impact experiment

NASA Astrophysics Data System (ADS)

Meenken, T.; Hiermaier, S.

2006-08-01

Measurement of strain rate dependent material data of low density low strength materials like polymeric foams and rubbers still poses challenges of a different kind to the experimental set up. For instance, in conventional Split Hopkinson Pressure Bar tests the impedance mismatch between the bars and the specimen makes strain measurement almost impossible. Application of viscoelastic bars poses new problems with wave dispersion. Also, maximum achievable strains and strain rates depend directly on the bar lengths, resulting in large experimental set ups in order to measure relevant data for automobile crash applications. In this paper a modified SHPB will be presented for testing low impedance materials. High strains can be achieved with nearly constant strain rate. A thin film stress measurement has been applied to the specimen/bar interfaces to investigate the initial sample ring up process. The process of stress homogeneity within the sample was investigated on EPDM and PU rubber.

Noise tests of a mixer nozzle-externally blown flap system

NASA Technical Reports Server (NTRS)

Goodykoontz, J. H.; Dorsch, R. G.; Groesbeck, D. E.

1973-01-01

Noise tests were conducted on a large scale model of an externally blown flap lift augmentation system, employing a mixer nozzle. The mixer nozzle consisted of seven flow passages with a total equivalent diameter of 40 centimeters. With the flaps in the 30 - 60 deg setting, the noise level below the wing was less with the mixer nozzle than when a standard circular nozzle was used. At the 10 - 20 deg flap setting, the noise levels were about the same when either nozzle was used. With retracted flaps, the noise level was higher when the mixer nozzle was used.

Parallel digital forensics infrastructure.

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

Liebrock, Lorie M.; Duggan, David Patrick

2009-10-01

This report documents the architecture and implementation of a Parallel Digital Forensics infrastructure. This infrastructure is necessary for supporting the design, implementation, and testing of new classes of parallel digital forensics tools. Digital Forensics has become extremely difficult with data sets of one terabyte and larger. The only way to overcome the processing time of these large sets is to identify and develop new parallel algorithms for performing the analysis. To support algorithm research, a flexible base infrastructure is required. A candidate architecture for this base infrastructure was designed, instantiated, and tested by this project, in collaboration with New Mexicomore » Tech. Previous infrastructures were not designed and built specifically for the development and testing of parallel algorithms. With the size of forensics data sets only expected to increase significantly, this type of infrastructure support is necessary for continued research in parallel digital forensics. This report documents the implementation of the parallel digital forensics (PDF) infrastructure architecture and implementation.« less

Large size GEM for Super Bigbite Spectrometer (SBS) polarimeter for Hall A 12GeV program at JLab

DOE PAGES

Gnanvo, Kondo; Liyanage, Nilanga; Nelyubin, Vladimir; ...

2015-05-01

We report on the R&D effort in the design and construction of a large size GEM chamber for the Proton Polarimeter of the Super Bigbite Spectrometer (SBS) in Hall A at Thomas Jefferson National Laboratory (JLab). The SBS Polarimeter trackers consist of two sets of four large chambers of size 200 cm x 60 cm 2. Each chamber is a vertical stack of four GEM modules with an active area of 60 cm x 50 cm. We have built and tested several GEM modules and we describe in this paper the design and construction of the final GEM as wellmore » as the preliminary results on performances from tests carried out in our detector lab and with test beams at (Fermilab).« less

Automatic classification of transiently evoked otoacoustic emissions using an artificial neural network.

PubMed

Buller, G; Lutman, M E

1998-08-01

The increasing use of transiently evoked otoacoustic emissions (TEOAE) in large neonatal hearing screening programmes makes a standardized method of response classification desirable. Until now methods have been either subjective or based on arbitrary response characteristics. This study takes an expert system approach to standardize the subjective judgements of an experienced scorer. The method that is developed comprises three stages. First, it transforms TEOAEs from waveforms in the time domain into a simplified parameter set. Second, the parameter set is classified by an artificial neural network that has been taught on a large database TEOAE waveforms and corresponding expert scores. Third, additional fuzzy logic rules automatically detect probable artefacts in the waveforms and synchronized spontaneous emission components. In this way, the knowledge of the experienced scorer is encapsulated in the expert system software and thereafter can be accessed by non-experts. Teaching and evaluation of the neural network was based on TEOAEs from a database totalling 2190 neonatal hearing screening tests. The database was divided into learning and test groups with 820 and 1370 waveforms respectively. From each recorded waveform a set of 12 parameters was calculated, representing signal static and dynamic properties. The artifical network was taught with parameter sets of only the learning groups. Reproduction of the human scorer classification by the neural net in the learning group showed a sensitivity for detecting screen fails of 99.3% (299 from 301 failed results on subjective scoring) and a specificity for detecting screen passes of 81.1% (421 of 519 pass results). To quantify the post hoc performance of the net (generalization), the test group was then presented to the network input. Sensitivity was 99.4% (474 from 477) and specificity was 87.3% (780 from 893). To check the efficiency of the classification method, a second learning group was selected out of the previous test group, and the previous learning group was used as the test group. Repeating learning and test procedures yielded 99.3% sensitivity and 80.7% specificity for reproduction, and 99.4% sensitivity and 86.7% specificity for generalization. In all respects, performance was better than for a previously optimized method based simply on cross-correlation between replicate non-linear waveforms. It is concluded that classification methods based on neural networks show promise for application to large neonatal screening programmes utilizing TEOAEs.

Reflection-plane tests of spoilers on an advanced technology wing with a large Fowler flap

NASA Technical Reports Server (NTRS)

Wentz, W. H., Jr.; Volk, C. G., Jr.

1976-01-01

Wind tunnel experiments were conducted to determine the effectiveness of spoilers applied to a finite-span wing which utilizes the GA(W)-1 airfoil section and a 30% chord full-span Fowler flap. A series of spoiler cross sectioned shapes were tested utilizing a reflection-plane model. Five-component force characteristics and hinge moment measurements were obtained. Results confirm earlier two-dimensional tests which showed that spoilers could provide large lift increments at any flap setting, and that spoiler control reversal tendencies could be eliminated by providing a vent path from lower surface to upper surface. Performance penalties due to spoiler leakage airflow were measured.

Use of thermal sieve to allow optical testing of cryogenic optical systems.

PubMed

Kim, Dae Wook; Cai, Wenrui; Burge, James H

2012-05-21

Full aperture testing of large cryogenic optical systems has been impractical due to the difficulty of operating a large collimator at cryogenic temperatures. The Thermal Sieve solves this problem by acting as a thermal barrier between an ambient temperature collimator and the cryogenic system under test. The Thermal Sieve uses a set of thermally controlled baffles with array of holes that are lined up to pass the light from the collimator without degrading the wavefront, while attenuating the thermal background by nearly 4 orders of magnitude. This paper provides the theory behind the Thermal Sieve system, evaluates the optimization for its optical and thermal performance, and presents the design and analysis for a specific system.

Total control: a critical analysis of mandatory HIV testing in U.S. prisons.

PubMed

Gagnon, Marilou; Jacob, Jean Daniel; Cormier, Luc

2013-01-01

The aim of this paper is to explore the relationship between mandatory HIV testing and the institutional management of inmates in U.S. prisons. Mandatory HIV testing has been largely overlooked by the nursing community even though it has important human rights and ethical implications. Drawing on the work of Goffman (1990) on the inner workings of total institutions, the present article critically examines the deployment of mandatory HIV testing in U.S. prisons. To set the stage, we define mandatory HIV testing and describe the methods of HIV testing currently used in U.S. prison settings. Then, we provide a brief overview of the concept of total institution and the mortification process. Finally, we expand on the relationship between mandatory HIV testing and much larger institutional objectives of total control, total structuring, total isolation, and separation of inmates from society (as summarized by Farrington, 1992). And lastly, we provide a brief discussion on the implications of mandatory HIV testing (as a method of HIV testing) from a nursing perspective.

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

NASA Astrophysics Data System (ADS)

Mardirossian, Narbe; Head-Gordon, Martin

2015-02-01

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 1010 choices carved out of a functional space of almost 1040 possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

U.S. Food safety and Inspection Service testing for Salmonella in selected raw meat and poultry products in the United States, 1998 through 2003: an establishment-level analysis.

PubMed

Eblen, Denise R; Barlow, Kristina E; Naugle, Alecia Larew

2006-11-01

The U.S. Food Safety and Inspection Service (FSIS) pathogen reduction-hazard analysis critical control point systems final rule, published in 1996, established Salmonella performance standards for broiler chicken, cow and bull, market hog, and steer and heifer carcasses and for ground beef, chicken, and turkey meat. In 1998, the FSIS began testing to verify that establishments are meeting performance standards. Samples are collected in sets in which the number of samples is defined but varies according to product class. A sample set fails when the number of positive Salmonella samples exceeds the maximum number of positive samples allowed under the performance standard. Salmonella sample sets collected at 1,584 establishments from 1998 through 2003 were examined to identify factors associated with failure of one or more sets. Overall, 1,282 (80.9%) of establishments never had failed sets. In establishments that did experience set failure(s), generally the failed sets were collected early in the establishment testing history, with the exception of broiler establishments where failure(s) occurred both early and late in the course of testing. Small establishments were more likely to have experienced a set failure than were large or very small establishments, and broiler establishments were more likely to have failed than were ground beef, market hog, or steer-heifer establishments. Agency response to failed Salmonella sample sets in the form of in-depth verification reviews and related establishment-initiated corrective actions have likely contributed to declines in the number of establishments that failed sets. A focus on food safety measures in small establishments and broiler processing establishments should further reduce the number of sample sets that fail to meet the Salmonella performance standard.

Item Selection and Pre-equating with Empirical Item Characteristic Curves.

ERIC Educational Resources Information Center

Livingston, Samuel A.

An empirical item characteristic curve shows the probability of a correct response as a function of the student's total test score. These curves can be estimated from large-scale pretest data. They enable test developers to select items that discriminate well in the score region where decisions are made. A similar set of curves can be used to…

School Context and Gender Differences in Mathematical Performance among School Graduates in Russia

ERIC Educational Resources Information Center

Bessudnov, Alexey; Makarov, Alexey

2015-01-01

Gender differences in mathematical performance have received considerable scrutiny in the fields of sociology, economics and psychology. We analyse a large data-set of high school graduates who took a standardised mathematical test in Russia in 2011 (n = 738,456) and find no substantial difference in mean test scores across boys and girls.…

Thermal/vacuum measurements of the Herschel space telescope by close-range photogrammetry

NASA Astrophysics Data System (ADS)

Parian, J. Amiri; Cozzani, A.; Appolloni, M.; Casarosa, G.

2017-11-01

In the frame of the development of a videogrammetric system to be used in thermal vacuum chambers at the European Space Research and Technology Centre (ESTEC) and other sites across Europe, the design of a network using micro-cameras was specified by the European Space agency (ESA)-ESTEC. The selected test set-up is the photogrammetric test of the Herschel Satellite Flight Model in the ESTEC Large Space Simulator. The photogrammetric system will be used to verify the Herschel Telescope alignment and Telescope positioning with respect to the Cryostat Vacuum Vessel (CVV) inside the Large Space Simulator during Thermal-Vacuum/Thermal-Balance test phases. We designed a close-range photogrammetric network by heuristic simulation and a videogrammetric system with an overall accuracy of 1:100,000. A semi-automated image acquisition system, which is able to work at low temperatures (-170°C) in order to acquire images according to the designed network has been constructed by ESA-ESTEC. In this paper we will present the videogrammetric system and sub-systems and the results of real measurements with a representative setup similar to the set-up of Herschel spacecraft which was realized in ESTEC Test Centre.

Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

PubMed

Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

2015-08-07

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.

Do Social Conditions Affect Capuchin Monkeys' (Cebus apella) Choices in a Quantity Judgment Task?

PubMed

Beran, Michael J; Perdue, Bonnie M; Parrish, Audrey E; Evans, Theodore A

2012-01-01

Beran et al. (2012) reported that capuchin monkeys closely matched the performance of humans in a quantity judgment test in which information was incomplete but a judgment still had to be made. In each test session, subjects first made quantity judgments between two known options. Then, they made choices where only one option was visible. Both humans and capuchin monkeys were guided by past outcomes, as they shifted from selecting a known option to selecting an unknown option at the point at which the known option went from being more than the average rate of return to less than the average rate of return from earlier choices in the test session. Here, we expanded this assessment of what guides quantity judgment choice behavior in the face of incomplete information to include manipulations to the unselected quantity. We manipulated the unchosen set in two ways: first, we showed the monkeys what they did not get (the unchosen set), anticipating that "losses" would weigh heavily on subsequent trials in which the same known quantity was presented. Second, we sometimes gave the unchosen set to another monkey, anticipating that this social manipulation might influence the risk-taking responses of the focal monkey when faced with incomplete information. However, neither manipulation caused difficulty for the monkeys who instead continued to use the rational strategy of choosing known sets when they were as large as or larger than the average rate of return in the session, and choosing the unknown (riskier) set when the known set was not sufficiently large. As in past experiments, this was true across a variety of daily ranges of quantities, indicating that monkeys were not using some absolute quantity as a threshold for selecting (or not) the known set, but instead continued to use the daily average rate of return to determine when to choose the known versus the unknown quantity.

Some Human Factors in Codebreaking

DTIC Science & Technology

2003-10-01

and backwards the signal span through the rotors and plugboard , finding the right exit at the illuminated panel and ending that stage of transit in...what its starting position was, moving on to discover where the alphabet rings had been set on the rotors. The plugboard settings were largely...using their tried and tested methods. Plugboard connections escalated to ten in January 1939. The Poles would have needed ten times their processing

Online Updating of Statistical Inference in the Big Data Setting.

PubMed

Schifano, Elizabeth D; Wu, Jing; Wang, Chun; Yan, Jun; Chen, Ming-Hui

2016-01-01

We present statistical methods for big data arising from online analytical processing, where large amounts of data arrive in streams and require fast analysis without storage/access to the historical data. In particular, we develop iterative estimating algorithms and statistical inferences for linear models and estimating equations that update as new data arrive. These algorithms are computationally efficient, minimally storage-intensive, and allow for possible rank deficiencies in the subset design matrices due to rare-event covariates. Within the linear model setting, the proposed online-updating framework leads to predictive residual tests that can be used to assess the goodness-of-fit of the hypothesized model. We also propose a new online-updating estimator under the estimating equation setting. Theoretical properties of the goodness-of-fit tests and proposed estimators are examined in detail. In simulation studies and real data applications, our estimator compares favorably with competing approaches under the estimating equation setting.

Experimental Applications of Automatic Test Markup Language (ATML)

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; McCartney, Patrick; Gorringe, Chris

2012-01-01

The authors describe challenging use-cases for Automatic Test Markup Language (ATML), and evaluate solutions. The first case uses ATML Test Results to deliver active features to support test procedure development and test flow, and bridging mixed software development environments. The second case examines adding attributes to Systems Modelling Language (SysML) to create a linkage for deriving information from a model to fill in an ATML document set. Both cases are outside the original concept of operations for ATML but are typical when integrating large heterogeneous systems with modular contributions from multiple disciplines.

A depth-first search algorithm to compute elementary flux modes by linear programming

PubMed Central

2014-01-01

Background The decomposition of complex metabolic networks into elementary flux modes (EFMs) provides a useful framework for exploring reaction interactions systematically. Generating a complete set of EFMs for large-scale models, however, is near impossible. Even for moderately-sized models (<400 reactions), existing approaches based on the Double Description method must iterate through a large number of combinatorial candidates, thus imposing an immense processor and memory demand. Results Based on an alternative elementarity test, we developed a depth-first search algorithm using linear programming (LP) to enumerate EFMs in an exhaustive fashion. Constraints can be introduced to directly generate a subset of EFMs satisfying the set of constraints. The depth-first search algorithm has a constant memory overhead. Using flux constraints, a large LP problem can be massively divided and parallelized into independent sub-jobs for deployment into computing clusters. Since the sub-jobs do not overlap, the approach scales to utilize all available computing nodes with minimal coordination overhead or memory limitations. Conclusions The speed of the algorithm was comparable to efmtool, a mainstream Double Description method, when enumerating all EFMs; the attrition power gained from performing flux feasibility tests offsets the increased computational demand of running an LP solver. Unlike the Double Description method, the algorithm enables accelerated enumeration of all EFMs satisfying a set of constraints. PMID:25074068

Access to chlamydia testing in remote and rural Scotland.

PubMed

Hawkins, Katherine E; Thompson, Lucy; Wilson, Philip

2016-01-01

The aim of this study was to assess access to sexual health care in remote and rural settings using Chlamydia testing as a focus by measuring the extent of Chlamydia testing and positivity across the Scottish Highlands in relation to the Scottish Index of Multiple Deprivation Quintile (SIMD) and Urban Rural 8-fold index (UR8). Tests processed through Raigmore Hospital in Inverness, the main testing laboratory for microbiology tests in North and West and South and Mid Highlands, were studied. Where people are tested in relation to where they live was assessed, as well as the type of test they opt for. Also assessed was the rate of positivity in male and female patients in rural compared with urban settings using the Scottish Government UR8 and in relation to the SIMD. 9644 results were analysed. 77.2% of the results were for females and 22.4% for males. 8.1% of the results were positive and 84.4% were negative. There were proportionately more positive tests from the sexual health sources than from general practice. The proportion of men who had positive tests was almost double that for women (12.7% vs 6.6%) although men made up only 27.9% of the total number of tests. There was no significant difference in positivity when compared with UR8 index or SIMD. 37.7% of people living in the most rural areas (UR8 7-8) had their test performed in a more urban setting (UR8 1-6), and 20.4% people had their test performed in a very urban setting (UR8 1-2). Of these tests, there was a tendency for UR8 7-8 patients to be more likely to have a positive test if tested in an urban setting. These results are similar to previous results in other countries that suggest that Chlamydia positivity is similar in rural and urban settings. A large proportion of people living in more rurally classified areas, and perhaps those with a higher risk, have their test in a central setting, suggesting that they may be bypassing local resources to get a test. The reason for this is not clear. The results also show that men are more likely to have their test in a genitourinary setting as well as have proportionately more positive results. These results support the case for customising sexual health services to the most rural areas and suggest that providing an anonymous testing service in these areas might be beneficial, especially for men.

Measurement of the UH-60A Hub Large Rotor Test Apparatus Control System Stiffness

NASA Technical Reports Server (NTRS)

Kufeld, Robert M.

2014-01-01

This purpose of this report is to provides details of the measurement of the control system stiffness of the UH-60A rotor hub mounted on the Large Rotor Test Apparatus (UH-60A/LRTA). The UH-60A/LRTA was used in the 40- by 80-Foot Wind Tunnel to complete the full-scale wind tunnel test portion of the NASA / ARMY UH-60A Airloads Program. This report describes the LRTA control system and highlights the differences between the LRTA and UH-60A aircraft. The test hardware, test setup, and test procedures are also described. Sample results are shown, including the azimuthal variation of the measured control system stiffness for three different loadings and two different dynamic actuator settings. Finally, the azimuthal stiffness is converted to fixed system values using multi-blade transformations for input to comprehensive rotorcraft prediction codes.

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, R. W.

1986-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on space shuttle flight STS-31D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, Richard W.

1986-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on Space Shuttle flight STS-31D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, Richard W.

1987-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures' dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on space shuttle flight STS-41D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Boeing infrared sensor (BIRS) calibration facility

NASA Technical Reports Server (NTRS)

Hazen, John D.; Scorsone, L. V.

1990-01-01

The Boeing Infrared Sensor (BIRS) Calibration Facility represents a major capital investment in optical and infrared technology. The facility was designed and built for the calibration and testing of the new generation large aperture long wave infrared (LWIR) sensors, seekers, and related technologies. Capability exists to perform both radiometric and goniometric calibrations of large infrared sensors under simulated environmental operating conditions. The system is presently configured for endoatmospheric calibrations with a uniform background field which can be set to simulate the expected mission background levels. During calibration, the sensor under test is also exposed to expected mission temperatures and pressures within the test chamber. Capability exists to convert the facility for exoatmospheric testing. The configuration of the system is described along with hardware elements and changes made to date are addressed.

The positive and negative consequences of multiple-choice testing.

PubMed

Roediger, Henry L; Marsh, Elizabeth J

2005-09-01

Multiple-choice tests are commonly used in educational settings but with unknown effects on students' knowledge. The authors examined the consequences of taking a multiple-choice test on a later general knowledge test in which students were warned not to guess. A large positive testing effect was obtained: Prior testing of facts aided final cued-recall performance. However, prior testing also had negative consequences. Prior reading of a greater number of multiple-choice lures decreased the positive testing effect and increased production of multiple-choice lures as incorrect answers on the final test. Multiple-choice testing may inadvertently lead to the creation of false knowledge.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE PAGES

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.; ...

2016-11-07

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

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

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Distributed computing methodology for training neural networks in an image-guided diagnostic application.

PubMed

Plagianakos, V P; Magoulas, G D; Vrahatis, M N

2006-03-01

Distributed computing is a process through which a set of computers connected by a network is used collectively to solve a single problem. In this paper, we propose a distributed computing methodology for training neural networks for the detection of lesions in colonoscopy. Our approach is based on partitioning the training set across multiple processors using a parallel virtual machine. In this way, interconnected computers of varied architectures can be used for the distributed evaluation of the error function and gradient values, and, thus, training neural networks utilizing various learning methods. The proposed methodology has large granularity and low synchronization, and has been implemented and tested. Our results indicate that the parallel virtual machine implementation of the training algorithms developed leads to considerable speedup, especially when large network architectures and training sets are used.

Set size and culture influence children's attention to number.

PubMed

Cantrell, Lisa; Kuwabara, Megumi; Smith, Linda B

2015-03-01

Much research evidences a system in adults and young children for approximately representing quantity. Here we provide evidence that the bias to attend to discrete quantity versus other dimensions may be mediated by set size and culture. Preschool-age English-speaking children in the United States and Japanese-speaking children in Japan were tested in a match-to-sample task where number was pitted against cumulative surface area in both large and small numerical set comparisons. Results showed that children from both cultures were biased to attend to the number of items for small sets. Large set responses also showed a general attention to number when ratio difficulty was easy. However, relative to the responses for small sets, attention to number decreased for both groups; moreover, both U.S. and Japanese children showed a significant bias to attend to total amount for difficult numerical ratio distances, although Japanese children shifted attention to total area at relatively smaller set sizes than U.S. children. These results add to our growing understanding of how quantity is represented and how such representation is influenced by context--both cultural and perceptual. Copyright © 2014 Elsevier Inc. All rights reserved.

Summary of LaRC 2-inch Erectable Joint Hardware Heritage Test Data

NASA Technical Reports Server (NTRS)

Dorsey, John T.; Watson, Judith J.

2016-01-01

As the National Space Transportation System (STS, also known as the Space Shuttle) went into service during the early 1980's, NASA envisioned many missions of exploration and discovery that could take advantage of the STS capabilities. These missions included: large orbiting space stations, large space science telescopes and large spacecraft for manned missions to the Moon and Mars. The missions required structures that were significantly larger than the payload volume available on the STS. NASA Langley Research Center (LaRC) conducted studies to design and develop the technology needed to assemble the large space structures in orbit. LaRC focused on technology for erectable truss structures, in particular, the joint that connects the truss struts at the truss nodes. When the NASA research in large erectable space structures ended in the early 1990's, a significant amount of structural testing had been performed on the LaRC 2-inch erectable joint that was never published. An extensive set of historical information and data has been reviewed and the joint structural testing results from this historical data are compiled and summarized in this report.

Participation of low-income women in genetic cancer risk assessment and BRCA 1/2 testing: the experience of a safety-net institution.

PubMed

Komenaka, Ian K; Nodora, Jesse N; Madlensky, Lisa; Winton, Lisa M; Heberer, Meredith A; Schwab, Richard B; Weitzel, Jeffrey N; Martinez, Maria Elena

2016-07-01

Some communities and populations lack access to genetic cancer risk assessment (GCRA) and testing. This is particularly evident in safety-net institutions, which serve a large segment of low-income, uninsured individuals. We describe the experience of a safety-net clinic with limited resources in providing GCRA and BRCA1/2 testing. We compared the proportion and characteristics of high-risk women who were offered and underwent GCRA and genetic testing. We also provide a description of the mutation profile for affected women. All 125 patients who were offered GCRA accepted to undergo GCRA. Of these, 72 % had a breast cancer diagnosis, 70 % were Hispanic, 52.8 % were non-English speakers, and 66 % did not have health insurance. Eighty four (67 %) were offered genetic testing and 81 (96 %) agreed. Hispanic women, those with no medical insurance, and those with a family history of breast cancer were significantly more likely to undergo testing (p > 0.01). Twelve of 81 (15 %) patients were found to have deleterious mutations, seven BRCA1, and five BRCA2. Our experience shows that it is possible to offer GCRA and genetic testing even in the setting of limited resources for these services. This is important given that a large majority of the low-income women in our study agreed to undergo counseling and testing. Our experience could serve as a model for similar low-resource safety-net health settings.

Pharmaceutical Raw Material Identification Using Miniature Near-Infrared (MicroNIR) Spectroscopy and Supervised Pattern Recognition Using Support Vector Machine

PubMed Central

Hsiung, Chang; Pederson, Christopher G.; Zou, Peng; Smith, Valton; von Gunten, Marc; O’Brien, Nada A.

2016-01-01

Near-infrared spectroscopy as a rapid and non-destructive analytical technique offers great advantages for pharmaceutical raw material identification (RMID) to fulfill the quality and safety requirements in pharmaceutical industry. In this study, we demonstrated the use of portable miniature near-infrared (MicroNIR) spectrometers for NIR-based pharmaceutical RMID and solved two challenges in this area, model transferability and large-scale classification, with the aid of support vector machine (SVM) modeling. We used a set of 19 pharmaceutical compounds including various active pharmaceutical ingredients (APIs) and excipients and six MicroNIR spectrometers to test model transferability. For the test of large-scale classification, we used another set of 253 pharmaceutical compounds comprised of both chemically and physically different APIs and excipients. We compared SVM with conventional chemometric modeling techniques, including soft independent modeling of class analogy, partial least squares discriminant analysis, linear discriminant analysis, and quadratic discriminant analysis. Support vector machine modeling using a linear kernel, especially when combined with a hierarchical scheme, exhibited excellent performance in both model transferability and large-scale classification. Hence, ultra-compact, portable and robust MicroNIR spectrometers coupled with SVM modeling can make on-site and in situ pharmaceutical RMID for large-volume applications highly achievable. PMID:27029624

Cosmological consistency tests of gravity theory and cosmic acceleration

NASA Astrophysics Data System (ADS)

Ishak-Boushaki, Mustapha B.

2017-01-01

Testing general relativity at cosmological scales and probing the cause of cosmic acceleration are among the important objectives targeted by incoming and future astronomical surveys and experiments. I present our recent results on consistency tests that can provide insights about the underlying gravity theory and cosmic acceleration using cosmological data sets. We use statistical measures, the rate of cosmic expansion, the growth rate of large scale structure, and the physical consistency of these probes with one another.

Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description.

PubMed

Auer, Lucas; Mariadassou, Mahendra; O'Donohue, Michael; Klopp, Christophe; Hernandez-Raquet, Guillermina

2017-11-01

Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α- and β-diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α- and β-community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates. © 2017 John Wiley & Sons Ltd.

An accelerated test design for use with synchronous orbit. [on Ni-Cd cell degradation behavior

NASA Technical Reports Server (NTRS)

Mcdermott, P. P.; Vasanth, K. L.

1980-01-01

The Naval Weapons Support Center at Crane, Indiana has conducted a large scale accelerated test of 6.0 Ah Ni-Cd cells. Data from the Crane test have been used to develop an equation for the description of Ni-Cd cell behavior in geosynchronous orbit. This equation relates the anticipated time to failure for a cell in synchronous orbit to temperature and overcharge rate sustained by the cell during the light period. A test design is suggested which uses this equation for setting test parameters for future accelerated testing.

ANALYZING CORRELATIONS BETWEEN STREAM AND WATERSHED ATTRIBUTES

EPA Science Inventory

Bivariate correlation analysis has been widely used to explore relationships between stream and watershed attributes that have all been measured on the same set of watersheds or sampling locations. Researchers routinely test H0: =0 for each correlation in a large table and then ...

Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach.

PubMed

Schneider, Nadine; Fechner, Nikolas; Landrum, Gregory A; Stiefl, Nikolaus

2017-08-28

Big data is one of the key transformative factors which increasingly influences all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: more and more data are being generated, for instance, by technologies such as DNA encoded libraries, peptide libraries, text mining of large literature corpora, and new in silico enumeration methods. Handling those huge sets of molecules effectively is quite challenging and requires compromises that often come at the expense of the interpretability of the results. In order to find an intuitive and meaningful approach to organizing large molecular data sets, we adopted a probabilistic framework called "topic modeling" from the text-mining field. Here we present the first chemistry-related implementation of this method, which allows large molecule sets to be assigned to "chemical topics" and investigating the relationships between those. In this first study, we thoroughly evaluate this novel method in different experiments and discuss both its disadvantages and advantages. We show very promising results in reproducing human-assigned concepts using the approach to identify and retrieve chemical series from sets of molecules. We have also created an intuitive visualization of the chemical topics output by the algorithm. This is a huge benefit compared to other unsupervised machine-learning methods, like clustering, which are commonly used to group sets of molecules. Finally, we applied the new method to the 1.6 million molecules of the ChEMBL22 data set to test its robustness and efficiency. In about 1 h we built a 100-topic model of this large data set in which we could identify interesting topics like "proteins", "DNA", or "steroids". Along with this publication we provide our data sets and an open-source implementation of the new method (CheTo) which will be part of an upcoming version of the open-source cheminformatics toolkit RDKit.

The development and validation of the Closed-set Mandarin Sentence (CMS) test.

PubMed

Tao, Duo-Duo; Fu, Qian-Jie; Galvin, John J; Yu, Ya-Feng

2017-09-01

Matrix-styled sentence tests offer a closed-set paradigm that may be useful when evaluating speech intelligibility. Ideally, sentence test materials should reflect the distribution of phonemes within the target language. We developed and validated the Closed-set Mandarin Sentence (CMS) test to assess Mandarin speech intelligibility in noise. CMS test materials were selected to be familiar words and to represent the natural distribution of vowels, consonants, and lexical tones found in Mandarin Chinese. Ten key words in each of five categories (Name, Verb, Number, Color, and Fruit) were produced by a native Mandarin talker, resulting in a total of 50 words that could be combined to produce 100,000 unique sentences. Normative data were collected in 10 normal-hearing, adult Mandarin-speaking Chinese listeners using a closed-set test paradigm. Two test runs were conducted for each subject, and 20 sentences per run were randomly generated while ensuring that each word was presented only twice in each run. First, the level of the words in each category were adjusted to produce equal intelligibility in noise. Test-retest reliability for word-in-sentence recognition was excellent according to Cronbach's alpha (0.952). After the category level adjustments, speech reception thresholds (SRTs) for sentences in noise, defined as the signal-to-noise ratio (SNR) that produced 50% correct whole sentence recognition, were adaptively measured by adjusting the SNR according to the correctness of response. The mean SRT was -7.9 (SE=0.41) and -8.1 (SE=0.34) dB for runs 1 and 2, respectively. The mean standard deviation across runs was 0.93 dB, and paired t-tests showed no significant difference between runs 1 and 2 (p=0.74) despite random sentences being generated for each run and each subject. The results suggest that the CMS provides large stimulus set with which to repeatedly and reliably measure Mandarin-speaking listeners' speech understanding in noise using a closed-set paradigm.

QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors.

PubMed

Tarasova, Olga A; Urusova, Aleksandra F; Filimonov, Dmitry A; Nicklaus, Marc C; Zakharov, Alexey V; Poroikov, Vladimir V

2015-07-27

Large-scale databases are important sources of training sets for various QSAR modeling approaches. Generally, these databases contain information extracted from different sources. This variety of sources can produce inconsistency in the data, defined as sometimes widely diverging activity results for the same compound against the same target. Because such inconsistency can reduce the accuracy of predictive models built from these data, we are addressing the question of how best to use data from publicly and commercially accessible databases to create accurate and predictive QSAR models. We investigate the suitability of commercially and publicly available databases to QSAR modeling of antiviral activity (HIV-1 reverse transcriptase (RT) inhibition). We present several methods for the creation of modeling (i.e., training and test) sets from two, either commercially or freely available, databases: Thomson Reuters Integrity and ChEMBL. We found that the typical predictivities of QSAR models obtained using these different modeling set compilation methods differ significantly from each other. The best results were obtained using training sets compiled for compounds tested using only one method and material (i.e., a specific type of biological assay). Compound sets aggregated by target only typically yielded poorly predictive models. We discuss the possibility of "mix-and-matching" assay data across aggregating databases such as ChEMBL and Integrity and their current severe limitations for this purpose. One of them is the general lack of complete and semantic/computer-parsable descriptions of assay methodology carried by these databases that would allow one to determine mix-and-matchability of result sets at the assay level.

Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.; Pappa, R. S.

1985-01-01

The ability of the ITD identification algorithm in identifying a complete set of structural modal parameters using a large number of free-response time histories simultaneously in one analysis, assuming a math model with a high number of degrees-of-freedom, has been studied. Identification results using simulated free responses of a uniform rectangular plate, with 225 measurement stations, and experimental responses from a ground vibration test of the Long Duration Exposure Facility (LDEF) Space Shuttle payload, with 142 measurement stations, are presented. As many as 300 degrees-of-freedom were allowed in analyzing these data. In general, the use of a significantly oversized math model in the identification process was found to maintain or increase identification accuracy and to identify modes of low response level that are not identified with smaller math model sizes. The concept of a Mode Shape Correlation Constant is introduced for use when more than one identification analysis of the same structure are conducted. This constant quantifies the degree of correlation between any two sets of complex mode shapes identified using different excitation conditions, different user-selectable algorithm constants, or overlapping sets of measurements.

Large modal survey testing using the Ibrahim time domain /ITD/ identification technique

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.; Pappa, R. S.

1981-01-01

The ability of the ITD identification algorithm in identifying a complete set of structural modal parameters using a large number of free-response time histories simultaneously in one analysis, assuming a math model with a high number of degrees-of-freedom, has been studied. Identification results using simulated free responses of a uniform rectangular plate, with 225 measurement stations, and experimental responses from a ground vibration test of the Long Duration Exposure Facility (LDEF) Space Shuttle payload, with 142 measurement stations, are presented. As many as 300 degrees-of-freedom were allowed in analyzing these data. In general, the use of a significantly oversized math model in the identification process was found to maintain or increase identification accuracy and to identify modes of low response level that are not identified with smaller math model sizes. The concept of a Mode Shape Correlation Constant is introduced for use when more than one identification analysis of the same structure are conducted. This constant quantifies the degree of correlation between any two sets of complex mode shapes identified using different excitation conditions, different user-selectable algorithm constants, or overlapping sets of measurements.

Coordinated platooning with multiple speeds

DOE PAGES

Luo, Fengqiao; Larson, Jeffrey; Munson, Todd

2018-03-22

In a platoon, vehicles travel one after another with small intervehicle distances; trailing vehicles in a platoon save fuel because they experience less aerodynamic drag. This work presents a coordinated platooning model with multiple speed options that integrates scheduling, routing, speed selection, and platoon formation/dissolution in a mixed-integer linear program that minimizes the total fuel consumed by a set of vehicles while traveling between their respective origins and destinations. The performance of this model is numerically tested on a grid network and the Chicago-area highway network. We find that the fuel-savings factor of a multivehicle system significantly depends on themore » time each vehicle is allowed to stay in the network; this time affects vehicles’ available speed choices, possible routes, and the amount of time for coordinating platoon formation. For problem instances with a large number of vehicles, we propose and test a heuristic decomposed approach that applies a clustering algorithm to partition the set of vehicles and then routes each group separately. When the set of vehicles is large and the available computational time is small, the decomposed approach finds significantly better solutions than does the full model.« less

Coordinated platooning with multiple speeds

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

Luo, Fengqiao; Larson, Jeffrey; Munson, Todd

In a platoon, vehicles travel one after another with small intervehicle distances; trailing vehicles in a platoon save fuel because they experience less aerodynamic drag. This work presents a coordinated platooning model with multiple speed options that integrates scheduling, routing, speed selection, and platoon formation/dissolution in a mixed-integer linear program that minimizes the total fuel consumed by a set of vehicles while traveling between their respective origins and destinations. The performance of this model is numerically tested on a grid network and the Chicago-area highway network. We find that the fuel-savings factor of a multivehicle system significantly depends on themore » time each vehicle is allowed to stay in the network; this time affects vehicles’ available speed choices, possible routes, and the amount of time for coordinating platoon formation. For problem instances with a large number of vehicles, we propose and test a heuristic decomposed approach that applies a clustering algorithm to partition the set of vehicles and then routes each group separately. When the set of vehicles is large and the available computational time is small, the decomposed approach finds significantly better solutions than does the full model.« less

A large-scale, long-term study of scale drift: The micro view and the macro view

NASA Astrophysics Data System (ADS)

He, W.; Li, S.; Kingsbury, G. G.

2016-11-01

The development of measurement scales for use across years and grades in educational settings provides unique challenges, as instructional approaches, instructional materials, and content standards all change periodically. This study examined the measurement stability of a set of Rasch measurement scales that have been in place for almost 40 years. In order to investigate the stability of these scales, item responses were collected from a large set of students who took operational adaptive tests using items calibrated to the measurement scales. For the four scales that were examined, item samples ranged from 2183 to 7923 items. Each item was administered to at least 500 students in each grade level, resulting in approximately 3000 responses per item. Stability was examined at the micro level analysing change in item parameter estimates that have occurred since the items were first calibrated. It was also examined at the macro level, involving groups of items and overall test scores for students. Results indicated that individual items had changes in their parameter estimates, which require further analysis and possible recalibration. At the same time, the results at the total score level indicate substantial stability in the measurement scales over the span of their use.

WND-CHARM: Multi-purpose image classification using compound image transforms

PubMed Central

Orlov, Nikita; Shamir, Lior; Macura, Tomasz; Johnston, Josiah; Eckley, D. Mark; Goldberg, Ilya G.

2008-01-01

We describe a multi-purpose image classifier that can be applied to a wide variety of image classification tasks without modifications or fine-tuning, and yet provide classification accuracy comparable to state-of-the-art task-specific image classifiers. The proposed image classifier first extracts a large set of 1025 image features including polynomial decompositions, high contrast features, pixel statistics, and textures. These features are computed on the raw image, transforms of the image, and transforms of transforms of the image. The feature values are then used to classify test images into a set of pre-defined image classes. This classifier was tested on several different problems including biological image classification and face recognition. Although we cannot make a claim of universality, our experimental results show that this classifier performs as well or better than classifiers developed specifically for these image classification tasks. Our classifier’s high performance on a variety of classification problems is attributed to (i) a large set of features extracted from images; and (ii) an effective feature selection and weighting algorithm sensitive to specific image classification problems. The algorithms are available for free download from openmicroscopy.org. PMID:18958301

Treatment of severe pulmonary hypertension in the setting of the large patent ductus arteriosus.

PubMed

Niu, Mary C; Mallory, George B; Justino, Henri; Ruiz, Fadel E; Petit, Christopher J

2013-05-01

Treatment of the large patent ductus arteriosus (PDA) in the setting of pulmonary hypertension (PH) is challenging. Left patent, the large PDA can result in irreversible pulmonary vascular disease. Occlusion, however, may lead to right ventricular failure for certain patients with severe PH. Our center has adopted a staged management strategy using medical management, noninvasive imaging, and invasive cardiac catheterization to treat PH in the presence of a large PDA. This approach determines the safety of ductal closure but also leverages medical therapy to create an opportunity for safe PDA occlusion. We reviewed our experience with this approach. Patients with both severe PH and PDAs were studied. PH treatment history and hemodynamic data obtained during catheterizations were reviewed. Repeat catheterizations, echocardiograms, and clinical status at latest follow-up were also reviewed. Seven patients had both PH and large, unrestrictive PDAs. At baseline, all patients had near-systemic right ventricular pressures. Nine catheterizations were performed. Two patients underwent 2 catheterizations each due to poor initial response to balloon test occlusion. Six of 7 patients exhibited subsystemic pulmonary pressures during test occlusion and underwent successful PDA occlusion. One patient did not undergo PDA occlusion. In follow-up, 2 additional catheterizations were performed after successful PDA occlusion for subsequent hemodynamic assessment. At the latest follow-up, the 6 patients who underwent PDA occlusion are well, with continued improvement in PH. Five patients remain on PH treatment. A staged approach to PDA closure for patients with severe PH is an effective treatment paradigm. Aggressive treatment of PH creates a window of opportunity for PDA occlusion, echocardiography assists in identifying the timing for closure, and balloon test occlusion during cardiac catheterization is critical in determining safety of closure. By safely eliminating the large PDA, this treatment algorithm can halt the perilous combination of the large shunting from the PDA and PH in a population at high risk of morbidity and mortality.

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

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

Mardirossian, Narbe; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

2015-02-21

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10{sup 10} choices carved out of a functional space of almost 10{sup 40} possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based onmore » a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.« less

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2015-02-20

We present a meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional. The functional form is selected from more than 10 10 choices carved out of a functional space of almost 10 40 possibilities. This raw data comes from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filteredmore » based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.« less

Turbulent and Laminar Flow in Karst Conduits Under Unsteady Flow Conditions: Interpretation of Pumping Tests by Discrete Conduit-Continuum Modeling

NASA Astrophysics Data System (ADS)

Giese, M.; Reimann, T.; Bailly-Comte, V.; Maréchal, J.-C.; Sauter, M.; Geyer, T.

2018-03-01

Due to the duality in terms of (1) the groundwater flow field and (2) the discharge conditions, flow patterns of karst aquifer systems are complex. Estimated aquifer parameters may differ by several orders of magnitude from local (borehole) to regional (catchment) scale because of the large contrast in hydraulic parameters between matrix and conduit, their heterogeneity and anisotropy. One approach to deal with the scale effect problem in the estimation of hydraulic parameters of karst aquifers is the application of large-scale experiments such as long-term high-abstraction conduit pumping tests, stimulating measurable groundwater drawdown in both, the karst conduit system as well as the fractured matrix. The numerical discrete conduit-continuum modeling approach MODFLOW-2005 Conduit Flow Process Mode 1 (CFPM1) is employed to simulate laminar and nonlaminar conduit flow, induced by large-scale experiments, in combination with Darcian matrix flow. Effects of large-scale experiments were simulated for idealized settings. Subsequently, diagnostic plots and analyses of different fluxes are applied to interpret differences in the simulated conduit drawdown and general flow patterns. The main focus is set on the question to which extent different conduit flow regimes will affect the drawdown in conduit and matrix depending on the hydraulic properties of the conduit system, i.e., conduit diameter and relative roughness. In this context, CFPM1 is applied to investigate the importance of considering turbulent conditions for the simulation of karst conduit flow. This work quantifies the relative error that results from assuming laminar conduit flow for the interpretation of a synthetic large-scale pumping test in karst.

Toward open set recognition.

PubMed

Scheirer, Walter J; de Rezende Rocha, Anderson; Sapkota, Archana; Boult, Terrance E

2013-07-01

To date, almost all experimental evaluations of machine learning-based recognition algorithms in computer vision have taken the form of "closed set" recognition, whereby all testing classes are known at training time. A more realistic scenario for vision applications is "open set" recognition, where incomplete knowledge of the world is present at training time, and unknown classes can be submitted to an algorithm during testing. This paper explores the nature of open set recognition and formalizes its definition as a constrained minimization problem. The open set recognition problem is not well addressed by existing algorithms because it requires strong generalization. As a step toward a solution, we introduce a novel "1-vs-set machine," which sculpts a decision space from the marginal distances of a 1-class or binary SVM with a linear kernel. This methodology applies to several different applications in computer vision where open set recognition is a challenging problem, including object recognition and face verification. We consider both in this work, with large scale cross-dataset experiments performed over the Caltech 256 and ImageNet sets, as well as face matching experiments performed over the Labeled Faces in the Wild set. The experiments highlight the effectiveness of machines adapted for open set evaluation compared to existing 1-class and binary SVMs for the same tasks.

The big fat LARS - a LArge Reservoir Simulator for hydrate formation and gas production

NASA Astrophysics Data System (ADS)

Beeskow-Strauch, Bettina; Spangenberg, Erik; Schicks, Judith M.; Giese, Ronny; Luzi-Helbing, Manja; Priegnitz, Mike; Klump, Jens; Thaler, Jan; Abendroth, Sven

2013-04-01

Simulating natural scenarios on lab scale is a common technique to gain insight into geological processes with moderate effort and expenses. Due to the remote occurrence of gas hydrates, their behavior in sedimentary deposits is largely investigated on experimental set ups in the laboratory. In the framework of the submarine gas hydrate research project (SUGAR) a large reservoir simulator (LARS) with an internal volume of 425 liter has been designed, built and tested. To our knowledge this is presently a word-wide unique set up. Because of its large volume it is suitable for pilot plant scale tests on hydrate behavior in sediments. That includes not only the option of systematic tests on gas hydrate formation in various sedimentary settings but also the possibility to mimic scenarios for the hydrate decomposition and subsequent natural gas extraction. Based on these experimental results various numerical simulations can be realized. Here, we present the design and the experimental set up of LARS. The prerequisites for the simulation of a natural gas hydrate reservoir are porous sediments, methane, water, low temperature and high pressure. The reservoir is supplied by methane-saturated and pre-cooled water. For its preparation an external gas-water mixing stage is available. The methane-loaded water is continuously flushed into LARS as finely dispersed fluid via bottom-and-top-located sparger. The LARS is equipped with a mantle cooling system and can be kept at a chosen set temperature. The temperature distribution is monitored at 14 reasonable locations throughout the reservoir by Pt100 sensors. Pressure needs are realized using syringe pump stands. A tomographic system, consisting of a 375-electrode-configuration is attached to the mantle for the monitoring of hydrate distribution throughout the entire reservoir volume. Two sets of tubular polydimethylsiloxan-membranes are applied to determine gas-water ratio within the reservoir using the effect of permeability differences between gaseous and dissolved methane (Zimmer et al., 2011). Gas hydrate is formed using a confined pressure of 12-15 MPa and a fluid pressure of 8-11 MPa with a set temperature of 275 K. The duration of the formation process depends on the required hydrate saturation and is usually in a range of several weeks. The subsequent decomposition experiments aiming at testing innovative production scenarios such as the application of a borehole tool for thermal stimulation of hydrate via catalytic oxidation of methane within an autothermal catalytic reactor (Schicks et al. 2011). Furthermore, experiments on hydrate decomposition via pressure reduction are performed to mimic realistic scenarios such as found during the production test in Mallik (Yasuda and Dallimore, 2007). In the near future it is planned to scale up existing results on CH4-CO2 exchange efficiency (e.g. Strauch and Schicks, 2012) by feeding CO2 to the hydrate reservoir. All experiments are due to the gain of high-resolution spatial and temporal data predestined as a base for numerical modeling. References Schicks, J. M., Spangenberg, E., Giese, R., Steinhauer, B., Klump, J., Luzi, M., 2011. Energies, 4, 1, 151-172. Zimmer, M., Erzinger, J., Kujawa, C., 2011. Int. J. of Greenhouse Gas Control, 5, 4, 995-1001. Yasuda, M., Dallimore, S. J., 2007. Jpn. Assoc. Pet. Technol., 72, 603-607. Beeskow-Strauch, B., Schicks, J.M., 2012. Energies, 5, 420-437.

Urine testing and urinary tract infections in febrile infants seen in office settings: the Pediatric Research in Office Settings' Febrile Infant Study.

PubMed

Newman, Thomas B; Bernzweig, Jane A; Takayama, John I; Finch, Stacia A; Wasserman, Richard C; Pantell, Robert H

2002-01-01

To determine the predictors and results of urine testing of young febrile infants seen in office settings. Prospective cohort study. Offices of 573 pediatric practitioners from 219 practices in the American Academy of Pediatrics Pediatric Research in Office Settings' research network. A total of 3066 infants 3 months or younger with temperatures of 38 degrees C or higher were evaluated and treated according to the judgment of their practitioners. Urine testing results, early and late urinary tract infections (UTIs), and UTIs with bacteremia. Fifty-four percent of the infants initially had urine tested, of whom 10% had a UTI. The height of the fever was associated with urine testing and a UTI among those tested (adjusted odds ratio per degree Celsius, 2.2 for both). Younger age, ill appearance, and lack of a fever source were associated with urine testing but not with a UTI, whereas lack of circumcision (adjusted odds ratio, 11.6), female sex (adjusted odds ratio, 5.4), and longer duration of fever (adjusted odds ratio, 1.8 for fever lasting > or = 24 hours) were not associated with urine testing but were associated with a UTI. Bacteremia accompanied the UTI in 10% of the patients, including 17% of those younger than 1 month. Among 807 infants not initially tested or treated with antibiotics, only 2 had a subsequent documented UTI; both did well. Practitioners order urine tests selectively, focusing on younger and more ill-appearing infants and on those without an apparent fever source. Such selective urine testing, with close follow-up, was associated with few late UTIs in this large study. Urine testing should focus particularly on uncircumcised boys, girls, the youngest and sickest infants, and those with persistent fever.

Detecting communities in large networks

NASA Astrophysics Data System (ADS)

Capocci, A.; Servedio, V. D. P.; Caldarelli, G.; Colaiori, F.

2005-07-01

We develop an algorithm to detect community structure in complex networks. The algorithm is based on spectral methods and takes into account weights and link orientation. Since the method detects efficiently clustered nodes in large networks even when these are not sharply partitioned, it turns to be specially suitable for the analysis of social and information networks. We test the algorithm on a large-scale data-set from a psychological experiment of word association. In this case, it proves to be successful both in clustering words, and in uncovering mental association patterns.

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

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design ofmore » the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust “high-speed” computational tool in theoretical chemistry and physics.« less

How to test validity in orthodontic research: a mixed dentition analysis example.

PubMed

Donatelli, Richard E; Lee, Shin-Jae

2015-02-01

The data used to test the validity of a prediction method should be different from the data used to generate the prediction model. In this study, we explored whether an independent data set is mandatory for testing the validity of a new prediction method and how validity can be tested without independent new data. Several validation methods were compared in an example using the data from a mixed dentition analysis with a regression model. The validation errors of real mixed dentition analysis data and simulation data were analyzed for increasingly large data sets. The validation results of both the real and the simulation studies demonstrated that the leave-1-out cross-validation method had the smallest errors. The largest errors occurred in the traditional simple validation method. The differences between the validation methods diminished as the sample size increased. The leave-1-out cross-validation method seems to be an optimal validation method for improving the prediction accuracy in a data set with limited sample sizes. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Express Testing Makes for More Effective Vet Visit

NASA Technical Reports Server (NTRS)

2003-01-01

This paper presents a discussion on Vetscan, a system designed to provide veterinarians with instant diagnostic information needed for rapid treatment decisions. VetScan is designed for point-of-care testing in any treatment setting, including mobile environments, where veterinarians can operate the analyzer from a car-lighter adapter. A full range of tests is available for almost every species normally treated by veterinarians, including cats, dogs, birds, reptiles, and large animals, such as those in the equine and bovine families.

A minimal standardization setting for language mapping tests: an Italian example.

PubMed

Rofes, Adrià; de Aguiar, Vânia; Miceli, Gabriele

2015-07-01

During awake surgery, picture-naming tests are administered to identify brain structures related to language function (language mapping), and to avoid iatrogenic damage. Before and after surgery, naming tests and other neuropsychological procedures aim at charting naming abilities, and at detecting which items the subject can respond to correctly. To achieve this goal, sufficiently large samples of normed and standardized stimuli must be available for preoperative and postoperative testing, and to prepare intraoperative tasks, the latter only including items named flawlessly preoperatively. To discuss design, norming and presentation of stimuli, and to describe the minimal standardization setting used to develop two sets of Italian stimuli, one for object naming and one for verb naming, respectively. The setting includes a naming study (to obtain picture-name agreement ratings), two on-line questionnaires (to acquire age-of-acquisition and imageability ratings for all test items), and the norming of other relevant language variables. The two sets of stimuli have >80 % picture-name agreement, high levels of internal consistency and reliability for imageability and age of acquisition ratings. They are normed for psycholinguistic variables known to affect lexical access and retrieval, and are validated in a clinical population. This framework can be used to increase the probability of reliably detecting language impairments before and after surgery, to prepare intraoperative tests based on sufficient knowledge of pre-surgical language abilities in each patient, and to decrease the probability of false positives during surgery. Examples of data usage are provided. Normative data can be found in the supplementary materials.

Metrology of Large Parts. Chapter 5

NASA Technical Reports Server (NTRS)

Stahl, H. Philip

2012-01-01

As discussed in the first chapter of this book, there are many different methods to measure a part using optical technology. Chapter 2 discussed the use of machine vision to measure macroscopic features such as length and position, which was extended to the use of interferometry as a linear measurement tool in chapter 3, and laser or other trackers to find the relation of key points on large parts in chapter 4. This chapter looks at measuring large parts to optical tolerances in the sub-micron range using interferometry, ranging, and optical tools discussed in the previous chapters. The purpose of this chapter is not to discuss specific metrology tools (such as interferometers or gauges), but to describe a systems engineering approach to testing large parts. Issues such as material warpage and temperature drifts that may be insignificant when measuring a part to micron levels under a microscope, as will be discussed in later chapters, can prove to be very important when making the same measurement over a larger part. In this chapter, we will define a set of guiding principles for successfully overcoming these challenges and illustrate the application of these principles with real world examples. While these examples are drawn from specific large optical testing applications, they inform the problems associated with testing any large part to optical tolerances. Manufacturing today relies on micrometer level part performance. Fields such as energy and transportation are demanding higher tolerances to provide increased efficiencies and fuel savings. By looking at how the optics industry approaches sub-micrometer metrology, one can gain a better understanding of the metrology challenges for any larger part specified to micrometer tolerances. Testing large parts, whether optical components or precision structures, to optical tolerances is just like testing small parts, only harder. Identical with what one does for small parts, a metrologist tests large parts and optics in particular to quantify their mechanical properties (such as dimensions, mass, etc); their optical prescription or design (i.e. radius of curvature, conic constant, vertex location, size); and their full part shape. And, just as with small parts, a metrologist accomplishes these tests using distance measuring instruments such as tape measures, inside micrometers, coordinate measuring machines, distance measuring interferometers; angle measuring instruments such as theodolites, autocollimators; and surface measuring instruments including interferometers, stylus profilers, interference microscopes, photogrammetric cameras, or other tools. However, while the methodology may be similar, it is more difficult to test a large object for the simple reason that most metrologists do not have the necessary intuition. The skills used to test small parts or optics in a laboratory do not extrapolate to testing large parts in an industrial setting any more than a backyard gardener might successfully operate a farm. But first, what is a large part? A simple definition might be the part's size or diameter. For optics and diffuse surface parts alike, the driving constraint is ability to illuminate the part's surface. For reflective convex mirrors, large is typically anything greater than 1 meter. But, for refractive optics, flats or convex mirrors, large is typically greater than 0.5 meter. While a size definition is simple, it may be less than universal. A more nuanced definition might be that a large part is any component which cannot be easily tested in a standard laboratory environment, on a standard vibration isolated table using standard laboratory infrastructure. A micro-switch or a precision lens might be easily measured to nanometer levels under a microscope in a lab, but a power turbine spline or a larger telescope mirror will not fit under that microscope and may not even fit on the table.

RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy

PubMed Central

Lo, Kitty K.; Boustred, Christopher; Chitty, Lyn S.; Plagnol, Vincent

2014-01-01

Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting. Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html. Contact: kitty.lo@ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24990604

Laboratory and Field Evaluation of Rapid Setting Cementitious Materials for Large Crater Repair

DTIC Science & Technology

2010-05-01

frame used within which to complete the repair was the current NATO standard of 4 hr. A total of 6 simulated craters were prepared, with each repair...Combat Command 129 Andrews Street Langley Air Force Base, VA 23665 ERDC TR-10-4 ii Abstract: Current practice for expedient runway repair...penalty. Numerous commercial products are available. A full-scale field test was conducted using rapid setting materials to repair simulated bomb craters

Fuels and Combustion Technologies for Aerospace Propulsion

DTIC Science & Technology

2016-09-01

20 °C) has a large effect on the extent of oxygen consumption . Increasing the JFTOT set point temperature normally results in increases in deposition...kinetics. Thus, the effect of the extent of oxygen consumption and temperature on deposition rates needs further study under JFTOT conditions to better...by 60 to 85 °C. Several fuels were tested at varying set point temperatures with complete oxygen consumption observed for all fuels by 320 °C; a wide

Process-based interpretation of conceptual hydrological model performance using a multinational catchment set

NASA Astrophysics Data System (ADS)

Poncelet, Carine; Merz, Ralf; Merz, Bruno; Parajka, Juraj; Oudin, Ludovic; Andréassian, Vazken; Perrin, Charles

2017-08-01

Most of previous assessments of hydrologic model performance are fragmented, based on small number of catchments, different methods or time periods and do not link the results to landscape or climate characteristics. This study uses large-sample hydrology to identify major catchment controls on daily runoff simulations. It is based on a conceptual lumped hydrological model (GR6J), a collection of 29 catchment characteristics, a multinational set of 1103 catchments located in Austria, France, and Germany and four runoff model efficiency criteria. Two analyses are conducted to assess how features and criteria are linked: (i) a one-dimensional analysis based on the Kruskal-Wallis test and (ii) a multidimensional analysis based on regression trees and investigating the interplay between features. The catchment features most affecting model performance are the flashiness of precipitation and streamflow (computed as the ratio of absolute day-to-day fluctuations by the total amount in a year), the seasonality of evaporation, the catchment area, and the catchment aridity. Nonflashy, nonseasonal, large, and nonarid catchments show the best performance for all the tested criteria. We argue that this higher performance is due to fewer nonlinear responses (higher correlation between precipitation and streamflow) and lower input and output variability for such catchments. Finally, we show that, compared to national sets, multinational sets increase results transferability because they explore a wider range of hydroclimatic conditions.

Universal computer test stand (recommended computer test requirements). [for space shuttle computer evaluation

NASA Technical Reports Server (NTRS)

1973-01-01

Techniques are considered which would be used to characterize areospace computers with the space shuttle application as end usage. The system level digital problems which have been encountered and documented are surveyed. From the large cross section of tests, an optimum set is recommended that has a high probability of discovering documented system level digital problems within laboratory environments. Defined is a baseline hardware, software system which is required as a laboratory tool to test aerospace computers. Hardware and software baselines and additions necessary to interface the UTE to aerospace computers for test purposes are outlined.

ACToR - Aggregated Computational Toxicology Resource ...

EPA Pesticide Factsheets

There are too many uncharacterized environmental chemicals to test with current in vivo protocols. Develop predictive in vitro screening assays that can be used to prioritize chemicals for detailed testing. ToxCast program requires large amounts of data: In vitro assays (mainly generated by ToxCast program) and In vivo data to develop and validate predictive signatures ACToR is compiling both sets of data for use in predictive algorithms.

Rhesus monkeys (Macaca mulatta) show robust primacy and recency in memory for lists from small, but not large, image sets.

PubMed

Basile, Benjamin M; Hampton, Robert R

2010-02-01

The combination of primacy and recency produces a U-shaped serial position curve typical of memory for lists. In humans, primacy is often thought to result from rehearsal, but there is little evidence for rehearsal in nonhumans. To further evaluate the possibility that rehearsal contributes to primacy in monkeys, we compared memory for lists of familiar stimuli (which may be easier to rehearse) to memory for unfamiliar stimuli (which are likely difficult to rehearse). Six rhesus monkeys saw lists of five images drawn from either large, medium, or small image sets. After presentation of each list, memory for one item was assessed using a serial probe recognition test. Across four experiments, we found robust primacy and recency with lists drawn from small and medium, but not large, image sets. This finding is consistent with the idea that familiar items are easier to rehearse and that rehearsal contributes to primacy, warranting further study of the possibility of rehearsal in monkeys. However, alternative interpretations are also viable and are discussed. Copyright 2009 Elsevier B.V. All rights reserved.

Search for supersymmetry in events with large missing transverse momentum, jets, and at least one tau lepton in 7 TeV proton-proton collision data with the ATLAS detector

DOE PAGES

Aad, G.; Abajyan, T.; Abbott, B.; ...

2012-11-20

A search for supersymmetry (SUSY) in events with large missing transverse momentum, jets, and at least one hadronically decaying τ lepton, with zero or one additional light lepton (e/μ), has been performed using 4.7 fb -1 of proton-proton collision data at √s = 7 TeV recorded with the ATLAS detector at the Large Hadron Collider. No excess above the Standard Model background expectation is observed and a 95 % confidence level visible cross-section upper limit for new phenomena is set. In the framework of gauge-mediated SUSY-breaking models, lower limits on the mass scale Λ are set at 54 TeV inmore » the regions where the τ 1 is the next-to-lightest SUSY particle (tanβ > 20). These limits provide the most stringent tests to date of GMSB models in a large part of the parameter space considered.« less

How Many Loci Does it Take to DNA Barcode a Crocus?

PubMed Central

Seberg, Ole; Petersen, Gitte

2009-01-01

Background DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. Methodology and Principal Findings Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will – as is the case in crocus – undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached – even in a taxonomic context. Conclusions/Significance The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting. PMID:19240801

How many loci does it take to DNA barcode a crocus?

PubMed

Seberg, Ole; Petersen, Gitte

2009-01-01

DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context. The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.

Experimental Study of Homogeneous Isotropic Slowly-Decaying Turbulence in Giant Grid-Wind Tunnel Set Up

NASA Astrophysics Data System (ADS)

Aliseda, Alberto; Bourgoin, Mickael; Eswirp Collaboration

2014-11-01

We present preliminary results from a recent grid turbulence experiment conducted at the ONERA wind tunnel in Modane, France. The ESWIRP Collaboration was conceived to probe the smallest scales of a canonical turbulent flow with very high Reynolds numbers. To achieve this, the largest scales of the turbulence need to be extremely big so that, even with the large separation of scales, the smallest scales would be well above the spatial and temporal resolution of the instruments. The ONERA wind tunnel in Modane (8 m -diameter test section) was chosen as a limit of the biggest large scales achievable in a laboratory setting. A giant inflatable grid (M = 0.8 m) was conceived to induce slowly-decaying homogeneous isotropic turbulence in a large region of the test section, with minimal structural risk. An international team or researchers collected hot wire anemometry, ultrasound anemometry, resonant cantilever anemometry, fast pitot tube anemometry, cold wire thermometry and high-speed particle tracking data of this canonical turbulent flow. While analysis of this large database, which will become publicly available over the next 2 years, has only started, the Taylor-scale Reynolds number is estimated to be between 400 and 800, with Kolmogorov scales as large as a few mm . The ESWIRP Collaboration is formed by an international team of scientists to investigate experimentally the smallest scales of turbulence. It was funded by the European Union to take advantage of the largest wind tunnel in Europe for fundamental research.

Prediction of Skin Sensitization with a Particle Swarm Optimized Support Vector Machine

PubMed Central

Yuan, Hua; Huang, Jianping; Cao, Chenzhong

2009-01-01

Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT) and murine local lymph node assay (LLNA) are the two most important in vivo models for identification of skin sensitizers. In order to reduce the number of animal tests, quantitative structure-activity relationships (QSARs) are strongly encouraged in the assessment of skin sensitization of chemicals. This paper has investigated the skin sensitization potential of 162 compounds with LLNA results and 92 compounds with GPMT results using a support vector machine. A particle swarm optimization algorithm was implemented for feature selection from a large number of molecular descriptors calculated by Dragon. For the LLNA data set, the classification accuracies are 95.37% and 88.89% for the training and the test sets, respectively. For the GPMT data set, the classification accuracies are 91.80% and 90.32% for the training and the test sets, respectively. The classification performances were greatly improved compared to those reported in the literature, indicating that the support vector machine optimized by particle swarm in this paper is competent for the identification of skin sensitizers. PMID:19742136

Scaling up Psycholinguistics

ERIC Educational Resources Information Center

Smith, Nathaniel J.

2011-01-01

This dissertation contains several projects, each addressing different questions with different techniques. In chapter 1, I argue that they are unified thematically by their goal of "scaling up psycholinguistics"; they are all aimed at analyzing large data-sets using tools that reveal patterns to propose and test mechanism-neutral hypotheses about…

VOLUMETRIC LEAK DETECTION IN LARGE UNDERGROUND STORAGE TANKS - VOLUME I

EPA Science Inventory

A set of experiments was conducted to determine whether volumetric leak detection system presently used to test underground storage tanks (USTs) up to 38,000 L (10,000 gal) in capacity could meet EPA's regulatory standards for tank tightness and automatic tank gauging systems whe...

A dynamic regularized gradient model of the subgrid-scale stress tensor for large-eddy simulation

NASA Astrophysics Data System (ADS)

Vollant, A.; Balarac, G.; Corre, C.

2016-02-01

Large-eddy simulation (LES) solves only the large scales part of turbulent flows by using a scales separation based on a filtering operation. The solution of the filtered Navier-Stokes equations requires then to model the subgrid-scale (SGS) stress tensor to take into account the effect of scales smaller than the filter size. In this work, a new model is proposed for the SGS stress model. The model formulation is based on a regularization procedure of the gradient model to correct its unstable behavior. The model is developed based on a priori tests to improve the accuracy of the modeling for both structural and functional performances, i.e., the model ability to locally approximate the SGS unknown term and to reproduce enough global SGS dissipation, respectively. LES is then performed for a posteriori validation. This work is an extension to the SGS stress tensor of the regularization procedure proposed by Balarac et al. ["A dynamic regularized gradient model of the subgrid-scale scalar flux for large eddy simulations," Phys. Fluids 25(7), 075107 (2013)] to model the SGS scalar flux. A set of dynamic regularized gradient (DRG) models is thus made available for both the momentum and the scalar equations. The second objective of this work is to compare this new set of DRG models with direct numerical simulations (DNS), filtered DNS in the case of classic flows simulated with a pseudo-spectral solver and with the standard set of models based on the dynamic Smagorinsky model. Various flow configurations are considered: decaying homogeneous isotropic turbulence, turbulent plane jet, and turbulent channel flows. These tests demonstrate the stable behavior provided by the regularization procedure, along with substantial improvement for velocity and scalar statistics predictions.

Designing a ruggedisation lab to characterise materials for harsh environments.

PubMed

Frazzette, Nicholas; Jethva, Janak; Mehta, Khanjan; Stapleton, Joshua J; Randall, Clive

Designing products for use in developing countries presents a unique set of challenges including harsh operating environments, costly repairs and maintenance, and users with varying degrees of education and device familiarity. For products to be robust, adaptable and durable, they need to be ruggedised for environmental factors such as high temperature and humidity as well as different operational conditions such as shock and chemical exposure. The product characterisation and ruggedisation processes require specific expertise and resources that are seldom available outside of large corporations and elite national research labs. There is no standardised process since product needs strongly depend on the context and user base, making it particularly onerous for underfunded start-ups and academic groups. Standardised protocols that identify essential lab testing regimens for specific contexts and user groups can complement field-testing and accelerate the product development process while reducing costs. This article synthesises current methods and strategies for product testing employed by large corporations as well as defence-related entities. A technological and organisational framework for a service-for-fee product characterisation and ruggedisation lab that reduces costs and shortens the timespan from product invention to commercial launch in harsh settings is presented.

Models for the hotspot distribution

NASA Technical Reports Server (NTRS)

Jurdy, Donna M.; Stefanick, Michael

1990-01-01

Published hotspot catalogs all show a hemispheric concentration beyond what can be expected by chance. Cumulative distributions about the center of concentration are described by a power law with a fractal dimension closer to 1 than 2. Random sets of the corresponding sizes do not show this effect. A simple shift of the random sets away from a point would produce distributions similar to those of hotspot sets. The possible relation of the hotspots to the locations of ridges and subduction zones is tested using large sets of randomly-generated points to estimate areas within given distances of the plate boundaries. The probability of finding the observed number of hotspots within 10 deg of the ridges is about what is expected.

Training set extension for SVM ensemble in P300-speller with familiar face paradigm.

PubMed

Li, Qi; Shi, Kaiyang; Gao, Ning; Li, Jian; Bai, Ou

2018-03-27

P300-spellers are brain-computer interface (BCI)-based character input systems. Support vector machine (SVM) ensembles are trained with large-scale training sets and used as classifiers in these systems. However, the required large-scale training data necessitate a prolonged collection time for each subject, which results in data collected toward the end of the period being contaminated by the subject's fatigue. This study aimed to develop a method for acquiring more training data based on a collected small training set. A new method was developed in which two corresponding training datasets in two sequences are superposed and averaged to extend the training set. The proposed method was tested offline on a P300-speller with the familiar face paradigm. The SVM ensemble with extended training set achieved 85% classification accuracy for the averaged results of four sequences, and 100% for 11 sequences in the P300-speller. In contrast, the conventional SVM ensemble with non-extended training set achieved only 65% accuracy for four sequences, and 92% for 11 sequences. The SVM ensemble with extended training set achieves higher classification accuracies than the conventional SVM ensemble, which verifies that the proposed method effectively improves the classification performance of BCI P300-spellers, thus enhancing their practicality.

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, T. K.; Chrostowski, Jon D.

1990-01-01

Uncertainty of frequency response using the fuzzy set method and on-orbit response prediction using laboratory test data to refine an analytical model are emphasized with respect to large space structures. Two aspects of the fuzzy set approach were investigated relative to its application to large structural dynamics problems: (1) minimizing the number of parameters involved in computing possible intervals; and (2) the treatment of extrema which may occur in the parameter space enclosed by all possible combinations of the important parameters of the model. Extensive printer graphics were added to the SSID code to help facilitate model verification, and an application of this code to the LaRC Ten Bay Truss is included in the appendix to illustrate this graphics capability.

Analyzing Real-World Light Duty Vehicle Efficiency Benefits

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

Gonder, Jeffrey; Wood, Eric; Chaney, Larry

Off-cycle technologies represent an important pathway to achieve real-world fuel savings, through which OEMs can potentially receive credit toward CAFE compliance. DOE national labs such as NREL are well positioned to provide objective input on these technologies using large, national data sets in conjunction with OEM- and technology-specific testing. This project demonstrates an approach that combines vehicle testing (dynamometer and on-road) with powertrain modeling and simulation over large, representative datasets to quantify real-world fuel economy. The approach can be applied to specific off-cycle technologies (engine encapsulation, start/stop, connected vehicle, etc.) in A/B comparisons to support calculation of realistic real-world impacts.more » Future work will focus on testing-based A/B technology comparisons that demonstrate the significance of this approach.« less

False Discovery Control in Large-Scale Spatial Multiple Testing

PubMed Central

Sun, Wenguang; Reich, Brian J.; Cai, T. Tony; Guindani, Michele; Schwartzman, Armin

2014-01-01

Summary This article develops a unified theoretical and computational framework for false discovery control in multiple testing of spatial signals. We consider both point-wise and cluster-wise spatial analyses, and derive oracle procedures which optimally control the false discovery rate, false discovery exceedance and false cluster rate, respectively. A data-driven finite approximation strategy is developed to mimic the oracle procedures on a continuous spatial domain. Our multiple testing procedures are asymptotically valid and can be effectively implemented using Bayesian computational algorithms for analysis of large spatial data sets. Numerical results show that the proposed procedures lead to more accurate error control and better power performance than conventional methods. We demonstrate our methods for analyzing the time trends in tropospheric ozone in eastern US. PMID:25642138

Observational methods to assess the effectiveness of screening colonoscopy in reducing right colon cancer mortality risk: SCOLAR.

PubMed

Goodman, Michael; Fletcher, Robert H; Doria-Rose, V Paul; Jensen, Christopher D; Zebrowski, Alexis M; Becerra, Tracy A; Quinn, Virginia P; Zauber, Ann G; Corley, Douglas A; Doubeni, Chyke A

2015-11-01

Screening colonoscopy's effectiveness in reducing risk of death from right colon cancers remains unclear. Methodological challenges of existing observational studies addressing this issue motivated the design of 'Effectiveness of Screening for Colorectal Cancer in Average-Risk Adults (SCOLAR)'. SCOLAR is a nested case-control study based on two large integrated health systems. This affords access to a large, well-defined historical cohort linked to integrated data on cancer outcomes, patient eligibility, test indications and important confounders. We found electronic data adequate for excluding ineligible patients (except family history), but not the detailed information needed for test indication assignment. The lessons of SCOLAR's design and implementation may be useful for future studies seeking to evaluate the effectiveness of screening tests in community settings.

Statistical characterization of a large geochemical database and effect of sample size

USGS Publications Warehouse

Zhang, C.; Manheim, F.T.; Hinde, J.; Grossman, J.N.

2005-01-01

The authors investigated statistical distributions for concentrations of chemical elements from the National Geochemical Survey (NGS) database of the U.S. Geological Survey. At the time of this study, the NGS data set encompasses 48,544 stream sediment and soil samples from the conterminous United States analyzed by ICP-AES following a 4-acid near-total digestion. This report includes 27 elements: Al, Ca, Fe, K, Mg, Na, P, Ti, Ba, Ce, Co, Cr, Cu, Ga, La, Li, Mn, Nb, Nd, Ni, Pb, Sc, Sr, Th, V, Y and Zn. The goal and challenge for the statistical overview was to delineate chemical distributions in a complex, heterogeneous data set spanning a large geographic range (the conterminous United States), and many different geological provinces and rock types. After declustering to create a uniform spatial sample distribution with 16,511 samples, histograms and quantile-quantile (Q-Q) plots were employed to delineate subpopulations that have coherent chemical and mineral affinities. Probability groupings are discerned by changes in slope (kinks) on the plots. Major rock-forming elements, e.g., Al, Ca, K and Na, tend to display linear segments on normal Q-Q plots. These segments can commonly be linked to petrologic or mineralogical associations. For example, linear segments on K and Na plots reflect dilution of clay minerals by quartz sand (low in K and Na). Minor and trace element relationships are best displayed on lognormal Q-Q plots. These sensitively reflect discrete relationships in subpopulations within the wide range of the data. For example, small but distinctly log-linear subpopulations for Pb, Cu, Zn and Ag are interpreted to represent ore-grade enrichment of naturally occurring minerals such as sulfides. None of the 27 chemical elements could pass the test for either normal or lognormal distribution on the declustered data set. Part of the reasons relate to the presence of mixtures of subpopulations and outliers. Random samples of the data set with successively smaller numbers of data points showed that few elements passed standard statistical tests for normality or log-normality until sample size decreased to a few hundred data points. Large sample size enhances the power of statistical tests, and leads to rejection of most statistical hypotheses for real data sets. For large sample sizes (e.g., n > 1000), graphical methods such as histogram, stem-and-leaf, and probability plots are recommended for rough judgement of probability distribution if needed. ?? 2005 Elsevier Ltd. All rights reserved.

Comparative study of biodegradability prediction of chemicals using decision trees, functional trees, and logistic regression.

PubMed

Chen, Guangchao; Li, Xuehua; Chen, Jingwen; Zhang, Ya-Nan; Peijnenburg, Willie J G M

2014-12-01

Biodegradation is the principal environmental dissipation process of chemicals. As such, it is a dominant factor determining the persistence and fate of organic chemicals in the environment, and is therefore of critical importance to chemical management and regulation. In the present study, the authors developed in silico methods assessing biodegradability based on a large heterogeneous set of 825 organic compounds, using the techniques of the C4.5 decision tree, the functional inner regression tree, and logistic regression. External validation was subsequently carried out by 2 independent test sets of 777 and 27 chemicals. As a result, the functional inner regression tree exhibited the best predictability with predictive accuracies of 81.5% and 81.0%, respectively, on the training set (825 chemicals) and test set I (777 chemicals). Performance of the developed models on the 2 test sets was subsequently compared with that of the Estimation Program Interface (EPI) Suite Biowin 5 and Biowin 6 models, which also showed a better predictability of the functional inner regression tree model. The model built in the present study exhibits a reasonable predictability compared with existing models while possessing a transparent algorithm. Interpretation of the mechanisms of biodegradation was also carried out based on the models developed. © 2014 SETAC.

Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in “Real-World” Settings

PubMed Central

Brenner, Bluma G.; Ibanescu, Ruxandra-Ilinca; Hardy, Isabelle; Roger, Michel

2017-01-01

HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings. PMID:29283390

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

Benchmarking contactless acquisition sensor reproducibility for latent fingerprint trace evidence

NASA Astrophysics Data System (ADS)

Hildebrandt, Mario; Dittmann, Jana

2015-03-01

Optical, nano-meter range, contactless, non-destructive sensor devices are promising acquisition techniques in crime scene trace forensics, e.g. for digitizing latent fingerprint traces. Before new approaches are introduced in crime investigations, innovations need to be positively tested and quality ensured. In this paper we investigate sensor reproducibility by studying different scans from four sensors: two chromatic white light sensors (CWL600/CWL1mm), one confocal laser scanning microscope, and one NIR/VIS/UV reflection spectrometer. Firstly, we perform an intra-sensor reproducibility testing for CWL600 with a privacy conform test set of artificial-sweat printed, computer generated fingerprints. We use 24 different fingerprint patterns as original samples (printing samples/templates) for printing with artificial sweat (physical trace samples) and their acquisition with contactless sensory resulting in 96 sensor images, called scan or acquired samples. The second test set for inter-sensor reproducibility assessment consists of the first three patterns from the first test set, acquired in two consecutive scans using each device. We suggest using a simple feature space set in spatial and frequency domain known from signal processing and test its suitability for six different classifiers classifying scan data into small differences (reproducible) and large differences (non-reproducible). Furthermore, we suggest comparing the classification results with biometric verification scores (calculated with NBIS, with threshold of 40) as biometric reproducibility score. The Bagging classifier is nearly for all cases the most reliable classifier in our experiments and the results are also confirmed with the biometric matching rates.

How To Promote Data Quality And Access? Publish It!

NASA Astrophysics Data System (ADS)

Carlson, D. J.; Pfeiffenberger, H.

2011-12-01

Started during IPY 2007-2008, the Earth System Science Data journal (Copernicus) has now 'tested the waters' of earth system data publishing for approximately 2 years with some success. The journal has published more than 30 data sets, of remarkable breadth and variety, all under a Creative Commons Attribution license. Users can now find well-described, quality-controlled and freely accessible data on soils, permafrost, sediment transport, ice sheets, surface radiation, ocean-atmosphere fluxes, ocean chemistry, gravity fields, and combined radar and web cam observations of the Eyjafjallajökull eruption plume. Several of the data sets derive specifically from IPY or from polar regions, but a large portion, including a substantial special issue on ocean carbon, cover broad temporal and geographic domains; the contributors themselves come from leading science institutions around the world. ESSD has attracted the particular interest of international research teams, particularly those who, as in the case of ocean carbon data, have spent many years gathering, collating and calibrating global data sets under long-term named programs, but who lack within those programs the mechanisms to distribute those data sets widely outside their specialist teams and to ensure proper citation credit for those remarkable collaborative data processing efforts. An in-progress special issue on global ocean plankton function types, again representing years of international data collaboration, provides a further example of ESSD utility to large research programs. We anticipate an interesting test case of parallel special issues with companion science journals - data sets in ESSD to accompany science publications in a prominent research journal. We see the ESSD practices and products as useful steps to increase quality of and access to important data sets.

Discriminative motif optimization based on perceptron training

PubMed Central

Patel, Ronak Y.; Stormo, Gary D.

2014-01-01

Motivation: Generating accurate transcription factor (TF) binding site motifs from data generated using the next-generation sequencing, especially ChIP-seq, is challenging. The challenge arises because a typical experiment reports a large number of sequences bound by a TF, and the length of each sequence is relatively long. Most traditional motif finders are slow in handling such enormous amount of data. To overcome this limitation, tools have been developed that compromise accuracy with speed by using heuristic discrete search strategies or limited optimization of identified seed motifs. However, such strategies may not fully use the information in input sequences to generate motifs. Such motifs often form good seeds and can be further improved with appropriate scoring functions and rapid optimization. Results: We report a tool named discriminative motif optimizer (DiMO). DiMO takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. We use area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. Using DiMO, on a large test set of 87 TFs from human, drosophila and yeast, we show that it is possible to significantly improve motifs identified by nine motif finders. The motifs are generated/optimized using training sets and evaluated on test sets. The AUC is improved for almost 90% of the TFs on test sets and the magnitude of increase is up to 39%. Availability and implementation: DiMO is available at http://stormo.wustl.edu/DiMO Contact: rpatel@genetics.wustl.edu, ronakypatel@gmail.com PMID:24369152

Rapid on-line detection and grading of wooden breast myopathy in chicken fillets by near-infrared spectroscopy.

PubMed

Wold, Jens Petter; Veiseth-Kent, Eva; Høst, Vibeke; Løvland, Atle

2017-01-01

The main objective of this work was to develop a method for rapid and non-destructive detection and grading of wooden breast (WB) syndrome in chicken breast fillets. Near-infrared (NIR) spectroscopy was chosen as detection method, and an industrial NIR scanner was applied and tested for large scale on-line detection of the syndrome. Two approaches were evaluated for discrimination of WB fillets: 1) Linear discriminant analysis based on NIR spectra only, and 2) a regression model for protein was made based on NIR spectra and the estimated concentrations of protein were used for discrimination. A sample set of 197 fillets was used for training and calibration. A test set was recorded under industrial conditions and contained spectra from 79 fillets. The classification methods obtained 99.5-100% correct classification of the calibration set and 100% correct classification of the test set. The NIR scanner was then installed in a commercial chicken processing plant and could detect incidence rates of WB in large batches of fillets. Examples of incidence are shown for three broiler flocks where a high number of fillets (9063, 6330 and 10483) were effectively measured. Prevalence of WB of 0.1%, 6.6% and 8.5% were estimated for these flocks based on the complete sample volumes. Such an on-line system can be used to alleviate the challenges WB represents to the poultry meat industry. It enables automatic quality sorting of chicken fillets to different product categories. Manual laborious grading can be avoided. Incidences of WB from different farms and flocks can be tracked and information can be used to understand and point out main causes for WB in the chicken production. This knowledge can be used to improve the production procedures and reduce today's extensive occurrence of WB.

Multiple regression and Artificial Neural Network for long-term rainfall forecasting using large scale climate modes

NASA Astrophysics Data System (ADS)

Mekanik, F.; Imteaz, M. A.; Gato-Trinidad, S.; Elmahdi, A.

2013-10-01

In this study, the application of Artificial Neural Networks (ANN) and Multiple regression analysis (MR) to forecast long-term seasonal spring rainfall in Victoria, Australia was investigated using lagged El Nino Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) as potential predictors. The use of dual (combined lagged ENSO-IOD) input sets for calibrating and validating ANN and MR Models is proposed to investigate the simultaneous effect of past values of these two major climate modes on long-term spring rainfall prediction. The MR models that did not violate the limits of statistical significance and multicollinearity were selected for future spring rainfall forecast. The ANN was developed in the form of multilayer perceptron using Levenberg-Marquardt algorithm. Both MR and ANN modelling were assessed statistically using mean square error (MSE), mean absolute error (MAE), Pearson correlation (r) and Willmott index of agreement (d). The developed MR and ANN models were tested on out-of-sample test sets; the MR models showed very poor generalisation ability for east Victoria with correlation coefficients of -0.99 to -0.90 compared to ANN with correlation coefficients of 0.42-0.93; ANN models also showed better generalisation ability for central and west Victoria with correlation coefficients of 0.68-0.85 and 0.58-0.97 respectively. The ability of multiple regression models to forecast out-of-sample sets is compatible with ANN for Daylesford in central Victoria and Kaniva in west Victoria (r = 0.92 and 0.67 respectively). The errors of the testing sets for ANN models are generally lower compared to multiple regression models. The statistical analysis suggest the potential of ANN over MR models for rainfall forecasting using large scale climate modes.

Data for Room Fire Model Comparisons

PubMed Central

Peacock, Richard D.; Davis, Sanford; Babrauskas, Vytenis

1991-01-01

With the development of models to predict fire growth and spread in buildings, there has been a concomitant evolution in the measurement and analysis of experimental data in real-scale fires. This report presents the types of analyses that can be used to examine large-scale room fire test data to prepare the data for comparison with zone-based fire models. Five sets of experimental data which can be used to test the limits of a typical two-zone fire model are detailed. A standard set of nomenclature describing the geometry of the building and the quantities measured in each experiment is presented. Availability of ancillary data (such as smaller-scale test results) is included. These descriptions, along with the data (available in computer-readable form) should allow comparisons between the experiment and model predictions. The base of experimental data ranges in complexity from one room tests with individual furniture items to a series of tests conducted in a multiple story hotel equipped with a zoned smoke control system. PMID:28184121

Data for Room Fire Model Comparisons.

PubMed

Peacock, Richard D; Davis, Sanford; Babrauskas, Vytenis

1991-01-01

With the development of models to predict fire growth and spread in buildings, there has been a concomitant evolution in the measurement and analysis of experimental data in real-scale fires. This report presents the types of analyses that can be used to examine large-scale room fire test data to prepare the data for comparison with zone-based fire models. Five sets of experimental data which can be used to test the limits of a typical two-zone fire model are detailed. A standard set of nomenclature describing the geometry of the building and the quantities measured in each experiment is presented. Availability of ancillary data (such as smaller-scale test results) is included. These descriptions, along with the data (available in computer-readable form) should allow comparisons between the experiment and model predictions. The base of experimental data ranges in complexity from one room tests with individual furniture items to a series of tests conducted in a multiple story hotel equipped with a zoned smoke control system.

Measuring Well What is Ill Defined?

ERIC Educational Resources Information Center

Torres Irribarra, David

2017-01-01

Maul's paper, "Rethinking Traditional Methods of Survey Validation," is a clever and pointed indictment of a set of specific but widespread practices in psychological measurement and the social sciences at large. Through it, Maul highlights central issues in the way to approach theory building and theory testing, bringing to mind the…

A Fast Turn-Around Facility for Very Large Scale Integration (VLSI)

DTIC Science & Technology

1982-06-01

statistics determination, the first test mask set will use the MATRIX chip design which was recently developed here at Stanford. This chip provides...reached when the basewidth is reduced to zero. Such devices, variably known as depleted- base transistors or bipolar static-induction transitors , have been

Leadership for Literacy: Teachers Raising Expectations and Opportunities

ERIC Educational Resources Information Center

Chilla, Nicole A.; Waff, Diane; Cook, Heleny

2007-01-01

The public is deeply concerned that students in urban settings are not achieving at high levels. Over the past twenty years, large urban districts have attempted to restructure massive school systems using educational policymaking processes that have focused on school structures, standards-driven curriculum, and test-based accountability measures.…

Neither Broad nor Bold

ERIC Educational Resources Information Center

Peterson, Paul E.

2012-01-01

Children raised in families with higher incomes score higher on math and reading tests. But is parental income the "cause" of a child's success? Or is the connection between income and achievement largely a symptom of something else: genetic heritage, parental skill, or a supportive educational setting? The Broader, Bolder Approach to Education, a…

Search and Seizure: What Your School's Rights Are.

ERIC Educational Resources Information Center

Stefkovich, Jacqueline A.; O'Brien, G. Michaele

1996-01-01

Unlike most school-security strategies, search and seizure procedures can be largely determined by studying landmark court cases. The U.S. Supreme Court set standards for conducting school searches in "New Jersey v. T.L.O." (1985) and for drug testing student athletes in "Vernonia School District v. Acton" (1995). School…

Towards a Deeper Assessment of Vocabulary Knowledge.

ERIC Educational Resources Information Center

Read, John

While interest in second language vocabulary knowledge has increased, vocabulary testing remains largely confined to the quantitative measurement of discrete items. More qualitative measures are needed to assess how well particular words are known. Research has characterized word knowledge in two ways: as a set of components or aspects, and as an…

The application of parameter estimation to flight measurements to obtain lateral-directional stability derivatives of an augmented jet-flap STOL airplane

NASA Technical Reports Server (NTRS)

Stephenson, J. D.

1983-01-01

Flight experiments with an augmented jet flap STOL aircraft provided data from which the lateral directional stability and control derivatives were calculated by applying a linear regression parameter estimation procedure. The tests, which were conducted with the jet flaps set at a 65 deg deflection, covered a large range of angles of attack and engine power settings. The effect of changing the angle of the jet thrust vector was also investigated. Test results are compared with stability derivatives that had been predicted. The roll damping derived from the tests was significantly larger than had been predicted, whereas the other derivatives were generally in agreement with the predictions. Results obtained using a maximum likelihood estimation procedure are compared with those from the linear regression solutions.

Evaluation of a 5-Marker Blood Test for Colorectal Cancer Early Detection in a Colorectal Cancer Screening Setting.

PubMed

Werner, Simone; Krause, Friedemann; Rolny, Vinzent; Strobl, Matthias; Morgenstern, David; Datz, Christian; Chen, Hongda; Brenner, Hermann

2016-04-01

In initial studies that included colorectal cancer patients undergoing diagnostic colonoscopy, we had identified a serum marker combination able to detect colorectal cancer with similar diagnostic performance as fecal immunochemical test (FIT). In this study, we aimed to validate the results in participants of a large colorectal cancer screening study conducted in the average-risk, asymptomatic screening population. We tested serum samples from 1,200 controls, 420 advanced adenoma patients, 4 carcinoma in situ patients, and 36 colorectal cancer patients with a 5-marker blood test [carcinoembryonic antigen (CEA)+anti-p53+osteopontin+seprase+ferritin]. The diagnostic performance of individual markers and marker combinations was assessed and compared with stool test results. AUCs for the detection of colorectal cancer and advanced adenomas with the 5-marker blood test were 0.78 [95% confidence interval (CI), 0.68-0.87] and 0.56 (95% CI, 0.53-0.59), respectively, which now is comparable with guaiac-based fecal occult blood test (gFOBT) but inferior to FIT. With cutoffs yielding specificities of 80%, 90%, and 95%, the sensitivities for the detection of colorectal cancer were 64%, 50%, and 42%, and early-stage cancers were detected as well as late-stage cancers. For osteopontin, seprase, and ferritin, the diagnostic performance in the screening setting was reduced compared with previous studies in diagnostic settings while CEA and anti-p53 showed similar diagnostic performance in both settings. Performance of the 5-marker blood test under screening conditions is inferior to FIT even though it is still comparable with the performance of gFOBT. CEA and anti-p53 could contribute to the development of a multiple marker blood-based test for early detection of colorectal cancer. ©2015 American Association for Cancer Research.

Reliability and validity of a self-administered tool for online neuropsychological testing: The Amsterdam Cognition Scan.

PubMed

Feenstra, Heleen E M; Murre, Jaap M J; Vermeulen, Ivar E; Kieffer, Jacobien M; Schagen, Sanne B

2018-04-01

To facilitate large-scale assessment of a variety of cognitive abilities in clinical studies, we developed a self-administered online neuropsychological test battery: the Amsterdam Cognition Scan (ACS). The current studies evaluate in a group of adult cancer patients: test-retest reliability of the ACS and the influence of test setting (home or hospital), and the relationship between our online and a traditional test battery (concurrent validity). Test-retest reliability was studied in 96 cancer patients (57 female; M age  = 51.8 years) who completed the ACS twice. Intraclass correlation coefficients (ICCs) were used to assess consistency over time. The test setting was counterbalanced between home and hospital; influence on test performance was assessed by repeated measures analyses of variance. Concurrent validity was studied in 201 cancer patients (112 female; M age  = 53.5 years) who completed both the online and an equivalent traditional neuropsychological test battery. Spearman or Pearson correlations were used to assess consistency between online and traditional tests. ICCs of the online tests ranged from .29 to .76, with an ICC of .78 for the ACS total score. These correlations are generally comparable with the test-retest correlations of the traditional tests as reported in the literature. Correlating online and traditional test scores, we observed medium to large concurrent validity (r/ρ = .42 to .70; total score r = .78), except for a visuospatial memory test (ρ = .36). Correlations were affected-as expected-by design differences between online tests and their offline counterparts. Although development and optimization of the ACS is an ongoing process, and reliability can be optimized for several tests, our results indicate that it is a highly usable tool to obtain (online) measures of various cognitive abilities. The ACS is expected to facilitate efficient gathering of data on cognitive functioning in the near future.

Estimation of the chemical-induced eye injury using a weight-of-evidence (WoE) battery of 21 artificial neural network (ANN) c-QSAR models (QSAR-21): part I: irritation potential.

PubMed

Verma, Rajeshwar P; Matthews, Edwin J

2015-03-01

Evaluation of potential chemical-induced eye injury through irritation and corrosion is required to ensure occupational and consumer safety for industrial, household and cosmetic ingredient chemicals. The historical method for evaluating eye irritant and corrosion potential of chemicals is the rabbit Draize test. However, the Draize test is controversial and its use is diminishing - the EU 7th Amendment to the Cosmetic Directive (76/768/EEC) and recast Regulation now bans marketing of new cosmetics having animal testing of their ingredients and requires non-animal alternative tests for safety assessments. Thus, in silico and/or in vitro tests are advocated. QSAR models for eye irritation have been reported for several small (congeneric) data sets; however, large global models have not been described. This report describes FDA/CFSAN's development of 21 ANN c-QSAR models (QSAR-21) to predict eye irritation using the ADMET Predictor program and a diverse training data set of 2928 chemicals. The 21 models had external (20% test set) and internal validation and average training/verification/test set statistics were: 88/88/85(%) sensitivity and 82/82/82(%) specificity, respectively. The new method utilized multiple artificial neural network (ANN) molecular descriptor selection functionalities to maximize the applicability domain of the battery. The eye irritation models will be used to provide information to fill the critical data gaps for the safety assessment of cosmetic ingredient chemicals. Copyright © 2014 Elsevier Inc. All rights reserved.

Automatic control of cryogenic wind tunnels

NASA Technical Reports Server (NTRS)

Balakrishna, S.

1989-01-01

Inadequate Reynolds number similarity in testing of scaled models affects the quality of aerodynamic data from wind tunnels. This is due to scale effects of boundary-layer shock wave interaction which is likely to be severe at transonic speeds. The idea of operation of wind tunnels using test gas cooled to cryogenic temperatures has yielded a quantrum jump in the ability to realize full scale Reynolds number flow similarity in small transonic tunnels. In such tunnels, the basic flow control problem consists of obtaining and maintaining the desired test section flow parameters. Mach number, Reynolds number, and dynamic pressure are the three flow parameters that are usually required to be kept constant during the period of model aerodynamic data acquisition. The series of activity involved in modeling, control law development, mechanization of the control laws on a microcomputer, and the performance of a globally stable automatic control system for the 0.3-m Transonic Cryogenic Tunnel (TCT) are discussed. A lumped multi-variable nonlinear dynamic model of the cryogenic tunnel, generation of a set of linear control laws for small perturbation, and nonlinear control strategy for large set point changes including tunnel trajectory control are described. The details of mechanization of the control laws on a 16 bit microcomputer system, the software features, operator interface, the display and safety are discussed. The controller is shown to provide globally stable and reliable temperature control to + or - 0.2 K, pressure to + or - 0.07 psi and Mach number to + or - 0.002 of the set point value. This performance is obtained both during large set point commands as for a tunnel cooldown, and during aerodynamic data acquisition with intrusive activity like geometrical changes in the test section such as angle of attack changes, drag rake movements, wall adaptation and sidewall boundary-layer removal. Feasibility of the use of an automatic Reynolds number control mode with fixed Mach number control is demonstrated.

Statistical Analysis of a Large Sample Size Pyroshock Test Data Set Including Post Flight Data Assessment. Revision 1

NASA Technical Reports Server (NTRS)

Hughes, William O.; McNelis, Anne M.

2010-01-01

The Earth Observing System (EOS) Terra spacecraft was launched on an Atlas IIAS launch vehicle on its mission to observe planet Earth in late 1999. Prior to launch, the new design of the spacecraft's pyroshock separation system was characterized by a series of 13 separation ground tests. The analysis methods used to evaluate this unusually large amount of shock data will be discussed in this paper, with particular emphasis on population distributions and finding statistically significant families of data, leading to an overall shock separation interface level. The wealth of ground test data also allowed a derivation of a Mission Assurance level for the flight. All of the flight shock measurements were below the EOS Terra Mission Assurance level thus contributing to the overall success of the EOS Terra mission. The effectiveness of the statistical methodology for characterizing the shock interface level and for developing a flight Mission Assurance level from a large sample size of shock data is demonstrated in this paper.

Model-independent test for scale-dependent non-Gaussianities in the cosmic microwave background.

PubMed

Räth, C; Morfill, G E; Rossmanith, G; Banday, A J; Górski, K M

2009-04-03

We present a model-independent method to test for scale-dependent non-Gaussianities in combination with scaling indices as test statistics. Therefore, surrogate data sets are generated, in which the power spectrum of the original data is preserved, while the higher order correlations are partly randomized by applying a scale-dependent shuffling procedure to the Fourier phases. We apply this method to the Wilkinson Microwave Anisotropy Probe data of the cosmic microwave background and find signatures for non-Gaussianities on large scales. Further tests are required to elucidate the origin of the detected anomalies.

Adhesion scratch testing - A round-robin experiment

NASA Technical Reports Server (NTRS)

Perry, A. J.; Valli, J.; Steinmann, P. A.

1988-01-01

Six sets of samples, TiN coated by chemical or physical vapor deposition methods (CVD or PVD) onto cemented carbide or high-speed steel (HSS), and TiC coated by CVD onto cemented carbide have been scratch tested using three types of commercially available scratch adhesion tester. With exception of one cemented carbide set, the reproducibility of the critical loads for any given set with a given stylus is excellent, about + or - 5 percent, and is about + or - 20 percent for different styli. Any differences in critical loads recorded for any given sample set can be attributed to the condition of the stylus (clean, new, etc.), the instrument used, the stylus itself (friction coefficient, etc.), and the sample set itself. One CVD set showed remarkably large differences in critical loads for different styli, which is thought to be related to a mechanical interaction between stylus and coating which is enhanced by a plastic deformability in the film related to the coating microstructure. The critical load for TiN on HSS increases with coating thickness, and differences in frictional conditions led to a systematic variation in the critical loads depending on the stylus used.

Active Learning to Overcome Sample Selection Bias: Application to Photometric Variable Star Classification

NASA Astrophysics Data System (ADS)

Richards, Joseph W.; Starr, Dan L.; Brink, Henrik; Miller, Adam A.; Bloom, Joshua S.; Butler, Nathaniel R.; James, J. Berian; Long, James P.; Rice, John

2012-01-01

Despite the great promise of machine-learning algorithms to classify and predict astrophysical parameters for the vast numbers of astrophysical sources and transients observed in large-scale surveys, the peculiarities of the training data often manifest as strongly biased predictions on the data of interest. Typically, training sets are derived from historical surveys of brighter, more nearby objects than those from more extensive, deeper surveys (testing data). This sample selection bias can cause catastrophic errors in predictions on the testing data because (1) standard assumptions for machine-learned model selection procedures break down and (2) dense regions of testing space might be completely devoid of training data. We explore possible remedies to sample selection bias, including importance weighting, co-training, and active learning (AL). We argue that AL—where the data whose inclusion in the training set would most improve predictions on the testing set are queried for manual follow-up—is an effective approach and is appropriate for many astronomical applications. For a variable star classification problem on a well-studied set of stars from Hipparcos and Optical Gravitational Lensing Experiment, AL is the optimal method in terms of error rate on the testing data, beating the off-the-shelf classifier by 3.4% and the other proposed methods by at least 3.0%. To aid with manual labeling of variable stars, we developed a Web interface which allows for easy light curve visualization and querying of external databases. Finally, we apply AL to classify variable stars in the All Sky Automated Survey, finding dramatic improvement in our agreement with the ASAS Catalog of Variable Stars, from 65.5% to 79.5%, and a significant increase in the classifier's average confidence for the testing set, from 14.6% to 42.9%, after a few AL iterations.

Development of pressure containment and damage tolerance technology for composite fuselage structures in large transport aircraft

NASA Technical Reports Server (NTRS)

Smith, P. J.; Thomson, L. W.; Wilson, R. D.

1986-01-01

NASA sponsored composites research and development programs were set in place to develop the critical engineering technologies in large transport aircraft structures. This NASA-Boeing program focused on the critical issues of damage tolerance and pressure containment generic to the fuselage structure of large pressurized aircraft. Skin-stringer and honeycomb sandwich composite fuselage shell designs were evaluated to resolve these issues. Analyses were developed to model the structural response of the fuselage shell designs, and a development test program evaluated the selected design configurations to appropriate load conditions.

Cellphone-based hand-held microplate reader for point-of-care ELISA testing (Conference Presentation)

NASA Astrophysics Data System (ADS)

Berg, Brandon; Cortazar, Bingen; Tseng, Derek; Ozkan, Haydar; Feng, Steve; Wei, Qingshan; Chan, Raymond Y.; Burbano, Jordi; Farooqui, Qamar; Lewinski, Michael; Di Carlo, Dino; Garner, Omai B.; Ozcan, Aydogan

2016-03-01

Enzyme-linked immunosorbent assay (ELISA) in a microplate format has been a gold standard first-line clinical test for diagnosis of various diseases including infectious diseases. However, this technology requires a relatively large and expensive multi-well scanning spectrophotometer to read and quantify the signal from each well, hindering its implementation in resource-limited-settings. Here, we demonstrate a cost-effective and handheld smartphone-based colorimetric microplate reader for rapid digitization and quantification of immunoserology-related ELISA tests in a conventional 96-well plate format at the point of care (POC). This device consists of a bundle of 96 optical fibers to collect the transmitted light from each well of the microplate and direct all the transmission signals from the wells onto the camera of the mobile-phone. Captured images are then transmitted to a remote server through a custom-designed app, and both quantitative and qualitative diagnostic results are returned back to the user within ~1 minute per 96-well plate by using a machine learning algorithm. We tested this mobile-phone based micro-plate reader in a clinical microbiology lab using FDA-approved mumps IgG, measles IgG, and herpes simplex virus IgG (HSV-1 and HSV-2) ELISA tests on 1138 remnant patient samples (roughly 50% training and 50% testing), and achieved an overall accuracy of ~99% or higher for each ELISA test. This handheld and cost-effective platform could be immediately useful for large-scale vaccination monitoring in low-infrastructure settings, and also for other high-throughput disease screening applications at POC.

Antepartum fetal heart rate feature extraction and classification using empirical mode decomposition and support vector machine

PubMed Central

2011-01-01

Background Cardiotocography (CTG) is the most widely used tool for fetal surveillance. The visual analysis of fetal heart rate (FHR) traces largely depends on the expertise and experience of the clinician involved. Several approaches have been proposed for the effective interpretation of FHR. In this paper, a new approach for FHR feature extraction based on empirical mode decomposition (EMD) is proposed, which was used along with support vector machine (SVM) for the classification of FHR recordings as 'normal' or 'at risk'. Methods The FHR were recorded from 15 subjects at a sampling rate of 4 Hz and a dataset consisting of 90 randomly selected records of 20 minutes duration was formed from these. All records were labelled as 'normal' or 'at risk' by two experienced obstetricians. A training set was formed by 60 records, the remaining 30 left as the testing set. The standard deviations of the EMD components are input as features to a support vector machine (SVM) to classify FHR samples. Results For the training set, a five-fold cross validation test resulted in an accuracy of 86% whereas the overall geometric mean of sensitivity and specificity was 94.8%. The Kappa value for the training set was .923. Application of the proposed method to the testing set (30 records) resulted in a geometric mean of 81.5%. The Kappa value for the testing set was .684. Conclusions Based on the overall performance of the system it can be stated that the proposed methodology is a promising new approach for the feature extraction and classification of FHR signals. PMID:21244712

Enhancement of the NMSU Channel Error Simulator to Provide User-Selectable Link Delays

NASA Technical Reports Server (NTRS)

Horan, Stephen; Wang, Ru-Hai

2000-01-01

This is the third in a continuing series of reports describing the development of the Space-to-Ground Link Simulator (SGLS) to be used for testing data transfers under simulated space channel conditions. The SGLS is based upon Virtual Instrument (VI) software techniques for managing the error generation, link data rate configuration, and, now, selection of the link delay value. In this report we detail the changes that needed to be made to the SGLS VI configuration to permit link delays to be added to the basic error generation and link data rate control capabilities. This was accomplished by modifying the rate-splitting VIs to include a buffer the hold the incoming data for the duration selected by the user to emulate the channel link delay. In sample tests of this configuration, the TCP/IP(sub ftp) service and the SCPS(sub fp) service were used to transmit 10-KB data files using both symmetric (both forward and return links set to 115200 bps) and unsymmetric (forward link set at 2400 bps and a return link set at 115200 bps) link configurations. Transmission times were recorded at bit error rates of 0 through 10(exp -5) to give an indication of the link performance. In these tests. we noted separate timings for the protocol setup time to initiate the file transfer and the variation in the actual file transfer time caused by channel errors. Both protocols showed similar performance to that seen earlier for the symmetric and unsymmetric channels. This time, the delays in establishing the file protocol also showed that these delays could double the transmission time and need to be accounted for in mission planning. Both protocols also showed a difficulty in transmitting large data files over large link delays. In these tests, there was no clear favorite between the TCP/IP(sub ftp) and the SCPS(sub fp). Based upon these tests, further testing is recommended to extend the results to different file transfer configurations.

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

PubMed

Kaplan, Noam; Vaaknin, Avishay; Linial, Michal

2003-10-01

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

Acoustic measurements from a rotor blade-vortex interaction noise experiment in the German-Dutch Wind Tunnel (DNW)

NASA Technical Reports Server (NTRS)

Martin, Ruth M.; Splettstoesser, W. R.; Elliott, J. W.; Schultz, K.-J.

1988-01-01

Acoustic data are presented from a 40 percent scale model of the 4-bladed BO-105 helicopter main rotor, measured in the large European aeroacoustic wind tunnel, the DNW. Rotor blade-vortex interaction (BVI) noise data in the low speed flight range were acquired using a traversing in-flow microphone array. The experimental apparatus, testing procedures, calibration results, and experimental objectives are fully described. A large representative set of averaged acoustic signals is presented.

Evaluating Gene Set Enrichment Analysis Via a Hybrid Data Model

PubMed Central

Hua, Jianping; Bittner, Michael L.; Dougherty, Edward R.

2014-01-01

Gene set enrichment analysis (GSA) methods have been widely adopted by biological labs to analyze data and generate hypotheses for validation. Most of the existing comparison studies focus on whether the existing GSA methods can produce accurate P-values; however, practitioners are often more concerned with the correct gene-set ranking generated by the methods. The ranking performance is closely related to two critical goals associated with GSA methods: the ability to reveal biological themes and ensuring reproducibility, especially for small-sample studies. We have conducted a comprehensive simulation study focusing on the ranking performance of seven representative GSA methods. We overcome the limitation on the availability of real data sets by creating hybrid data models from existing large data sets. To build the data model, we pick a master gene from the data set to form the ground truth and artificially generate the phenotype labels. Multiple hybrid data models can be constructed from one data set and multiple data sets of smaller sizes can be generated by resampling the original data set. This approach enables us to generate a large batch of data sets to check the ranking performance of GSA methods. Our simulation study reveals that for the proposed data model, the Q2 type GSA methods have in general better performance than other GSA methods and the global test has the most robust results. The properties of a data set play a critical role in the performance. For the data sets with highly connected genes, all GSA methods suffer significantly in performance. PMID:24558298

A surrogate-based metaheuristic global search method for beam angle selection in radiation treatment planning.

PubMed

Zhang, H H; Gao, S; Chen, W; Shi, L; D'Souza, W D; Meyer, R R

2013-03-21

An important element of radiation treatment planning for cancer therapy is the selection of beam angles (out of all possible coplanar and non-coplanar angles in relation to the patient) in order to maximize the delivery of radiation to the tumor site and minimize radiation damage to nearby organs-at-risk. This category of combinatorial optimization problem is particularly difficult because direct evaluation of the quality of treatment corresponding to any proposed selection of beams requires the solution of a large-scale dose optimization problem involving many thousands of variables that represent doses delivered to volume elements (voxels) in the patient. However, if the quality of angle sets can be accurately estimated without expensive computation, a large number of angle sets can be considered, increasing the likelihood of identifying a very high quality set. Using a computationally efficient surrogate beam set evaluation procedure based on single-beam data extracted from plans employing equallyspaced beams (eplans), we have developed a global search metaheuristic process based on the nested partitions framework for this combinatorial optimization problem. The surrogate scoring mechanism allows us to assess thousands of beam set samples within a clinically acceptable time frame. Tests on difficult clinical cases demonstrate that the beam sets obtained via our method are of superior quality.

A surrogate-based metaheuristic global search method for beam angle selection in radiation treatment planning

PubMed Central

Zhang, H H; Gao, S; Chen, W; Shi, L; D’Souza, W D; Meyer, R R

2013-01-01

An important element of radiation treatment planning for cancer therapy is the selection of beam angles (out of all possible coplanar and non-coplanar angles in relation to the patient) in order to maximize the delivery of radiation to the tumor site and minimize radiation damage to nearby organs-at-risk. This category of combinatorial optimization problem is particularly difficult because direct evaluation of the quality of treatment corresponding to any proposed selection of beams requires the solution of a large-scale dose optimization problem involving many thousands of variables that represent doses delivered to volume elements (voxels) in the patient. However, if the quality of angle sets can be accurately estimated without expensive computation, a large number of angle sets can be considered, increasing the likelihood of identifying a very high quality set. Using a computationally efficient surrogate beam set evaluation procedure based on single-beam data extracted from plans employing equally-spaced beams (eplans), we have developed a global search metaheuristic process based on the Nested Partitions framework for this combinatorial optimization problem. The surrogate scoring mechanism allows us to assess thousands of beam set samples within a clinically acceptable time frame. Tests on difficult clinical cases demonstrate that the beam sets obtained via our method are superior quality. PMID:23459411

Construction and application of a new dual-hybrid random phase approximation.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Kállay, Mihály

2015-10-13

The direct random phase approximation (dRPA) combined with Kohn-Sham reference orbitals is among the most promising tools in computational chemistry and applicable in many areas of chemistry and physics. The reason for this is that it scales as N(4) with the system size, which is a considerable advantage over the accurate ab initio wave function methods like standard coupled-cluster. dRPA also yields a considerably more accurate description of thermodynamic and electronic properties than standard density-functional theory methods. It is also able to describe strong static electron correlation effects even in large systems with a small or vanishing band gap missed by common single-reference methods. However, dRPA has several flaws due to its self-correlation error. In order to obtain accurate and precise reaction energies, barriers and noncovalent intra- and intermolecular interactions, we construct a new dual-hybrid dRPA (hybridization of exact and semilocal exchange in both the energy and the orbitals) and test the performance of this new functional on isogyric, isodesmic, hypohomodesmotic, homodesmotic, and hyperhomodesmotic reaction classes. We also use a test set of 14 Diels-Alder reactions, six atomization energies (AE6), 38 hydrocarbon atomization energies, and 100 reaction barrier heights (DBH24, HT-BH38, and NHT-BH38). For noncovalent complexes, we use the NCCE31 and S22 test sets. To test the intramolecular interactions, we use a set of alkane, cysteine, phenylalanine-glycine-glycine tripeptide, and monosaccharide conformers. We also discuss the delocalization and static correlation errors. We show that a universally accurate description of chemical properties can be provided by a large, 75% exact exchange mixing both in the calculation of the reference orbitals and the final energy.

Alignment-independent technique for 3D QSAR analysis

NASA Astrophysics Data System (ADS)

Wilkes, Jon G.; Stoyanova-Slavova, Iva B.; Buzatu, Dan A.

2016-04-01

Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test 2 = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test 2 = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test 2 = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

Usability-driven pruning of large ontologies: the case of SNOMED CT.

PubMed

López-García, Pablo; Boeker, Martin; Illarramendi, Arantza; Schulz, Stefan

2012-06-01

To study ontology modularization techniques when applied to SNOMED CT in a scenario in which no previous corpus of information exists and to examine if frequency-based filtering using MEDLINE can reduce subset size without discarding relevant concepts. Subsets were first extracted using four graph-traversal heuristics and one logic-based technique, and were subsequently filtered with frequency information from MEDLINE. Twenty manually coded discharge summaries from cardiology patients were used as signatures and test sets. The coverage, size, and precision of extracted subsets were measured. Graph-traversal heuristics provided high coverage (71-96% of terms in the test sets of discharge summaries) at the expense of subset size (17-51% of the size of SNOMED CT). Pre-computed subsets and logic-based techniques extracted small subsets (1%), but coverage was limited (24-55%). Filtering reduced the size of large subsets to 10% while still providing 80% coverage. Extracting subsets to annotate discharge summaries is challenging when no previous corpus exists. Ontology modularization provides valuable techniques, but the resulting modules grow as signatures spread across subhierarchies, yielding a very low precision. Graph-traversal strategies and frequency data from an authoritative source can prune large biomedical ontologies and produce useful subsets that still exhibit acceptable coverage. However, a clinical corpus closer to the specific use case is preferred when available.

Advanced Distributed Measurements and Data Processing at the Vibro-Acoustic Test Facility, GRC Space Power Facility, Sandusky, Ohio - an Architecture and an Example

NASA Technical Reports Server (NTRS)

Hill, Gerald M.; Evans, Richard K.

2009-01-01

A large-scale, distributed, high-speed data acquisition system (HSDAS) is currently being installed at the Space Power Facility (SPF) at NASA Glenn Research Center s Plum Brook Station in Sandusky, OH. This installation is being done as part of a facility construction project to add Vibro-acoustic Test Capabilities (VTC) to the current thermal-vacuum testing capability of SPF in support of the Orion Project s requirement for Space Environments Testing (SET). The HSDAS architecture is a modular design, which utilizes fully-remotely managed components, enables the system to support multiple test locations with a wide-range of measurement types and a very large system channel count. The architecture of the system is presented along with details on system scalability and measurement verification. In addition, the ability of the system to automate many of its processes such as measurement verification and measurement system analysis is also discussed.

Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies

PubMed Central

2010-01-01

Background All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloidosis would actually occur under physiological conditions depends largely on the amino acid composition of a protein. We explore using a naive Bayesian classifier and a weighted decision tree for predicting the amyloidogenicity of immunoglobulin sequences. Results The average accuracy based on leave-one-out (LOO) cross validation of a Bayesian classifier generated from 143 amyloidogenic sequences is 60.84%. This is consistent with the average accuracy of 61.15% for a holdout test set comprised of 103 AM and 28 non-amyloidogenic sequences. The LOO cross validation accuracy increases to 81.08% when the training set is augmented by the holdout test set. In comparison, the average classification accuracy for the holdout test set obtained using a decision tree is 78.64%. Non-amyloidogenic sequences are predicted with average LOO cross validation accuracies between 74.05% and 77.24% using the Bayesian classifier, depending on the training set size. The accuracy for the holdout test set was 89%. For the decision tree, the non-amyloidogenic prediction accuracy is 75.00%. Conclusions This exploratory study indicates that both classification methods may be promising in providing straightforward predictions on the amyloidogenicity of a sequence. Nevertheless, the number of available sequences that satisfy the premises of this study are limited, and are consequently smaller than the ideal training set size. Increasing the size of the training set clearly increases the accuracy, and the expansion of the training set to include not only more derivatives, but more alignments, would make the method more sound. The accuracy of the classifiers may also be improved when additional factors, such as structural and physico-chemical data, are considered. The development of this type of classifier has significant applications in evaluating engineered antibodies, and may be adapted for evaluating engineered proteins in general. PMID:20144194

Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies.

PubMed

David, Maria Pamela C; Concepcion, Gisela P; Padlan, Eduardo A

2010-02-08

All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloidosis would actually occur under physiological conditions depends largely on the amino acid composition of a protein. We explore using a naive Bayesian classifier and a weighted decision tree for predicting the amyloidogenicity of immunoglobulin sequences. The average accuracy based on leave-one-out (LOO) cross validation of a Bayesian classifier generated from 143 amyloidogenic sequences is 60.84%. This is consistent with the average accuracy of 61.15% for a holdout test set comprised of 103 AM and 28 non-amyloidogenic sequences. The LOO cross validation accuracy increases to 81.08% when the training set is augmented by the holdout test set. In comparison, the average classification accuracy for the holdout test set obtained using a decision tree is 78.64%. Non-amyloidogenic sequences are predicted with average LOO cross validation accuracies between 74.05% and 77.24% using the Bayesian classifier, depending on the training set size. The accuracy for the holdout test set was 89%. For the decision tree, the non-amyloidogenic prediction accuracy is 75.00%. This exploratory study indicates that both classification methods may be promising in providing straightforward predictions on the amyloidogenicity of a sequence. Nevertheless, the number of available sequences that satisfy the premises of this study are limited, and are consequently smaller than the ideal training set size. Increasing the size of the training set clearly increases the accuracy, and the expansion of the training set to include not only more derivatives, but more alignments, would make the method more sound. The accuracy of the classifiers may also be improved when additional factors, such as structural and physico-chemical data, are considered. The development of this type of classifier has significant applications in evaluating engineered antibodies, and may be adapted for evaluating engineered proteins in general.

AGARD Flight Test Techniques Series. Volume 7. Air-to-Air Radar Flight Testing

DTIC Science & Technology

1988-06-01

enters the beam ), a different tilt angle should be used. The emphasis on setting the tilt angle may require a non - standard high accuracy tilt angle...is: the time from pilot designation on a non -maneuvering target to the time that the system achieves target range, range rate and angle tracking...minimal attenuation, distortion, or boresight Shift effects on the radar beam . Thus, radome design for airborne application io largely a process of

Investigating the Effects of Magnetic Variations on Inertial/Magnetic Orientation Sensors

DTIC Science & Technology

2007-09-01

caused by test objects, a track was constructed using nonferrous materials and set so that the orientation of an inertial/magnetic sensor module...states ◆ metal filing cabinet ◆ mobile robot, unpowered, powered, and motor engaged. The MicroStrain 3DM-G sensor module is factory calibrated and...triad of the sensor module approached a large metal filing cabinet. The deviations for this test object are the largest of any observed in the

Management of Electronic Test Equipment. Volume 3. Organizations, Policies, and Procedures.

DTIC Science & Technology

1986-07-01

is not guaranteed. The best example, probably, is the UH - 60 Black Hawk program, where the specific tools used by organizational maintainers were nailed...tools. This innovative and highly effective approach was large!i, Successful. even though it became obvious once the UH - 60 was fielded, that a special...test set was necessary to cope with the electronic control unit assembly of the turbine engine. The UH - 60 example, however, does illustrate that support

Global-scale regionalization of hydrological model parameters using streamflow data from many small catchments

NASA Astrophysics Data System (ADS)

Beck, Hylke; de Roo, Ad; van Dijk, Albert; McVicar, Tim; Miralles, Diego; Schellekens, Jaap; Bruijnzeel, Sampurno; de Jeu, Richard

2015-04-01

Motivated by the lack of large-scale model parameter regionalization studies, a large set of 3328 small catchments (< 10000 km2) around the globe was used to set up and evaluate five model parameterization schemes at global scale. The HBV-light model was chosen because of its parsimony and flexibility to test the schemes. The catchments were calibrated against observed streamflow (Q) using an objective function incorporating both behavioral and goodness-of-fit measures, after which the catchment set was split into subsets of 1215 donor and 2113 evaluation catchments based on the calibration performance. The donor catchments were subsequently used to derive parameter sets that were transferred to similar grid cells based on a similarity measure incorporating climatic and physiographic characteristics, thereby producing parameter maps with global coverage. Overall, there was a lack of suitable donor catchments for mountainous and tropical environments. The schemes with spatially-uniform parameter sets (EXP2 and EXP3) achieved the worst Q estimation performance in the evaluation catchments, emphasizing the importance of parameter regionalization. The direct transfer of calibrated parameter sets from donor catchments to similar grid cells (scheme EXP1) performed best, although there was still a large performance gap between EXP1 and HBV-light calibrated against observed Q. The schemes with parameter sets obtained by simultaneously calibrating clusters of similar donor catchments (NC10 and NC58) performed worse than EXP1. The relatively poor Q estimation performance achieved by two (uncalibrated) macro-scale hydrological models suggests there is considerable merit in regionalizing the parameters of such models. The global HBV-light parameter maps and ancillary data are freely available via http://water.jrc.ec.europa.eu.

Caught you: threats to confidentiality due to the public release of large-scale genetic data sets

PubMed Central

2010-01-01

Background Large-scale genetic data sets are frequently shared with other research groups and even released on the Internet to allow for secondary analysis. Study participants are usually not informed about such data sharing because data sets are assumed to be anonymous after stripping off personal identifiers. Discussion The assumption of anonymity of genetic data sets, however, is tenuous because genetic data are intrinsically self-identifying. Two types of re-identification are possible: the "Netflix" type and the "profiling" type. The "Netflix" type needs another small genetic data set, usually with less than 100 SNPs but including a personal identifier. This second data set might originate from another clinical examination, a study of leftover samples or forensic testing. When merged to the primary, unidentified set it will re-identify all samples of that individual. Even with no second data set at hand, a "profiling" strategy can be developed to extract as much information as possible from a sample collection. Starting with the identification of ethnic subgroups along with predictions of body characteristics and diseases, the asthma kids case as a real-life example is used to illustrate that approach. Summary Depending on the degree of supplemental information, there is a good chance that at least a few individuals can be identified from an anonymized data set. Any re-identification, however, may potentially harm study participants because it will release individual genetic disease risks to the public. PMID:21190545

Caught you: threats to confidentiality due to the public release of large-scale genetic data sets.

PubMed

Wjst, Matthias

2010-12-29

Large-scale genetic data sets are frequently shared with other research groups and even released on the Internet to allow for secondary analysis. Study participants are usually not informed about such data sharing because data sets are assumed to be anonymous after stripping off personal identifiers. The assumption of anonymity of genetic data sets, however, is tenuous because genetic data are intrinsically self-identifying. Two types of re-identification are possible: the "Netflix" type and the "profiling" type. The "Netflix" type needs another small genetic data set, usually with less than 100 SNPs but including a personal identifier. This second data set might originate from another clinical examination, a study of leftover samples or forensic testing. When merged to the primary, unidentified set it will re-identify all samples of that individual. Even with no second data set at hand, a "profiling" strategy can be developed to extract as much information as possible from a sample collection. Starting with the identification of ethnic subgroups along with predictions of body characteristics and diseases, the asthma kids case as a real-life example is used to illustrate that approach. Depending on the degree of supplemental information, there is a good chance that at least a few individuals can be identified from an anonymized data set. Any re-identification, however, may potentially harm study participants because it will release individual genetic disease risks to the public.

Experimental Evaluation of Suitability of Selected Multi-Criteria Decision-Making Methods for Large-Scale Agent-Based Simulations.

PubMed

Tučník, Petr; Bureš, Vladimír

2016-01-01

Multi-criteria decision-making (MCDM) can be formally implemented by various methods. This study compares suitability of four selected MCDM methods, namely WPM, TOPSIS, VIKOR, and PROMETHEE, for future applications in agent-based computational economic (ACE) models of larger scale (i.e., over 10 000 agents in one geographical region). These four MCDM methods were selected according to their appropriateness for computational processing in ACE applications. Tests of the selected methods were conducted on four hardware configurations. For each method, 100 tests were performed, which represented one testing iteration. With four testing iterations conducted on each hardware setting and separated testing of all configurations with the-server parameter de/activated, altogether, 12800 data points were collected and consequently analyzed. An illustrational decision-making scenario was used which allows the mutual comparison of all of the selected decision making methods. Our test results suggest that although all methods are convenient and can be used in practice, the VIKOR method accomplished the tests with the best results and thus can be recommended as the most suitable for simulations of large-scale agent-based models.

Evaluation of interpolation techniques for the creation of gridded daily precipitation (1 × 1 km2); Cyprus, 1980-2010

NASA Astrophysics Data System (ADS)

Camera, Corrado; Bruggeman, Adriana; Hadjinicolaou, Panos; Pashiardis, Stelios; Lange, Manfred A.

2014-01-01

High-resolution gridded daily data sets are essential for natural resource management and the analyses of climate changes and their effects. This study aims to evaluate the performance of 15 simple or complex interpolation techniques in reproducing daily precipitation at a resolution of 1 km2 over topographically complex areas. Methods are tested considering two different sets of observation densities and different rainfall amounts. We used rainfall data that were recorded at 74 and 145 observational stations, respectively, spread over the 5760 km2 of the Republic of Cyprus, in the Eastern Mediterranean. Regression analyses utilizing geographical copredictors and neighboring interpolation techniques were evaluated both in isolation and combined. Linear multiple regression (LMR) and geographically weighted regression methods (GWR) were tested. These included a step-wise selection of covariables, as well as inverse distance weighting (IDW), kriging, and 3D-thin plate splines (TPS). The relative rank of the different techniques changes with different station density and rainfall amounts. Our results indicate that TPS performs well for low station density and large-scale events and also when coupled with regression models. It performs poorly for high station density. The opposite is observed when using IDW. Simple IDW performs best for local events, while a combination of step-wise GWR and IDW proves to be the best method for large-scale events and high station density. This study indicates that the use of step-wise regression with a variable set of geographic parameters can improve the interpolation of large-scale events because it facilitates the representation of local climate dynamics.

Methods and apparatus of analyzing electrical power grid data

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

Hafen, Ryan P.; Critchlow, Terence J.; Gibson, Tara D.

Apparatus and methods of processing large-scale data regarding an electrical power grid are described. According to one aspect, a method of processing large-scale data regarding an electrical power grid includes accessing a large-scale data set comprising information regarding an electrical power grid; processing data of the large-scale data set to identify a filter which is configured to remove erroneous data from the large-scale data set; using the filter, removing erroneous data from the large-scale data set; and after the removing, processing data of the large-scale data set to identify an event detector which is configured to identify events of interestmore » in the large-scale data set.« less

Prediction of protein tertiary structure from sequences using a very large back-propagation neural network

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

Liu, X.; Wilcox, G.L.

1993-12-31

We have implemented large scale back-propagation neural networks on a 544 node Connection Machine, CM-5, using the C language in MIMD mode. The program running on 512 processors performs backpropagation learning at 0.53 Gflops, which provides 76 million connection updates per second. We have applied the network to the prediction of protein tertiary structure from sequence information alone. A neural network with one hidden layer and 40 million connections is trained to learn the relationship between sequence and tertiary structure. The trained network yields predicted structures of some proteins on which it has not been trained given only their sequences.more » Presentation of the Fourier transform of the sequences accentuates periodicity in the sequence and yields good generalization with greatly increased training efficiency. Training simulations with a large, heterologous set of protein structures (111 proteins from CM-5 time) to solutions with under 2% RMS residual error within the training set (random responses give an RMS error of about 20%). Presentation of 15 sequences of related proteins in a testing set of 24 proteins yields predicted structures with less than 8% RMS residual error, indicating good apparent generalization.« less

Seeking the Cause of Correlations among Mental Abilities: Large Twin Analysis in a National Testing Program.

ERIC Educational Resources Information Center

Page, Ellis B.; Jarjoura, David

1979-01-01

A computer scan of ACT Assessment records identified 3,427 sets of twins. The Hardy-Weinberg rule was used to estimate the proportion of monozygotic twins in the sample. Matrices of genetic and environmental influences were produced. The heaviest loadings were clearly in the genetic matrix. (SJL)

Application of the National Assessment of Educational Progress Philosophy in San Bernardino City Unified School District.

ERIC Educational Resources Information Center

Bonney, Lewis A.

the steps taken by a large urban school district to develop and implement an objectives-based curriculum with criterion-referenced assessment of student progress are described. These steps include: goal setting, development of curriculum objectives, construction of assessment exercises, matrix sampling in test administration, and reporting of…

A Test of the Teaching-Learning Style Mesh Hypothesis in a Chinese MBA

ERIC Educational Resources Information Center

Andres, Hayward P.; Akan, Obasi H.

2015-01-01

Purpose: The purpose of this paper is to determine if "fit" and "non-fit" between authoritarian versus demonstrator teaching and visual versus verbal learning preferences differ in impact on Chinese MBA student academic performance in a large local urban Chinese university setting. In addition, the role of Chinese cultural…

Interactive visual analysis promotes exploration of long-term ecological data

Treesearch

T.N. Pham; J.A. Jones; R. Metoyer; F.J. Swanson; R.J. Pabst

2013-01-01

Long-term ecological data are crucial in helping ecologists understand ecosystem function and environmental change. Nevertheless, these kinds of data sets are difficult to analyze because they are usually large, multivariate, and spatiotemporal. Although existing analysis tools such as statistical methods and spreadsheet software permit rigorous tests of pre-conceived...

Remote sensing techniques in cultural resource management archaeology

NASA Astrophysics Data System (ADS)

Johnson, Jay K.; Haley, Bryan S.

2003-04-01

Cultural resource management archaeology in the United States concerns compliance with legislation set in place to protect archaeological resources from the impact of modern activities. Traditionally, surface collection, shovel testing, test excavation, and mechanical stripping are used in these projects. These methods are expensive, time consuming, and may poorly represent the features within archaeological sites. The use of remote sensing techniques in cultural resource management archaeology may provide an answer to these problems. Near-surface geophysical techniques, including magnetometry, resistivity, electromagnetics, and ground penetrating radar, have proven to be particularly successful at efficiently locating archaeological features. Research has also indicated airborne and satellite remote sensing may hold some promise in the future for large-scale archaeological survey, although this is difficult in many areas of the world where ground cover reflect archaeological features in an indirect manner. A cost simulation of a hypothetical data recovery project on a large complex site in Mississippi is presented to illustrate the potential advantages of remote sensing in a cultural resource management setting. The results indicate these techniques can save a substantial amount of time and money for these projects.

Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens

PubMed Central

Huang, Shan-Han; Tung, Chun-Wei

2017-01-01

The assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation. PMID:28117354

Search for diphoton events with large missing transverse energy with 36 pb-1 of 7 TeV proton-proton collision data with the ATLAS detector

NASA Astrophysics Data System (ADS)

Aad, G.; Abbott, B.; Abdallah, J.; Abdelalim, A. A.; Abdesselam, A.; Abdinov, O.; Abi, B.; Abolins, M.; Abramowicz, H.; Abreu, H.; Acerbi, E.; Acharya, B. S.; Adams, D. L.; Addy, T. N.; Adelman, J.; Aderholz, M.; Adomeit, S.; Adragna, P.; Adye, T.; Aefsky, S.; Aguilar-Saavedra, J. A.; Aharrouche, M.; Ahlen, S. P.; Ahles, F.; Ahmad, A.; Ahsan, M.; Aielli, G.; Akdogan, T.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Akiyama, A.; Alam, M. S.; Alam, M. A.; Albert, J.; Albrand, S.; Aleksa, M.; Aleksandrov, I. N.; Alessandria, F.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Aliev, M.; Alimonti, G.; Alison, J.; Aliyev, M.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alviggi, M. G.; Amako, K.; Amaral, P.; Amelung, C.; Ammosov, V. V.; Amorim, A.; Amorós, G.; Amram, N.; Anastopoulos, C.; Andari, N.; Andeen, T.; Anders, C. F.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Andrieux, M.-L.; Anduaga, X. S.; Angerami, A.; Anghinolfi, F.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonov, A.; Antos, J.; Anulli, F.; Aoun, S.; Aperio Bella, L.; Apolle, R.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A. T. H.; Archambault, J. P.; Arfaoui, S.; Arguin, J.-F.; Arik, E.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnault, C.; Artamonov, A.; Artoni, G.; Arutinov, D.; Asai, S.; Asfandiyarov, R.; Ask, S.; Åsman, B.; Asquith, L.; Assamagan, K.; Astbury, A.; Astvatsatourov, A.; Atoian, G.; Aubert, B.; Auerbach, B.; Auge, E.; Augsten, K.; Aurousseau, M.; Austin, N.; Avramidou, R.; Axen, D.; Ay, C.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Baccaglioni, G.; Bacci, C.; Bach, A. M.; Bachacou, H.; Bachas, K.; Bachy, G.; Backes, M.; Backhaus, M.; Badescu, E.; Bagnaia, P.; Bahinipati, S.; Bai, Y.; Bailey, D. C.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, M. D.; Baker, S.; Dos Santos Pedrosa, F. Baltasar; Banas, E.; Banerjee, P.; Banerjee, Sw.; Banfi, D.; Bangert, A.; Bansal, V.; Bansil, H. S.; Barak, L.; Baranov, S. P.; Barashkou, A.; Barbaro Galtieri, A.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Bardin, D. Y.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Barrillon, P.; Bartoldus, R.; Barton, A. E.; Bartsch, D.; Bartsch, V.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battaglia, A.; Battistin, M.; Battistoni, G.; Bauer, F.; Bawa, H. S.; Beare, B.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Bechtle, P.; Beck, H. P.; Beckingham, M.; Becks, K. H.; Beddall, A. J.; Beddall, A.; Bedikian, S.; Bednyakov, V. A.; Bee, C. P.; Begel, M.; Harpaz, S. Behar; Behera, P. K.; Beimforde, M.; Belanger-Champagne, C.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellagamba, L.; Bellina, F.; Bellomo, M.; Belloni, A.; Beloborodova, O.; Belotskiy, K.; Beltramello, O.; Ami, S. Ben; Benary, O.; Benchekroun, D.; Benchouk, C.; Bendel, M.; Benedict, B. H.; Benekos, N.; Benhammou, Y.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernardet, K.; Bernat, P.; Bernhard, R.; Bernius, C.; Berry, T.; Bertin, A.; Bertinelli, F.; Bertolucci, F.; Besana, M. I.; Besson, N.; Bethke, S.; Bhimji, W.; Bianchi, R. M.; Bianco, M.; Biebel, O.; Bieniek, S. P.; Biesiada, J.; Biglietti, M.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Biscarat, C.; Bitenc, U.; Black, K. M.; Blair, R. E.; Blanchard, J.-B.; Blanchot, G.; Blazek, T.; Blocker, C.; Blocki, J.; Blondel, A.; Blum, W.; Blumenschein, U.; Bobbink, G. J.; Bobrovnikov, V. B.; Bocchetta, S. S.; Bocci, A.; Boddy, C. R.; Boehler, M.; Boek, J.; Boelaert, N.; Böser, S.; Bogaerts, J. A.; Bogdanchikov, A.; Bogouch, A.; Bohm, C.; Boisvert, V.; Bold, T.; Boldea, V.; Bolnet, N. M.; Bona, M.; Bondarenko, V. G.; Boonekamp, M.; Boorman, G.; Booth, C. 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A.; Budick, B.; Büscher, V.; Bugge, L.; Buira-Clark, D.; Bulekov, O.; Bunse, M.; Buran, T.; Burckhart, H.; Burdin, S.; Burgess, T.; Burke, S.; Busato, E.; Bussey, P.; Buszello, C. P.; Butin, F.; Butler, B.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Buttinger, W.; Byatt, T.; Cabrera Urbán, S.; Caforio, D.; Cakir, O.; Calafiura, P.; Calderini, G.; Calfayan, P.; Calkins, R.; Caloba, L. P.; Caloi, R.; Calvet, D.; Calvet, S.; Camacho Toro, R.; Camarri, P.; Cambiaghi, M.; Cameron, D.; Campana, S.; Campanelli, M.; Canale, V.; Canelli, F.; Canepa, A.; Cantero, J.; Capasso, L.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capriotti, D.; Capua, M.; Caputo, R.; Caramarcu, C.; Cardarelli, R.; Carli, T.; Carlino, G.; Carminati, L.; Caron, B.; Caron, S.; Carrillo Montoya, G. D.; Carter, A. A.; Carter, J. R.; Carvalho, J.; Casadei, D.; Casado, M. P.; Cascella, M.; Caso, C.; Castaneda Hernandez, A. M.; Castaneda-Miranda, E.; Castillo Gimenez, V.; Castro, N. F.; Cataldi, G.; Cataneo, F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Cattani, G.; Caughron, S.; Cauz, D.; Cavalleri, P.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Ceradini, F.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cetin, S. A.; Cevenini, F.; Chafaq, A.; Chakraborty, D.; Chan, K.; Chapleau, B.; Chapman, J. D.; Chapman, J. W.; Chareyre, E.; Charlton, D. G.; Chavda, V.; Barajas, C. A. Chavez; Cheatham, S.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, S.; Chen, T.; Chen, X.; Cheng, S.; Cheplakov, A.; Chepurnov, V. F.; Cherkaoui El Moursli, R.; Chernyatin, V.; Cheu, E.; Cheung, S. L.; Chevalier, L.; Chiefari, G.; Chikovani, L.; Childers, J. T.; Chilingarov, A.; Chiodini, G.; Chizhov, M. V.; Choudalakis, G.; Chouridou, S.; Christidi, I. A.; Christov, A.; Chromek-Burckhart, D.; Chu, M. L.; Chudoba, J.; Ciapetti, G.; Ciba, K.; Ciftci, A. K.; Ciftci, R.; Cinca, D.; Cindro, V.; Ciobotaru, M. D.; Ciocca, C.; Ciocio, A.; Cirilli, M.; Ciubancan, M.; Clark, A.; Clark, P. J.; Cleland, W.; Clemens, J. C.; Clement, B.; Clement, C.; Clifft, R. W.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coe, P.; Cogan, J. G.; Coggeshall, J.; Cogneras, E.; Cojocaru, C. D.; Colas, J.; Colijn, A. P.; Collard, C.; Collins, N. J.; Collins-Tooth, C.; Collot, J.; Colon, G.; Conde Muiño, P.; Coniavitis, E.; Conidi, M. C.; Consonni, M.; Consorti, V.; Constantinescu, S.; Conta, C.; Conventi, F.; Cook, J.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cooper-Smith, N. J.; Copic, K.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Costin, T.; Côté, D.; Coura Torres, R.; Courneyea, L.; Cowan, G.; Cowden, C.; Cox, B. E.; Cranmer, K.; Crescioli, F.; Cristinziani, M.; Crosetti, G.; Crupi, R.; Crépé-Renaudin, S.; Cuciuc, C.-M.; Almenar, C. Cuenca; Cuhadar Donszelmann, T.; Cuneo, S.; Curatolo, M.; Curtis, C. J.; Cwetanski, P.; Czirr, H.; Czyczula, Z.; D'Auria, S.; D'Onofrio, M.; D'Orazio, A.; Da Silva, P. V. M.; Da Via, C.; Dabrowski, W.; Dai, T.; Dallapiccola, C.; Dam, M.; Dameri, M.; Damiani, D. S.; Danielsson, H. O.; Dannheim, D.; Dao, V.; Darbo, G.; Darlea, G. L.; Daum, C.; Dauvergne, J. P.; Davey, W.; Davidek, T.; Davidson, N.; Davidson, R.; Davies, E.; Davies, M.; Davison, A. R.; Davygora, Y.; Dawe, E.; Dawson, I.; Dawson, J. W.; Daya, R. K.; De, K.; de Asmundis, R.; De Castro, S.; De Castro Faria Salgado, P. E.; De Cecco, S.; de Graat, J.; De Groot, N.; de Jong, P.; De La Taille, C.; De la Torre, H.; De Lotto, B.; De Mora, L.; De Nooij, L.; De Oliveira Branco, M.; De Pedis, D.; de Saintignon, P.; De Salvo, A.; De Sanctis, U.; De Santo, A.; De Vivie De Regie, J. B.; Dean, S.; Dedovich, D. V.; Degenhardt, J.; Dehchar, M.; Deile, M.; Del Papa, C.; Del Peso, J.; Del Prete, T.; Deliyergiyev, M.; Dell'Acqua, A.; Dell'Asta, L.; Della Pietra, M.; della Volpe, D.; Delmastro, M.; Delpierre, P.; Delruelle, N.; Delsart, P. A.; Deluca, C.; Demers, S.; Demichev, M.; Demirkoz, B.; Deng, J.; Denisov, S. P.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Devetak, E.; Deviveiros, P. O.; Dewhurst, A.; DeWilde, B.; Dhaliwal, S.; Dhullipudi, R.; Di Ciaccio, A.; Di Ciaccio, L.; Di Girolamo, A.; Di Girolamo, B.; Di Luise, S.; Di Mattia, A.; Di Micco, B.; Di Nardo, R.; Di Simone, A.; Di Sipio, R.; Diaz, M. A.; Diblen, F.; Diehl, E. B.; Dietrich, J.; Dietzsch, T. A.; Diglio, S.; Dindar Yagci, K.; Dingfelder, J.; Dionisi, C.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; do Vale, M. A. B.; Do Valle Wemans, A.; Doan, T. K. O.; Dobbs, M.; Dobinson, R.; Dobos, D.; Dobson, E.; Dobson, M.; Dodd, J.; Doglioni, C.; Doherty, T.; Doi, Y.; Dolejsi, J.; Dolenc, I.; Dolezal, Z.; Dolgoshein, B. A.; Dohmae, T.; Donadelli, M.; Donega, M.; Donini, J.; Dopke, J.; Doria, A.; Dos Anjos, A.; Dosil, M.; Dotti, A.; Dova, M. T.; Dowell, J. D.; Doxiadis, A. D.; Doyle, A. T.; Drasal, Z.; Drees, J.; Dressnandt, N.; Drevermann, H.; Driouichi, C.; Dris, M.; Dubbert, J.; Dubbs, T.; Dube, S.; Duchovni, E.; Duckeck, G.; Dudarev, A.; Dudziak, F.; Dührssen, M.; Duerdoth, I. P.; Duflot, L.; Dufour, M.-A.; Dunford, M.; Yildiz, H. Duran; Duxfield, R.; Dwuznik, M.; Dydak, F.; Dzahini, D.; Düren, M.; Ebenstein, W. L.; Ebke, J.; Eckert, S.; Eckweiler, S.; Edmonds, K.; Edwards, C. A.; Edwards, N. C.; Ehrenfeld, W.; Ehrich, T.; Eifert, T.; Eigen, G.; Einsweiler, K.; Eisenhandler, E.; Ekelof, T.; El Kacimi, M.; Ellert, M.; Elles, S.; Ellinghaus, F.; Ellis, K.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Ely, R.; Emeliyanov, D.; Engelmann, R.; Engl, A.; Epp, B.; Eppig, A.; Erdmann, J.; Ereditato, A.; Eriksson, D.; Ernst, J.; Ernst, M.; Ernwein, J.; Errede, D.; Errede, S.; Ertel, E.; Escalier, M.; Escobar, C.; Espinal Curull, X.; Esposito, B.; Etienne, F.; Etienvre, A. I.; Etzion, E.; Evangelakou, D.; Evans, H.; Fabbri, L.; Fabre, C.; Fakhrutdinov, R. M.; Falciano, S.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farley, J.; Farooque, T.; Farrington, S. M.; Farthouat, P.; Fassnacht, P.; Fassouliotis, D.; Fatholahzadeh, B.; Favareto, A.; Fayard, L.; Fazio, S.; Febbraro, R.; Federic, P.; Fedin, O. L.; Fedorko, W.; Fehling-Kaschek, M.; Feligioni, L.; Fellmann, D.; Felzmann, C. U.; Feng, C.; Feng, E. J.; Fenyuk, A. B.; Ferencei, J.; Ferland, J.; Fernando, W.; Ferrag, S.; Ferrando, J.; Ferrara, V.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferrer, A.; Ferrer, M. L.; Ferrere, D.; Ferretti, C.; Ferretto Parodi, A.; Fiascaris, M.; Fiedler, F.; Filipčič, A.; Filippas, A.; Filthaut, F.; Fincke-Keeler, M.; Fiolhais, M. C. N.; Fiorini, L.; Firan, A.; Fischer, G.; Fischer, P.; Fisher, M. J.; Fisher, S. M.; Flechl, M.; Fleck, I.; Fleckner, J.; Fleischmann, P.; Fleischmann, S.; Flick, T.; Flores Castillo, L. R.; Flowerdew, M. J.; Föhlisch, F.; Fokitis, M.; Martin, T. Fonseca; Forbush, D. A.; Formica, A.; Forti, A.; Fortin, D.; Foster, J. M.; Fournier, D.; Foussat, A.; Fowler, A. J.; Fowler, K.; Fox, H.; Francavilla, P.; Franchino, S.; Francis, D.; Frank, T.; Franklin, M.; Franz, S.; Fraternali, M.; Fratina, S.; French, S. T.; Froeschl, R.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fullana Torregrosa, E.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gadfort, T.; Gadomski, S.; Gagliardi, G.; Gagnon, P.; Galea, C.; Gallas, E. J.; Gallas, M. V.; Gallo, V.; Gallop, B. J.; Gallus, P.; Galyaev, E.; Gan, K. K.; Gao, Y. S.; Gapienko, V. A.; Gaponenko, A.; Garberson, F.; Garcia-Sciveres, M.; García, C.; Navarro, J. E. García; Gardner, R. W.; Garelli, N.; Garitaonandia, H.; Garonne, V.; Garvey, J.; Gatti, C.; Gaudio, G.; Gaumer, O.; Gaur, B.; Gauthier, L.; Gavrilenko, I. L.; Gay, C.; Gaycken, G.; Gayde, J.-C.; Gazis, E. N.; Ge, P.; Gee, C. N. P.; Geerts, D. A. A.; Geich-Gimbel, Ch.; Gellerstedt, K.; Gemme, C.; Gemmell, A.; Genest, M. H.; Gentile, S.; George, M.; George, S.; Gerlach, P.; Gershon, A.; Geweniger, C.; Ghazlane, H.; Ghez, P.; Ghodbane, N.; Giacobbe, B.; Giagu, S.; Giakoumopoulou, V.; Giangiobbe, V.; Gianotti, F.; Gibbard, B.; Gibson, A.; Gibson, S. M.; Gilbert, L. M.; Gilchriese, M.; Gilewsky, V.; Gillberg, D.; Gillman, A. R.; Gingrich, D. M.; Ginzburg, J.; Giokaris, N.; Giordano, R.; Giorgi, F. M.; Giovannini, P.; Giraud, P. F.; Giugni, D.; Giunta, M.; Giusti, P.; Gjelsten, B. K.; Gladilin, L. K.; Glasman, C.; Glatzer, J.; Glazov, A.; Glitza, K. W.; Glonti, G. L.; Godfrey, J.; Godlewski, J.; Goebel, M.; Göpfert, T.; Goeringer, C.; Gössling, C.; Göttfert, T.; Goldfarb, S.; Goldin, D.; Golling, T.; Golovnia, S. N.; Gomes, A.; Fajardo, L. S. Gomez; Gonçalo, R.; Goncalves Pinto Firmino Da Costa, J.; Gonella, L.; Gonidec, A.; Gonzalez, S.; González de la Hoz, S.; Silva, M. L. Gonzalez; Gonzalez-Sevilla, S.; Goodson, J. J.; Goossens, L.; Gorbounov, P. A.; Gordon, H. A.; Gorelov, I.; Gorfine, G.; Gorini, B.; Gorini, E.; Gorišek, A.; Gornicki, E.; Gorokhov, S. A.; Goryachev, V. N.; Gosdzik, B.; Gosselink, M.; Gostkin, M. I.; Gouanère, M.; Eschrich, I. Gough; Gouighri, M.; Goujdami, D.; Goulette, M. P.; Goussiou, A. G.; Goy, C.; Grabowska-Bold, I.; Grabski, V.; Grafström, P.; Grah, C.; Grahn, K.-J.; Grancagnolo, F.; Grancagnolo, S.; Grassi, V.; Gratchev, V.; Grau, N.; Gray, H. M.; Gray, J. A.; Graziani, E.; Grebenyuk, O. G.; Greenfield, D.; Greenshaw, T.; Greenwood, Z. D.; Gregor, I. M.; Grenier, P.; Griffiths, J.; Grigalashvili, N.; Grillo, A. A.; Grinstein, S.; Grishkevich, Y. V.; Grivaz, J.-F.; Grognuz, J.; Groh, M.; Gross, E.; Grosse-Knetter, J.; Groth-Jensen, J.; Grybel, K.; Guarino, V. J.; Guest, D.; Guicheney, C.; Guida, A.; Guillemin, T.; Guindon, S.; Guler, H.; Gunther, J.; Guo, B.; Guo, J.; Gupta, A.; Gusakov, Y.; Gushchin, V. N.; Gutierrez, A.; Gutierrez, P.; Guttman, N.; Gutzwiller, O.; Guyot, C.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haas, S.; Haber, C.; Hackenburg, R.; Hadavand, H. K.; Hadley, D. R.; Haefner, P.; Hahn, F.; Haider, S.; Hajduk, Z.; Hakobyan, H.; Haller, J.; Hamacher, K.; Hamal, P.; Hamilton, A.; Hamilton, S.; Han, H.; Han, L.; Hanagaki, K.; Hance, M.; Handel, C.; Hanke, P.; Hansen, J. R.; Hansen, J. B.; Hansen, J. D.; Hansen, P. H.; Hansson, P.; Hara, K.; Hare, G. A.; Harenberg, T.; Harkusha, S.; Harper, D.; Harrington, R. D.; Harris, O. M.; Harrison, K.; Hartert, J.; Hartjes, F.; Haruyama, T.; Harvey, A.; Hasegawa, S.; Hasegawa, Y.; Hassani, S.; Hatch, M.; Hauff, D.; Haug, S.; Hauschild, M.; Hauser, R.; Havranek, M.; Hawes, B. M.; Hawkes, C. M.; Hawkings, R. J.; Hawkins, D.; Hayakawa, T.; Hayden, D.; Hayward, H. S.; Haywood, S. J.; Hazen, E.; He, M.; Head, S. J.; Hedberg, V.; Heelan, L.; Heim, S.; Heinemann, B.; Heisterkamp, S.; Helary, L.; Heller, M.; Hellman, S.; Hellmich, D.; Helsens, C.; Henderson, R. C. W.; Henke, M.; Henrichs, A.; Correia, A. M. Henriques; Henrot-Versille, S.; Henry-Couannier, F.; Hensel, C.; Henß, T.; Hernandez, C. M.; Hernández Jiménez, Y.; Herrberg, R.; Hershenhorn, A. D.; Herten, G.; Hertenberger, R.; Hervas, L.; Hessey, N. P.; Hidvegi, A.; Higón-Rodriguez, E.; Hill, D.; Hill, J. C.; Hill, N.; Hiller, K. H.; Hillert, S.; Hillier, S. J.; Hinchliffe, I.; Hines, E.; Hirose, M.; Hirsch, F.; Hirschbuehl, D.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M. R.; Hoffman, J.; Hoffmann, D.; Hohlfeld, M.; Holder, M.; Holmes, A.; Holmgren, S. O.; Holy, T.; Holzbauer, J. L.; Homma, Y.; Hong, T. M.; Hooft van Huysduynen, L.; Horazdovsky, T.; Horn, C.; Horner, S.; Horton, K.; Hostachy, J.-Y.; Hou, S.; Houlden, M. A.; Hoummada, A.; Howarth, J.; Howell, D. F.; Hristova, I.; Hrivnac, J.; Hruska, I.; Hryn'ova, T.; Hsu, P. J.; Hsu, S.-C.; Huang, G. S.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Huffman, T. B.; Hughes, E. W.; Hughes, G.; Hughes-Jones, R. 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L.; Renaud, A.; Renkel, P.; Rescigno, M.; Resconi, S.; Resende, B.; Reznicek, P.; Rezvani, R.; Richards, A.; Richter, R.; Richter-Was, E.; Ridel, M.; Rieke, S.; Rijpstra, M.; Rijssenbeek, M.; Rimoldi, A.; Rinaldi, L.; Rios, R. R.; Riu, I.; Rivoltella, G.; Rizatdinova, F.; Rizvi, E.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robinson, M.; Robson, A.; Rocha de Lima, J. G.; Roda, C.; Dos Santos, D. Roda; Rodier, S.; Rodriguez, D.; Garcia, Y. Rodriguez; Roe, A.; Roe, S.; Røhne, O.; Rojo, V.; Rolli, S.; Romaniouk, A.; Romanov, V. M.; Romeo, G.; Romero Maltrana, D.; Roos, L.; Ros, E.; Rosati, S.; Rosbach, K.; Rose, M.; Rosenbaum, G. A.; Rosenberg, E. I.; Rosendahl, P. L.; Rosselet, L.; Rossetti, V.; Rossi, E.; Rossi, L. P.; Rossi, L.; Rotaru, M.; Roth, I.; Rothberg, J.; Rousseau, D.; Royon, C. R.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubinskiy, I.; Ruckert, B.; Ruckstuhl, N.; Rud, V. I.; Rudolph, C.; Rudolph, G.; Rühr, F.; Ruggieri, F.; Ruiz-Martinez, A.; Rulikowska-Zarebska, E.; Rumiantsev, V.; Rumyantsev, L.; Runge, K.; Runolfsson, O.; Rurikova, Z.; Rusakovich, N. A.; Rust, D. R.; Rutherfoord, J. P.; Ruwiedel, C.; Ruzicka, P.; Ryabov, Y. F.; Ryadovikov, V.; Ryan, P.; Rybar, M.; Rybkin, G.; Ryder, N. C.; Rzaeva, S.; Saavedra, A. F.; Sadeh, I.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Sakamoto, H.; Salamanna, G.; Salamon, A.; Saleem, M.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvachua Ferrando, B. M.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sampsonidis, D.; Samset, B. H.; Sanchez, A.; Sandaker, H.; Sander, H. G.; Sanders, M. P.; Sandhoff, M.; Sandoval, T.; Sandstroem, R.; Sandvoss, S.; Sankey, D. P. C.; Sansoni, A.; Santamarina Rios, C.; Santoni, C.; Santonico, R.; Santos, H.; Saraiva, J. G.; Sarangi, T.; Sarkisyan-Grinbaum, E.; Sarri, F.; Sartisohn, G.; Sasaki, O.; Sasaki, T.; Sasao, N.; Satsounkevitch, I.; Sauvage, G.; Sauvan, E.; Sauvan, J. B.; Savard, P.; Savinov, V.; Savu, D. O.; Savva, P.; Sawyer, L.; Saxon, D. H.; Says, L. P.; Sbarra, C.; Sbrizzi, A.; Scallon, O.; Scannicchio, D. A.; Schaarschmidt, J.; Schacht, P.; Schäfer, U.; Schaepe, S.; Schaetzel, S.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Schamov, A. G.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Scherzer, M. I.; Schiavi, C.; Schieck, J.; Schioppa, M.; Schlenker, S.; Schlereth, J. L.; Schmidt, E.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, M.; Schöning, A.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schroeder, C.; Schroer, N.; Schuh, S.; Schuler, G.; Schultes, J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, J. W.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schwemling, Ph.; Schwienhorst, R.; Schwierz, R.; Schwindling, J.; Schwindt, T.; Scott, W. G.; Searcy, J.; Sedykh, E.; Segura, E.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Seliverstov, D. M.; Sellden, B.; Sellers, G.; Seman, M.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Seuster, R.; Severini, H.; Sevior, M. E.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L. Y.; Shank, J. T.; Shao, Q. T.; Shapiro, M.; Shatalov, P. B.; Shaver, L.; Shaw, C.; Shaw, K.; Sherman, D.; Sherwood, P.; Shibata, A.; Shichi, H.; Shimizu, S.; Shimojima, M.; Shin, T.; Shmeleva, A.; Shochet, M. J.; Short, D.; Shupe, M. A.; Sicho, P.; Sidoti, A.; Siebel, A.; Siegert, F.; Siegrist, J.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S. B.; Simak, V.; Simard, O.; Simic, Lj.; Simion, S.; Simmons, B.; Simonyan, M.; Sinervo, P.; Sinev, N. B.; Sipica, V.; Siragusa, G.; Sisakyan, A. N.; Sivoklokov, S. Yu.; Sjölin, J.; Sjursen, T. B.; Skinnari, L. A.; Skovpen, K.; Skubic, P.; Skvorodnev, N.; Slater, M.; Slavicek, T.; Sliwa, K.; Sloan, T. J.; Sloper, J.; Smakhtin, V.; Smirnov, S. Yu.; Smirnova, L. N.; Smirnova, O.; Smith, B. C.; Smith, D.; Smith, K. M.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snow, S. W.; Snow, J.; Snuverink, J.; Snyder, S.; Soares, M.; Sobie, R.; Sodomka, J.; Soffer, A.; Solans, C. A.; Solar, M.; Solc, J.; Soldatov, E.; Soldevila, U.; Solfaroli Camillocci, E.; Solodkov, A. A.; Solovyanov, O. V.; Sondericker, J.; Soni, N.; Sopko, V.; Sopko, B.; Sorbi, M.; Sosebee, M.; Soukharev, A.; Spagnolo, S.; Spanò, F.; Spighi, R.; Spigo, G.; Spila, F.; Spiriti, E.; Spiwoks, R.; Spousta, M.; Spreitzer, T.; Spurlock, B.; Denis, R. D. St.; Stahl, T.; Stahlman, J.; Stamen, R.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stapnes, S.; Starchenko, E. A.; Stark, J.; Staroba, P.; Starovoitov, P.; Staude, A.; Stavina, P.; Stavropoulos, G.; Steele, G.; Steinbach, P.; Steinberg, P.; Stekl, I.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stevenson, K.; Stewart, G. A.; Stillings, J. A.; Stockmanns, T.; Stockton, M. C.; Stoerig, K.; Stoicea, G.; Stonjek, S.; Strachota, P.; Stradling, A. R.; Straessner, A.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strang, M.; Strauss, E.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Strong, J. A.; Stroynowski, R.; Strube, J.; Stugu, B.; Stumer, I.; Stupak, J.; Sturm, P.; Soh, D. A.; Su, D.; Subramania, H. S.; Succurro, A.; Sugaya, Y.; Sugimoto, T.; Suhr, C.; Suita, K.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, X.; Sundermann, J. E.; Suruliz, K.; Sushkov, S.; Susinno, G.; Sutton, M. R.; Suzuki, Y.; Svatos, M.; Sviridov, Yu. M.; Swedish, S.; Sykora, I.; Sykora, T.; Szeless, B.; Sánchez, J.; Ta, D.; Tackmann, K.; Taffard, A.; Tafirout, R.; Taga, A.; Taiblum, N.; Takahashi, Y.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Talby, M.; Talyshev, A.; Tamsett, M. C.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tanaka, Y.; Tani, K.; Tannoury, N.; Tappern, G. P.; Tapprogge, S.; Tardif, D.; Tarem, S.; Tarrade, F.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tassi, E.; Tatarkhanov, M.; Taylor, C.; Taylor, F. E.; Taylor, G. N.; Taylor, W.; Castanheira, M. Teixeira Dias; Teixeira-Dias, P.; Temming, K. K.; Ten Kate, H.; Teng, P. K.; Terada, S.; Terashi, K.; Terron, J.; Terwort, M.; Testa, M.; Teuscher, R. J.; Thadome, J.; Therhaag, J.; Theveneaux-Pelzer, T.; Thioye, M.; Thoma, S.; Thomas, J. P.; Thompson, E. N.; Thompson, P. D.; Thompson, P. D.; Thompson, A. S.; Thomson, E.; Thomson, M.; Thun, R. P.; Tic, T.; Tikhomirov, V. O.; Tikhonov, Y. A.; Timmermans, C. J. W. P.; Tipton, P.; Tique Aires Viegas, F. J.; Tisserant, S.; Tobias, J.; Toczek, B.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokár, S.; Tokunaga, K.; Tokushuku, K.; Tollefson, K.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, G.; Tonoyan, A.; Topfel, C.; Topilin, N. D.; Torchiani, I.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Traynor, D.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Trinh, T. N.; Tripiana, M. F.; Trischuk, W.; Trivedi, A.; Trocmé, B.; Troncon, C.; Trottier-McDonald, M.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C.-L.; Tsiakiris, M.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsung, J.-W.; Tsuno, S.; Tsybychev, D.; Tua, A.; Tuggle, J. M.; Turala, M.; Turecek, D.; Turk Cakir, I.; Turlay, E.; Turra, R.; Tuts, P. M.; Tykhonov, A.; Tylmad, M.; Tyndel, M.; Tyrvainen, H.; Tzanakos, G.; Uchida, K.; Ueda, I.; Ueno, R.; Ugland, M.; Uhlenbrock, M.; Uhrmacher, M.; Ukegawa, F.; Unal, G.; Underwood, D. G.; Undrus, A.; Unel, G.; Unno, Y.; Urbaniec, D.; Urkovsky, E.; Urrejola, P.; Usai, G.; Uslenghi, M.; Vacavant, L.; Vacek, V.; Vachon, B.; Vahsen, S.; Valenta, J.; Valente, P.; Valentinetti, S.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; van der Graaf, H.; van der Kraaij, E.; Van Der Leeuw, R.; van der Poel, E.; van der Ster, D.; Van Eijk, B.; van Eldik, N.; van Gemmeren, P.; van Kesteren, Z.; van Vulpen, I.; Vandelli, W.; Vandoni, G.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Varela Rodriguez, F.; Vari, R.; Varnes, E. W.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vassilakopoulos, V. I.; Vazeille, F.; Vegni, G.; Veillet, J. J.; Vellidis, C.; Veloso, F.; Veness, R.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vest, A.; Vetterli, M. C.; Vichou, I.; Vickey, T.; Viehhauser, G. H. A.; Viel, S.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinek, E.; Vinogradov, V. B.; Virchaux, M.; Virzi, J.; Vitells, O.; Viti, M.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vlasak, M.; Vlasov, N.; Vogel, A.; Vokac, P.; Volpi, G.; Volpi, M.; Volpini, G.; von der Schmitt, H.; von Loeben, J.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorobiev, A. P.; Vorwerk, V.; Vos, M.; Voss, R.; Voss, T. T.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Anh, T. Vu; Vuillermet, R.; Vukotic, I.; Wagner, W.; Wagner, P.; Wahlen, H.; Wakabayashi, J.; Walbersloh, J.; Walch, S.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Waller, P.; Wang, C.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, J. C.; Wang, R.; Wang, S. M.; Warburton, A.; Ward, C. P.; Warsinsky, M.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, A. T.; Waugh, B. M.; Weber, J.; Weber, M.; Weber, M. S.; Weber, P.; Weidberg, A. R.; Weigell, P.; Weingarten, J.; Weiser, C.; Wellenstein, H.; Wells, P. S.; Wen, M.; Wenaus, T.; Wendler, S.; Weng, Z.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Werth, M.; Wessels, M.; Weydert, C.; Whalen, K.; Wheeler-Ellis, S. J.; Whitaker, S. P.; White, A.; White, M. J.; White, S.; Whitehead, S. R.; Whiteson, D.; Whittington, D.; Wicek, F.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik, L. A. M.; Wijeratne, P. A.; Wildauer, A.; Wildt, M. A.; Wilhelm, I.; Wilkens, H. G.; Will, J. Z.; Williams, E.; Williams, H. H.; Willis, W.; Willocq, S.; Wilson, J. A.; Wilson, M. G.; Wilson, A.; Wingerter-Seez, I.; Winkelmann, S.; Winklmeier, F.; Wittgen, M.; Wolter, M. W.; Wolters, H.; Wooden, G.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wraight, K.; Wright, C.; Wrona, B.; Wu, S. L.; Wu, X.; Wu, Y.; Wulf, E.; Wunstorf, R.; Wynne, B. M.; Xaplanteris, L.; Xella, S.; Xie, S.; Xie, Y.; Xu, C.; Xu, D.; Xu, G.; Yabsley, B.; Yamada, M.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamaoka, J.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, U. K.; Yang, Y.; Yang, Y.; Yang, Z.; Yanush, S.; Yao, W.-M.; Yao, Y.; Yasu, Y.; Ybeles Smit, G. V.; Ye, J.; Ye, S.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Young, C.; Youssef, S.; Yu, D.; Yu, J.; Yu, J.; Yuan, L.; Yurkewicz, A.; Zaets, V. G.; Zaidan, R.; Zaitsev, A. M.; Zajacova, Z.; Zalite, Yo. K.; Zanello, L.; Zarzhitsky, P.; Zaytsev, A.; Zeitnitz, C.; Zeller, M.; Zemla, A.; Zendler, C.; Zenin, A. V.; Zenin, O.; Ženiš, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; della Porta, G. Zevi; Zhan, Z.; Zhang, D.; Zhang, H.; Zhang, J.; Zhang, X.; Zhang, Z.; Zhao, L.; Zhao, T.; Zhao, Z.; Zhemchugov, A.; Zheng, S.; Zhong, J.; Zhou, B.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhuravlov, V.; Zieminska, D.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Ziolkowski, M.; Zitoun, R.; Živković, L.; Zmouchko, V. V.; Zobernig, G.; Zoccoli, A.; Zolnierowski, Y.; Zsenei, A.; zur Nedden, M.; Zutshi, V.; Zwalinski, L.

2011-10-01

Making use of 36 pb-1 of proton-proton collision data at sqrt{s} =7 TeV, the ATLAS Collaboration has performed a search for diphoton events with large missing transverse energy. Observing no excess of events above the Standard Model prediction, a 95% Confidence Level (CL) upper limit is set on the cross section for new physics of σ<0.38-0.65 pb in the context of a generalised model of gauge-mediated supersymmetry breaking (GGM) with a bino-like lightest neutralino, and of σ<0.18-0.23 pb in the context of a specific model with one universal extra dimension (UED). A 95% CL lower limit of 560 GeV, for bino masses above 50 GeV, is set on the GGM gluino mass, while a lower limit of 1/ R>961 GeV is set on the UED compactification radius R. These limits provide the most stringent tests of these models to date.

Measuring hospital care from the patients' perspective: an overview of the CAHPS Hospital Survey development process.

PubMed

Goldstein, Elizabeth; Farquhar, Marybeth; Crofton, Christine; Darby, Charles; Garfinkel, Steven

2005-12-01

To describe the developmental process for the CAHPS Hospital Survey. A pilot was conducted in three states with 19,720 hospital discharges. A rigorous, multi-step process was used to develop the CAHPS Hospital Survey. It included a public call for measures, multiple Federal Register notices soliciting public input, a review of the relevant literature, meetings with hospitals, consumers and survey vendors, cognitive interviews with consumer, a large-scale pilot test in three states and consumer testing and numerous small-scale field tests. The current version of the CAHPS Hospital Survey has survey items in seven domains, two overall ratings of the hospital and five items used for adjusting for the mix of patients across hospitals and for analytical purposes. The CAHPS Hospital Survey is a core set of questions that can be administered as a stand-alone questionnaire or combined with a broader set of hospital specific items.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

PubMed

Edgar, Robert C

2004-01-01

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

Direct Validation of the Wall Interference Correction System of the Ames 11-Foot Transonic Wind Tunnel

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert; Boone, Alan R.

2003-01-01

Data from the test of a large semispan model was used to perform a direct validation of a wall interference correction system for a transonic slotted wall wind tunnel. At first, different sets of uncorrected aerodynamic coefficients were generated by physically changing the boundary condition of the test section walls. Then, wall interference corrections were computed and applied to all data points. Finally, an interpolation of the corrected aerodynamic coefficients was performed. This interpolation made sure that the corrected Mach number of a given run would be constant. Overall, the agreement between corresponding interpolated lift, drag, and pitching moment coefficient sets was very good. Buoyancy corrections were also investigated. These studies showed that the accuracy goal of one drag count may only be achieved if reliable estimates of the wall interference induced buoyancy correction are available during a test.

Multiple Phenotype Association Tests Using Summary Statistics in Genome-Wide Association Studies

PubMed Central

Liu, Zhonghua; Lin, Xihong

2017-01-01

Summary We study in this paper jointly testing the associations of a genetic variant with correlated multiple phenotypes using the summary statistics of individual phenotype analysis from Genome-Wide Association Studies (GWASs). We estimated the between-phenotype correlation matrix using the summary statistics of individual phenotype GWAS analyses, and developed genetic association tests for multiple phenotypes by accounting for between-phenotype correlation without the need to access individual-level data. Since genetic variants often affect multiple phenotypes differently across the genome and the between-phenotype correlation can be arbitrary, we proposed robust and powerful multiple phenotype testing procedures by jointly testing a common mean and a variance component in linear mixed models for summary statistics. We computed the p-values of the proposed tests analytically. This computational advantage makes our methods practically appealing in large-scale GWASs. We performed simulation studies to show that the proposed tests maintained correct type I error rates, and to compare their powers in various settings with the existing methods. We applied the proposed tests to a GWAS Global Lipids Genetics Consortium summary statistics data set and identified additional genetic variants that were missed by the original single-trait analysis. PMID:28653391

Multiple phenotype association tests using summary statistics in genome-wide association studies.

PubMed

Liu, Zhonghua; Lin, Xihong

2018-03-01

We study in this article jointly testing the associations of a genetic variant with correlated multiple phenotypes using the summary statistics of individual phenotype analysis from Genome-Wide Association Studies (GWASs). We estimated the between-phenotype correlation matrix using the summary statistics of individual phenotype GWAS analyses, and developed genetic association tests for multiple phenotypes by accounting for between-phenotype correlation without the need to access individual-level data. Since genetic variants often affect multiple phenotypes differently across the genome and the between-phenotype correlation can be arbitrary, we proposed robust and powerful multiple phenotype testing procedures by jointly testing a common mean and a variance component in linear mixed models for summary statistics. We computed the p-values of the proposed tests analytically. This computational advantage makes our methods practically appealing in large-scale GWASs. We performed simulation studies to show that the proposed tests maintained correct type I error rates, and to compare their powers in various settings with the existing methods. We applied the proposed tests to a GWAS Global Lipids Genetics Consortium summary statistics data set and identified additional genetic variants that were missed by the original single-trait analysis. © 2017, The International Biometric Society.

Vision-based mobile robot navigation through deep convolutional neural networks and end-to-end learning

NASA Astrophysics Data System (ADS)

Zhang, Yachu; Zhao, Yuejin; Liu, Ming; Dong, Liquan; Kong, Lingqin; Liu, Lingling

2017-09-01

In contrast to humans, who use only visual information for navigation, many mobile robots use laser scanners and ultrasonic sensors along with vision cameras to navigate. This work proposes a vision-based robot control algorithm based on deep convolutional neural networks. We create a large 15-layer convolutional neural network learning system and achieve the advanced recognition performance. Our system is trained from end to end to map raw input images to direction in supervised mode. The images of data sets are collected in a wide variety of weather conditions and lighting conditions. Besides, the data sets are augmented by adding Gaussian noise and Salt-and-pepper noise to avoid overfitting. The algorithm is verified by two experiments, which are line tracking and obstacle avoidance. The line tracking experiment is proceeded in order to track the desired path which is composed of straight and curved lines. The goal of obstacle avoidance experiment is to avoid the obstacles indoor. Finally, we get 3.29% error rate on the training set and 5.1% error rate on the test set in the line tracking experiment, 1.8% error rate on the training set and less than 5% error rate on the test set in the obstacle avoidance experiment. During the actual test, the robot can follow the runway centerline outdoor and avoid the obstacle in the room accurately. The result confirms the effectiveness of the algorithm and our improvement in the network structure and train parameters

Evaluation of differences in quality of experience features for test stimuli of good-only and bad-only overall audiovisual quality

NASA Astrophysics Data System (ADS)

Strohmeier, Dominik; Kunze, Kristina; Göbel, Klemens; Liebetrau, Judith

2013-01-01

Assessing audiovisual Quality of Experience (QoE) is a key element to ensure quality acceptance of today's multimedia products. The use of descriptive evaluation methods allows evaluating QoE preferences and the underlying QoE features jointly. From our previous evaluations on QoE for mobile 3D video we found that mainly one dimension, video quality, dominates the descriptive models. Large variations of the visual video quality in the tests may be the reason for these findings. A new study was conducted to investigate whether test sets of low QoE are described differently than those of high audiovisual QoE. Reanalysis of previous data sets seems to confirm this hypothesis. Our new study consists of a pre-test and a main test, using the Descriptive Sorted Napping method. Data sets of good-only and bad-only video quality were evaluated separately. The results show that the perception of bad QoE is mainly determined one-dimensionally by visual artifacts, whereas the perception of good quality shows multiple dimensions. Here, mainly semantic-related features of the content and affective descriptors are used by the naïve test participants. The results show that, with increasing QoE of audiovisual systems, content semantics and users' a_ective involvement will become important for assessing QoE differences.

Characterizing interspecies uncertainty using data from studies of anti-neoplastic agents in animals and humans

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

Price, Paul S.; Keenan, Russell E.; Swartout, Jeffrey C.

For most chemicals, the Reference Dose (RfD) is based on data from animal testing. The uncertainty introduced by the use of animal models has been termed interspecies uncertainty. The magnitude of the differences between the toxicity of a chemical in humans and test animals and its uncertainty can be investigated by evaluating the inter-chemical variation in the ratios of the doses associated with similar toxicological endpoints in test animals and humans. This study performs such an evaluation on a data set of 64 anti-neoplastic drugs. The data set provides matched responses in humans and four species of test animals: mice,more » rats, monkeys, and dogs. While the data have a number of limitations, the data show that when the drugs are evaluated on a body weight basis: 1) toxicity generally increases with a species' body weight; however, humans are not always more sensitive than test animals; 2) the animal to human dose ratios were less than 10 for most, but not all, drugs; 3) the current practice of using data from multiple species when setting RfDs lowers the probability of having a large value for the ratio. These findings provide insight into inter-chemical variation in animal to human extrapolations and suggest the need for additional collection and analysis of matched toxicity data in humans and test animals.« less

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G∗∗, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the α-helix and β-strand.

Analysis of soil moisture extraction algorithm using data from aircraft experiments

NASA Technical Reports Server (NTRS)

Burke, H. H. K.; Ho, J. H.

1981-01-01

A soil moisture extraction algorithm is developed using a statistical parameter inversion method. Data sets from two aircraft experiments are utilized for the test. Multifrequency microwave radiometric data surface temperature, and soil moisture information are contained in the data sets. The surface and near surface ( or = 5 cm) soil moisture content can be extracted with accuracy of approximately 5% to 6% for bare fields and fields with grass cover by using L, C, and X band radiometer data. This technique is used for handling large amounts of remote sensing data from space.

CMS results in the Combined Computing Readiness Challenge CCRC'08

NASA Astrophysics Data System (ADS)

Bonacorsi, D.; Bauerdick, L.; CMS Collaboration

2009-12-01

During February and May 2008, CMS participated to the Combined Computing Readiness Challenge (CCRC'08) together with all other LHC experiments. The purpose of this worldwide exercise was to check the readiness of the Computing infrastructure for LHC data taking. Another set of major CMS tests called Computing, Software and Analysis challenge (CSA'08) - as well as CMS cosmic runs - were also running at the same time: CCRC augmented the load on computing with additional tests to validate and stress-test all CMS computing workflows at full data taking scale, also extending this to the global WLCG community. CMS exercised most aspects of the CMS computing model, with very comprehensive tests. During May 2008, CMS moved more than 3.6 Petabytes among more than 300 links in the complex Grid topology. CMS demonstrated that is able to safely move data out of CERN to the Tier-1 sites, sustaining more than 600 MB/s as a daily average for more than seven days in a row, with enough headroom and with hourly peaks of up to 1.7 GB/s. CMS ran hundreds of simultaneous jobs at each Tier-1 site, re-reconstructing and skimming hundreds of millions of events. After re-reconstruction the fresh AOD (Analysis Object Data) has to be synchronized between Tier-1 centers: CMS demonstrated that the required inter-Tier-1 transfers are achievable within a few days. CMS also showed that skimmed analysis data sets can be transferred to Tier-2 sites for analysis at sufficient rate, regionally as well as inter-regionally, achieving all goals in about 90% of >200 links. Simultaneously, CMS also ran a large Tier-2 analysis exercise, where realistic analysis jobs were submitted to a large set of Tier-2 sites by a large number of people to produce a chaotic workload across the systems, and with more than 400 analysis users in May. Taken all together, CMS routinely achieved submissions of 100k jobs/day, with peaks up to 200k jobs/day. The achieved results in CCRC'08 - focussing on the distributed workflows - are presented and discussed.

[Testing the efficacy of disinfectants during drinking water treatment. A new experimental set-up at the German EPA (Umweltbundesamt - UBA)].

PubMed

Grützmacher, G; Bartel, H; Althoff, H W; Clemen, S

2007-03-01

A set-up for experiments in the flow-through mode was constructed in order to test the efficacy of substances used for disinfecting water during drinking water treatment. A flow-through mode - in contrast to experiments under stationary conditions (so-called batch experiments) - was chosen, because this experimental design allows experiments to be carried out under constant conditions for an extended time (up to one week) and because efficacy testing is possible repeatedly, simultaneously and under exactly the same conditions for short (about 0.5 min) and also longer (about 47 min) contact times. With this experimental design the effect of biofilms along the inner pipe surfaces can be included in the observations. The construction of the experimental set-up is based on experience with laboratory flow-through systems that were installed by the UBA's drinking water department (formerly Institute for Water-, Soil- and Air Hygiene (WaBoLu) Institute) for testing disinfection with chlorine. In the first step, a test pipe for the simulation of a water works situation was installed. Water of different qualities can be mixed in large volumes beforehand so that the experimental procedure can be run with constant water quality for a minimum of one week. The kinetics of the disinfection reaction can be observed by extracting samples from eight sampling ports situated along the test pipe. In order to assign exact residence times to each of the sampling ports, tracer experiments were performed prior to testing disinfectant efficacy. This paper gives the technical details of the experimental set-up and presents the results of the tracer experiments to provide an introduction with respect to its potential.

Does choice of angular velocity affect pain level during isokinetic strength testing of knee osteoarthritis patients?

PubMed

Almosnino, S; Brandon, S C E; Sled, E A

2012-12-01

Thigh musculature strength assessment in individuals with knee osteoarthritis is routinely performed in rehabilitative settings. A factor that may influence results is pain experienced during testing. To assess whether pain experienced during isokinetic testing in individuals with knee osteoarthritis is dependent on the angular velocity prescribed. Experimental, repeated measures. University laboratory. Thirty-five individuals (19 women, 16 men) with tibiofemoral osteoarthritis. Participants performed three randomized sets of five maximal concentric extension-flexion repetitions at 60°/s, 90°/s and 120°/s. Pain intensity was measured immediately after the completion of each set. Strength outcomes for each set were the average peak moment. Across gender, pain level was not significantly affected by testing velocity (P=0.18, η(p)(2) =0.05). There was a trend of women reporting more pain than men across all testing velocities, however this comparison did not reach statistical significance (P=0.18, η(p)(2)=0.05). There was a significant main effect of testing velocity on strength, with the highest level attained at 60°/s. However, no difference in strength was noted when testing was performed at 90°/s or 120°/s. A large variation in pain scores within and across conditions and gender was noted, suggesting that at the current stage: 1) isokinetic angular velocity prescription be performed on an individual patient basis; and 2) improvements in the manner pain is recorded are needed in order to reduce the variations in pain scores. Individual prescription of angular velocity may be necessary for optimal strength output and reduction of pain during effort exertion in this patient population.

The development of a patient-specific method for physiotherapy goal setting: a user-centered design.

PubMed

Stevens, Anita; Köke, Albère; van der Weijden, Trudy; Beurskens, Anna

2018-08-01

To deliver client-centered care, physiotherapists need to identify the patients' individual treatment goals. However, practical tools for involving patients in goal setting are lacking. The purpose of this study was to improve the frequently used Patient-Specific Complaints instrument in Dutch physiotherapy, and to develop it into a feasible method to improve physiotherapy goal setting. An iterative user-centered design was conducted in co-creation with the physiotherapists and patients, in three phases. Their needs and preferences were identified by means of group meetings and questionnaires. The new method was tested in several field tests in physiotherapy practices. Four main objectives for improvement were formulated: clear instructions for the administration procedure, targeted use across the physiotherapy process, client-activating communication skills, and a client-centered attitude of the physiotherapist. A theoretical goal-setting framework and elements of shared decision making were integrated into the new-called, Patient-Specific Goal-setting method, together with a practical training course. The user-centered approach resulted in a goal-setting method that is fully integrated in the physiotherapy process. The new goal-setting method contributes to a more structured approach to goal setting and enables patient participation and goal-oriented physiotherapy. Before large-scale implementation, its feasibility in physiotherapy practice needs to be investigated. Implications for rehabilitation Involving patients and physiotherapists in the development and testing of a goal-setting method, increases the likelihood of its feasibility in practice. The integration of a goal-setting method into the physiotherapy process offers the opportunity to focus more fully on the patient's goals. Patients should be informed about the aim of every step of the goal-setting process in order to increase their awareness and involvement. Training physiotherapists to use a patient-specific method for goal setting is crucial for a correct application.

Association of high proliferation marker Ki-67 expression with DCEMR imaging features of breast: a large scale evaluation

NASA Astrophysics Data System (ADS)

Saha, Ashirbani; Harowicz, Michael R.; Grimm, Lars J.; Kim, Connie E.; Ghate, Sujata V.; Walsh, Ruth; Mazurowski, Maciej A.

2018-02-01

One of the methods widely used to measure the proliferative activity of cells in breast cancer patients is the immunohistochemical (IHC) measurement of the percentage of cells stained for nuclear antigen Ki-67. Use of Ki-67 expression as a prognostic marker is still under investigation. However, numerous clinical studies have reported an association between a high Ki-67 and overall survival (OS) and disease free survival (DFS). On the other hand, to offer non-invasive alternative in determining Ki-67 expression, researchers have made recent attempts to study the association of Ki-67 expression with magnetic resonance (MR) imaging features of breast cancer in small cohorts (<30). Here, we present a large scale evaluation of the relationship between imaging features and Ki-67 score as: (a) we used a set of 450 invasive breast cancer patients, (b) we extracted a set of 529 imaging features of shape and enhancement from breast, tumor and fibroglandular tissue of the patients, (c) used a subset of patients as the training set to select features and trained a multivariate logistic regression model to predict high versus low Ki-67 values, and (d) we validated the performance of the trained model in an independent test set using the area-under the receiver operating characteristics (ROC) curve (AUC) of the values predicted. Our model was able to predict high versus low Ki-67 in the test set with an AUC of 0.67 (95% CI: 0.58-0.75, p<1.1e-04). Thus, a moderate strength of association of Ki-67 values and MRextracted imaging features was demonstrated in our experiments.

Single Event Effects (SEE) Testing of Embedded DSP Cores within Microsemi RTAX4000D Field Programmable Gate Array (FPGA) Devices

NASA Technical Reports Server (NTRS)

Perez, Christopher E.; Berg, Melanie D.; Friendlich, Mark R.

2011-01-01

Motivation for this work is: (1) Accurately characterize digital signal processor (DSP) core single-event effect (SEE) behavior (2) Test DSP cores across a large frequency range and across various input conditions (3) Isolate SEE analysis to DSP cores alone (4) Interpret SEE analysis in terms of single-event upsets (SEUs) and single-event transients (SETs) (5) Provide flight missions with accurate estimate of DSP core error rates and error signatures.

High-level neutron coincidence counter maintenance manual

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

Swansen, J.; Collinsworth, P.

1983-05-01

High-level neutron coincidence counter operational (field) calibration and usage is well known. This manual makes explicit basic (shop) check-out, calibration, and testing of new units and is a guide for repair of failed in-service units. Operational criteria for the major electronic functions are detailed, as are adjustments and calibration procedures, and recurrent mechanical/electromechanical problems are addressed. Some system tests are included for quality assurance. Data on nonstandard large-scale integrated (circuit) components and a schematic set are also included.

Movement control tests of the low back; evaluation of the difference between patients with low back pain and healthy controls

PubMed Central

Luomajoki, Hannu; Kool, Jan; de Bruin, Eling D; Airaksinen, Olavi

2008-01-01

Background To determine whether there is a difference between patients with low back pain and healthy controls in a test battery score for movement control of the lumbar spine. Methods This was a case control study, carried out in five outpatient physiotherapy practices in the German-speaking part of Switzerland. Twelve physiotherapists tested the ability of 210 subjects (108 patients with non-specific low back pain and 102 control subjects without back pain) to control their movements in the lumbar spine using a set of six tests. We observed the number of positive tests out of six (mean, standard deviation and 95% confidence interval of the mean). The significance of the differences between the groups was calculated with Mann-Whitney U test and p was set on <0.05. The effect size (d) between the groups was calculated and d>0.8 was considered a large difference. Results On average, patients with low back pain had 2.21(95%CI 1.94–2.48) positive tests and the healthy controls 0.75 (95%CI 0.55–0.95). The effect size was d = 1.18 (p < 0.001). There was a significant difference between acute and chronic (p < 0.01), as well as between subacute and chronic patient groups (p < 0.03), but not between acute and subacute patient groups (p > 0.7). Conclusion This is the first study demonstrating a significant difference between patients with low back pain and subjects without back pain regarding their ability to actively control the movements of the low back. The effect size between patients with low back pain and healthy controls in movement control is large. PMID:19108735

Measurements and predictions of flyover and static noise of a TF30 afterburning turbofan engine

NASA Technical Reports Server (NTRS)

Burcham, F. W., Jr.; Lasagna, P. L.; Oas, S. C.

1978-01-01

The noise of the TF30 afterburning turbofan engine in an F-111 airplane was determined from static (ground) and flyover tests. A survey was made to measure the exhaust temperature and velocity profiles for a range of power settings. Comparisons were made between predicted and measured jet mixing, internal, and shock noise. It was found that the noise produced at static conditions was dominated by jet mixing noise, and was adequately predicted by current methods. The noise produced during flyovers exhibited large contributions from internally generated noise in the forward arc. For flyovers with the engine at nonafterburning power, the internal noise, shock noise, and jet mixing noise were accurately predicted. During flyovers with afterburning power settings, however, additional internal noise believed to be due to the afterburning process was evident; its level was as much as 8 decibels above the nonafterburning internal noise. Power settings that produced exhausts with inverted velocity profiles appeared to be slightly less noisy than power settings of equal thrust that produced uniform exhaust velocity profiles both in flight and in static testing.

A software framework for developing measurement applications under variable requirements.

PubMed

Arpaia, Pasquale; Buzio, Marco; Fiscarelli, Lucio; Inglese, Vitaliano

2012-11-01

A framework for easily developing software for measurement and test applications under highly and fast-varying requirements is proposed. The framework allows the software quality, in terms of flexibility, usability, and maintainability, to be maximized. Furthermore, the development effort is reduced and finalized, by relieving the test engineer of development details. The framework can be configured for satisfying a large set of measurement applications in a generic field for an industrial test division, a test laboratory, or a research center. As an experimental case study, the design, the implementation, and the assessment inside the application to a measurement scenario of magnet testing at the European Organization for Nuclear Research is reported.

The gradient boosting algorithm and random boosting for genome-assisted evaluation in large data sets.

PubMed

González-Recio, O; Jiménez-Montero, J A; Alenda, R

2013-01-01

In the next few years, with the advent of high-density single nucleotide polymorphism (SNP) arrays and genome sequencing, genomic evaluation methods will need to deal with a large number of genetic variants and an increasing sample size. The boosting algorithm is a machine-learning technique that may alleviate the drawbacks of dealing with such large data sets. This algorithm combines different predictors in a sequential manner with some shrinkage on them; each predictor is applied consecutively to the residuals from the committee formed by the previous ones to form a final prediction based on a subset of covariates. Here, a detailed description is provided and examples using a toy data set are included. A modification of the algorithm called "random boosting" was proposed to increase predictive ability and decrease computation time of genome-assisted evaluation in large data sets. Random boosting uses a random selection of markers to add a subsequent weak learner to the predictive model. These modifications were applied to a real data set composed of 1,797 bulls genotyped for 39,714 SNP. Deregressed proofs of 4 yield traits and 1 type trait from January 2009 routine evaluations were used as dependent variables. A 2-fold cross-validation scenario was implemented. Sires born before 2005 were used as a training sample (1,576 and 1,562 for production and type traits, respectively), whereas younger sires were used as a testing sample to evaluate predictive ability of the algorithm on yet-to-be-observed phenotypes. Comparison with the original algorithm was provided. The predictive ability of the algorithm was measured as Pearson correlations between observed and predicted responses. Further, estimated bias was computed as the average difference between observed and predicted phenotypes. The results showed that the modification of the original boosting algorithm could be run in 1% of the time used with the original algorithm and with negligible differences in accuracy and bias. This modification may be used to speed the calculus of genome-assisted evaluation in large data sets such us those obtained from consortiums. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The Wilcoxon signed rank test for paired comparisons of clustered data.

PubMed

Rosner, Bernard; Glynn, Robert J; Lee, Mei-Ling T

2006-03-01

The Wilcoxon signed rank test is a frequently used nonparametric test for paired data (e.g., consisting of pre- and posttreatment measurements) based on independent units of analysis. This test cannot be used for paired comparisons arising from clustered data (e.g., if paired comparisons are available for each of two eyes of an individual). To incorporate clustering, a generalization of the randomization test formulation for the signed rank test is proposed, where the unit of randomization is at the cluster level (e.g., person), while the individual paired units of analysis are at the subunit within cluster level (e.g., eye within person). An adjusted variance estimate of the signed rank test statistic is then derived, which can be used for either balanced (same number of subunits per cluster) or unbalanced (different number of subunits per cluster) data, with an exchangeable correlation structure, with or without tied values. The resulting test statistic is shown to be asymptotically normal as the number of clusters becomes large, if the cluster size is bounded. Simulation studies are performed based on simulating correlated ranked data from a signed log-normal distribution. These studies indicate appropriate type I error for data sets with > or =20 clusters and a superior power profile compared with either the ordinary signed rank test based on the average cluster difference score or the multivariate signed rank test of Puri and Sen. Finally, the methods are illustrated with two data sets, (i) an ophthalmologic data set involving a comparison of electroretinogram (ERG) data in retinitis pigmentosa (RP) patients before and after undergoing an experimental surgical procedure, and (ii) a nutritional data set based on a randomized prospective study of nutritional supplements in RP patients where vitamin E intake outside of study capsules is compared before and after randomization to monitor compliance with nutritional protocols.

Similitude assessment method for comparing PMHS response data from impact loading across multiple test devices.

PubMed

Dooley, Christopher J; Tenore, Francesco V; Gayzik, F Scott; Merkle, Andrew C

2018-04-27

Biological tissue testing is inherently susceptible to the wide range of variability specimen to specimen. A primary resource for encapsulating this range of variability is the biofidelity response corridor or BRC. In the field of injury biomechanics, BRCs are often used for development and validation of both physical, such as anthropomorphic test devices, and computational models. For the purpose of generating corridors, post-mortem human surrogates were tested across a range of loading conditions relevant to under-body blast events. To sufficiently cover the wide range of input conditions, a relatively small number of tests were performed across a large spread of conditions. The high volume of required testing called for leveraging the capabilities of multiple impact test facilities, all with slight variations in test devices. A method for assessing similitude of responses between test devices was created as a metric for inclusion of a response in the resulting BRC. The goal of this method was to supply a statistically sound, objective method to assess the similitude of an individual response against a set of responses to ensure that the BRC created from the set was affected primarily by biological variability, not anomalies or differences stemming from test devices. Copyright © 2018 Elsevier Ltd. All rights reserved.

Segmenting data sets for RIP.

PubMed

de Sanctis, Daniele; Nanao, Max H

2012-09-01

Specific radiation damage can be used for the phasing of macromolecular crystal structures. In practice, however, the optimization of the X-ray dose used to `burn' the crystal to induce specific damage can be difficult. Here, a method is presented in which a single large data set that has not been optimized in any way for radiation-damage-induced phasing (RIP) is segmented into multiple sub-data sets, which can then be used for RIP. The efficacy of this method is demonstrated using two model systems and two test systems. A method to improve the success of this type of phasing experiment by varying the composition of the two sub-data sets with respect to their separation by image number, and hence by absorbed dose, as well as their individual completeness is illustrated.

Model verification of large structural systems. [space shuttle model response

NASA Technical Reports Server (NTRS)

Lee, L. T.; Hasselman, T. K.

1978-01-01

A computer program for the application of parameter identification on the structural dynamic models of space shuttle and other large models with hundreds of degrees of freedom is described. Finite element, dynamic, analytic, and modal models are used to represent the structural system. The interface with math models is such that output from any structural analysis program applied to any structural configuration can be used directly. Processed data from either sine-sweep tests or resonant dwell tests are directly usable. The program uses measured modal data to condition the prior analystic model so as to improve the frequency match between model and test. A Bayesian estimator generates an improved analytical model and a linear estimator is used in an iterative fashion on highly nonlinear equations. Mass and stiffness scaling parameters are generated for an improved finite element model, and the optimum set of parameters is obtained in one step.

Performance testing of 3D point cloud software

NASA Astrophysics Data System (ADS)

Varela-González, M.; González-Jorge, H.; Riveiro, B.; Arias, P.

2013-10-01

LiDAR systems are being used widely in recent years for many applications in the engineering field: civil engineering, cultural heritage, mining, industry and environmental engineering. One of the most important limitations of this technology is the large computational requirements involved in data processing, especially for large mobile LiDAR datasets. Several software solutions for data managing are available in the market, including open source suites, however, users often unknown methodologies to verify their performance properly. In this work a methodology for LiDAR software performance testing is presented and four different suites are studied: QT Modeler, VR Mesh, AutoCAD 3D Civil and the Point Cloud Library running in software developed at the University of Vigo (SITEGI). The software based on the Point Cloud Library shows better results in the loading time of the point clouds and CPU usage. However, it is not as strong as commercial suites in working set and commit size tests.

A Center for Extraterrestrial Engineering and Construction (CETEC)

NASA Technical Reports Server (NTRS)

Leigh, Gerald G.

1992-01-01

A group of knowledgeable scientists and engineers in New Mexico has recognized the need for such a testing capability and has proposed a project to evelop an extraterrestrial surface simulation facility. A group of universities, national laboratories, and private industrial firms is proposing to establish a Center for Extraterrestrial Engineering and Construction (CETEC) and to develop large extraterrestrial surface simulation facilities in which this needed testing can be realistically performed. The CETEC is envisioned to be both a center of knowledge and data regarding engineering, construction, mining, and material process operations on extraterrestrial bodies and a set of extraterrestrial surface simulation facilities. The primary CETEC facility is proposed to be a large domed building made of steel reinforced concrete with more than one acre of test floor area covered with several feet of simulated lunar soil and dust. Various aspects of the project are presented in viewgraph form.

Detecting a Weak Association by Testing its Multiple Perturbations: a Data Mining Approach

NASA Astrophysics Data System (ADS)

Lo, Min-Tzu; Lee, Wen-Chung

2014-05-01

Many risk factors/interventions in epidemiologic/biomedical studies are of minuscule effects. To detect such weak associations, one needs a study with a very large sample size (the number of subjects, n). The n of a study can be increased but unfortunately only to an extent. Here, we propose a novel method which hinges on increasing sample size in a different direction-the total number of variables (p). We construct a p-based `multiple perturbation test', and conduct power calculations and computer simulations to show that it can achieve a very high power to detect weak associations when p can be made very large. As a demonstration, we apply the method to analyze a genome-wide association study on age-related macular degeneration and identify two novel genetic variants that are significantly associated with the disease. The p-based method may set a stage for a new paradigm of statistical tests.

The Stellar IMF from Isothermal MHD Turbulence

NASA Astrophysics Data System (ADS)

Haugbølle, Troels; Padoan, Paolo; Nordlund, Åke

2018-02-01

We address the turbulent fragmentation scenario for the origin of the stellar initial mass function (IMF), using a large set of numerical simulations of randomly driven supersonic MHD turbulence. The turbulent fragmentation model successfully predicts the main features of the observed stellar IMF assuming an isothermal equation of state without any stellar feedback. As a test of the model, we focus on the case of a magnetized isothermal gas, neglecting stellar feedback, while pursuing a large dynamic range in both space and timescales covering the full spectrum of stellar masses from brown dwarfs to massive stars. Our simulations represent a generic 4 pc region within a typical Galactic molecular cloud, with a mass of 3000 M ⊙ and an rms velocity 10 times the isothermal sound speed and 5 times the average Alfvén velocity, in agreement with observations. We achieve a maximum resolution of 50 au and a maximum duration of star formation of 4.0 Myr, forming up to a thousand sink particles whose mass distribution closely matches the observed stellar IMF. A large set of medium-size simulations is used to test the sink particle algorithm, while larger simulations are used to test the numerical convergence of the IMF and the dependence of the IMF turnover on physical parameters predicted by the turbulent fragmentation model. We find a clear trend toward numerical convergence and strong support for the model predictions, including the initial time evolution of the IMF. We conclude that the physics of isothermal MHD turbulence is sufficient to explain the origin of the IMF.

MABAL: a Novel Deep-Learning Architecture for Machine-Assisted Bone Age Labeling.

PubMed

Mutasa, Simukayi; Chang, Peter D; Ruzal-Shapiro, Carrie; Ayyala, Rama

2018-02-05

Bone age assessment (BAA) is a commonly performed diagnostic study in pediatric radiology to assess skeletal maturity. The most commonly utilized method for assessment of BAA is the Greulich and Pyle method (Pediatr Radiol 46.9:1269-1274, 2016; Arch Dis Child 81.2:172-173, 1999) atlas. The evaluation of BAA can be a tedious and time-consuming process for the radiologist. As such, several computer-assisted detection/diagnosis (CAD) methods have been proposed for automation of BAA. Classical CAD tools have traditionally relied on hard-coded algorithmic features for BAA which suffer from a variety of drawbacks. Recently, the advent and proliferation of convolutional neural networks (CNNs) has shown promise in a variety of medical imaging applications. There have been at least two published applications of using deep learning for evaluation of bone age (Med Image Anal 36:41-51, 2017; JDI 1-5, 2017). However, current implementations are limited by a combination of both architecture design and relatively small datasets. The purpose of this study is to demonstrate the benefits of a customized neural network algorithm carefully calibrated to the evaluation of bone age utilizing a relatively large institutional dataset. In doing so, this study will aim to show that advanced architectures can be successfully trained from scratch in the medical imaging domain and can generate results that outperform any existing proposed algorithm. The training data consisted of 10,289 images of different skeletal age examinations, 8909 from the hospital Picture Archiving and Communication System at our institution and 1383 from the public Digital Hand Atlas Database. The data was separated into four cohorts, one each for male and female children above the age of 8, and one each for male and female children below the age of 10. The testing set consisted of 20 radiographs of each 1-year-age cohort from 0 to 1 years to 14-15+ years, half male and half female. The testing set included left-hand radiographs done for bone age assessment, trauma evaluation without significant findings, and skeletal surveys. A 14 hidden layer-customized neural network was designed for this study. The network included several state of the art techniques including residual-style connections, inception layers, and spatial transformer layers. Data augmentation was applied to the network inputs to prevent overfitting. A linear regression output was utilized. Mean square error was used as the network loss function and mean absolute error (MAE) was utilized as the primary performance metric. MAE accuracies on the validation and test sets for young females were 0.654 and 0.561 respectively. For older females, validation and test accuracies were 0.662 and 0.497 respectively. For young males, validation and test accuracies were 0.649 and 0.585 respectively. Finally, for older males, validation and test set accuracies were 0.581 and 0.501 respectively. The female cohorts were trained for 900 epochs each and the male cohorts were trained for 600 epochs. An eightfold cross-validation set was employed for hyperparameter tuning. Test error was obtained after training on a full data set with the selected hyperparameters. Using our proposed customized neural network architecture on our large available data, we achieved an aggregate validation and test set mean absolute errors of 0.637 and 0.536 respectively. To date, this is the best published performance on utilizing deep learning for bone age assessment. Our results support our initial hypothesis that customized, purpose-built neural networks provide improved performance over networks derived from pre-trained imaging data sets. We build on that initial work by showing that the addition of state-of-the-art techniques such as residual connections and inception architecture further improves prediction accuracy. This is important because the current assumption for use of residual and/or inception architectures is that a large pre-trained network is required for successful implementation given the relatively small datasets in medical imaging. Instead we show that a small, customized architecture incorporating advanced CNN strategies can indeed be trained from scratch, yielding significant improvements in algorithm accuracy. It should be noted that for all four cohorts, testing error outperformed validation error. One reason for this is that our ground truth for our test set was obtained by averaging two pediatric radiologist reads compared to our training data for which only a single read was used. This suggests that despite relatively noisy training data, the algorithm could successfully model the variation between observers and generate estimates that are close to the expected ground truth.

Comparisons of false negative rates from a trend test alone and from a trend test jointly with a control-high groups pairwise test in the determination of the carcinogenicity of new drugs.

PubMed

Lin, Karl K; Rahman, Mohammad A

2018-05-21

Interest has been expressed in using a joint test procedure that requires that the results of both a trend test and a pairwise comparison test between the control and the high groups be statistically significant simultaneously at the levels of significance recommended in the FDA 2001 draft guidance for industry document for the separate tests in order for the drug effect on the development of an individual tumor type to be considered as statistically significant. Results of our simulation studies show that there is a serious consequence of large inflations of the false negative rate through large decreases of false positive rate in the use of the above joint test procedure in the final interpretation of the carcinogenicity potential of a new drug if the levels of significance recommended for separate tests are used. The inflation can be as high as 204.5% of the false negative rate when the trend test alone is required to test if the effect is statistically significant. To correct the problem, new sets of levels of significance have also been developed for those who want to use the joint test in reviews of carcinogenicity studies.

How "Boundaryless" Are the Careers of High Potentials, Key Experts and Average Performers?

ERIC Educational Resources Information Center

Dries, Nicky; Van Acker, Frederik; Verbruggen, Marijke

2012-01-01

The talent management literature declares talent management a prime concern for HRM professionals while the careers literature calls talent management archaic. Three sets of assumptions identified through comparative review of both streams of the literature were tested in a large-scale survey (n = 941). We found more support for the assumptions…

Classical, Generalizability, and Multifaceted Rasch Detection of Interrater Variability in Large, Sparse Data Sets.

ERIC Educational Resources Information Center

MacMillan, Peter D.

2000-01-01

Compared classical test theory (CTT), generalizability theory (GT), and multifaceted Rasch model (MFRM) approaches to detecting and correcting for rater variability using responses of 4,930 high school students graded by 3 raters on 9 scales. The MFRM approach identified far more raters as different than did the CTT analysis. GT and Rasch…

Item Difficulty in the Evaluation of Computer-Based Instruction: An Example from Neuroanatomy

ERIC Educational Resources Information Center

Chariker, Julia H.; Naaz, Farah; Pani, John R.

2012-01-01

This article reports large item effects in a study of computer-based learning of neuroanatomy. Outcome measures of the efficiency of learning, transfer of learning, and generalization of knowledge diverged by a wide margin across test items, with certain sets of items emerging as particularly difficult to master. In addition, the outcomes of…

The Importance of Institutional Image to Student Satisfaction and Loyalty within Higher Education

ERIC Educational Resources Information Center

Brown, Robert M.; Mazzarol, Timothy William

2009-01-01

This paper outlines the findings of a study employing a partial least squares (PLS) structural equation methodology to test a customer satisfaction model of the drivers of student satisfaction and loyalty in higher education settings. Drawing upon a moderately large sample of students enrolled in four "types" of Australian universities,…

Testing ecoregions in Kentucky and Tennessee with satellite imagery and Forest Inventory data

Treesearch

W. Henry McNab; F. Thomas Lloyd

2009-01-01

Ecoregions are large mapped areas of hypothesized ecological uniformity that are delineated subjectively based on multiple physical and biological components. Ecoregion maps are seldom evaluated because suitable data sets are often lacking. Landsat imagery is a readily available, low-cost source of archived data that can be used to calculate the normalized difference...

Analysis of Large Data Sets in Brazil: A Study on Selection Procedures to College Admission.

ERIC Educational Resources Information Center

Rodrigues, Aroldo

Because the achievement battery traditionally administered to Brazilian college bound students may discriminate against those who cannot afford to attend the best high schools or preparatory courses, tests were developed to measure aptitude for higher education, independent of ability or actual knowledge of course content. The focus of the…

School Correlates of Academic Behaviors and Performance among McKinney-Vento Identified Youth

ERIC Educational Resources Information Center

Stone, Susan; Uretsky, Mathew

2016-01-01

We utilized a pooled sample of elementary, middle, and high school-aged children identified as homeless via definitions set forth by McKinney-Vento legislation in a large urban district in California to estimate the extent to which school factors contributed to student attendance, suspensions, test-taking behaviors, and performance on state…

School Subtracts Math Texts to Add E-Lessons, Tests

ERIC Educational Resources Information Center

Trotter, Andrew

2007-01-01

This article discusses how math teachers at San Marcos High School turned to an online curriculum and in-class assessments to increase student achievement. Setting aside their 7-year-old textbooks, teachers filled the void largely with an online math curriculum, called Agile Mind, that comes equipped with an array of assessment tools. The idea was…

Profiles of Observed Infant Anger Predict Preschool Behavior Problems: Moderation by Life Stress

ERIC Educational Resources Information Center

Brooker, Rebecca J.; Buss, Kristin A.; Lemery-Chalfant, Kathryn; Aksan, Nazan; Davidson, Richard J.; Goldsmith, H. Hill

2014-01-01

Using both traditional composites and novel profiles of anger, we examined associations between infant anger and preschool behavior problems in a large, longitudinal data set (N = 966). We also tested the role of life stress as a moderator of the link between early anger and the development of behavior problems. Although traditional measures of…

Acoustic characteristics of externally blown flap systems with mixer nozzles

NASA Technical Reports Server (NTRS)

Goodykoontz, J. H.; Dorsch, R. G.; Wagner, J. M.

1974-01-01

Noise tests were conducted on a large scale, cold flow model of an engine-under-the-wing externally blown flap lift augmentation system employing a mixer nozzle. The mixer nozzle was used to reduce the flap impingement velocity and, consequently, try to attenuate the additional noise caused by the interaction between the jet exhaust and the wing flap. Results from the mixer nozzle tests are summarized and compared with the results for a conical nozzle. The comparison showed that with the mixer nozzle, less noise was generated when the trailing flap was in a typical landing setting (e.g., 60 deg). However, for a takeoff flap setting (20 deg), there was little or no difference in the acoustic characteristics when either the mixer or conical nozzle was used.

RAVE: Rapid Visualization Environment

NASA Technical Reports Server (NTRS)

Klumpar, D. M.; Anderson, Kevin; Simoudis, Avangelos

1994-01-01

Visualization is used in the process of analyzing large, multidimensional data sets. However, the selection and creation of visualizations that are appropriate for the characteristics of a particular data set and the satisfaction of the analyst's goals is difficult. The process consists of three tasks that are performed iteratively: generate, test, and refine. The performance of these tasks requires the utilization of several types of domain knowledge that data analysts do not often have. Existing visualization systems and frameworks do not adequately support the performance of these tasks. In this paper we present the RApid Visualization Environment (RAVE), a knowledge-based system that interfaces with commercial visualization frameworks and assists a data analyst in quickly and easily generating, testing, and refining visualizations. RAVE was used for the visualization of in situ measurement data captured by spacecraft.

Genomic Prediction of Seed Quality Traits Using Advanced Barley Breeding Lines.

PubMed

Nielsen, Nanna Hellum; Jahoor, Ahmed; Jensen, Jens Due; Orabi, Jihad; Cericola, Fabio; Edriss, Vahid; Jensen, Just

2016-01-01

Genomic selection was recently introduced in plant breeding. The objective of this study was to develop genomic prediction for important seed quality parameters in spring barley. The aim was to predict breeding values without expensive phenotyping of large sets of lines. A total number of 309 advanced spring barley lines tested at two locations each with three replicates were phenotyped and each line was genotyped by Illumina iSelect 9Kbarley chip. The population originated from two different breeding sets, which were phenotyped in two different years. Phenotypic measurements considered were: seed size, protein content, protein yield, test weight and ergosterol content. A leave-one-out cross-validation strategy revealed high prediction accuracies ranging between 0.40 and 0.83. Prediction across breeding sets resulted in reduced accuracies compared to the leave-one-out strategy. Furthermore, predicting across full and half-sib-families resulted in reduced prediction accuracies. Additionally, predictions were performed using reduced marker sets and reduced training population sets. In conclusion, using less than 200 lines in the training set can result in low prediction accuracy, and the accuracy will then be highly dependent on the family structure of the selected training set. However, the results also indicate that relatively small training sets (200 lines) are sufficient for genomic prediction in commercial barley breeding. In addition, our results indicate a minimum marker set of 1,000 to decrease the risk of low prediction accuracy for some traits or some families.

Genomic Prediction of Seed Quality Traits Using Advanced Barley Breeding Lines

PubMed Central

Nielsen, Nanna Hellum; Jahoor, Ahmed; Jensen, Jens Due; Orabi, Jihad; Cericola, Fabio; Edriss, Vahid; Jensen, Just

2016-01-01

Genomic selection was recently introduced in plant breeding. The objective of this study was to develop genomic prediction for important seed quality parameters in spring barley. The aim was to predict breeding values without expensive phenotyping of large sets of lines. A total number of 309 advanced spring barley lines tested at two locations each with three replicates were phenotyped and each line was genotyped by Illumina iSelect 9Kbarley chip. The population originated from two different breeding sets, which were phenotyped in two different years. Phenotypic measurements considered were: seed size, protein content, protein yield, test weight and ergosterol content. A leave-one-out cross-validation strategy revealed high prediction accuracies ranging between 0.40 and 0.83. Prediction across breeding sets resulted in reduced accuracies compared to the leave-one-out strategy. Furthermore, predicting across full and half-sib-families resulted in reduced prediction accuracies. Additionally, predictions were performed using reduced marker sets and reduced training population sets. In conclusion, using less than 200 lines in the training set can result in low prediction accuracy, and the accuracy will then be highly dependent on the family structure of the selected training set. However, the results also indicate that relatively small training sets (200 lines) are sufficient for genomic prediction in commercial barley breeding. In addition, our results indicate a minimum marker set of 1,000 to decrease the risk of low prediction accuracy for some traits or some families. PMID:27783639

Single Event Transients in Voltage Regulators for FPGA Power Supply Applications

NASA Technical Reports Server (NTRS)

Poivey, Christian; Sanders, Anthony; Kim, Hak; Phan, Anthony; Forney, Jim; LaBel, Kenneth A.; Karsh, Jeremy; Pursley, Scott; Kleyner, Igor; Katz, Richard

2006-01-01

As with other bipolar analog devices, voltage regulators are known to be sensitive to single event transients (SET). In typical applications, large output capacitors are used to provide noise immunity. Therefore, since SET amplitude and duration are generally small, they are often of secondary importance due to this capacitance filtering. In low voltage applications, however, even small SET are a concern. Over-voltages may cause destructive conditions. Under-voltages may cause functional interrupts and may also trigger electrical latchup conditions. In addition, internal protection circuits which are affected by load as well as internal thermal effects can also be triggered from heavy ions, causing dropouts or shutdown ranging from milliseconds to seconds. In the case of FPGA power supplies applications, SETS are critical. For example, in the case of Actel FPGA RTAX family, core power supply voltage is 1.5V. Manufacturer specifies an absolute maximum rating of 1.6V and recommended operating conditions between 1.425V and 1.575V. Therefore, according to the manufacturer, any transient of amplitude greater than 75 mV can disrupt normal circuit functions, and overvoltages greater than 100 mV may damage the FPGA. We tested five low dropout voltage regulators for SET sensitivity under a large range of circuit application conditions.

New Evidence on Self-Affirmation Effects and Theorized Sources of Heterogeneity from Large-Scale Replications

PubMed Central

Hanselman, Paul; Rozek, Christopher S.; Grigg, Jeffrey; Borman, Geoffrey D.

2016-01-01

Brief, targeted self-affirmation writing exercises have recently been offered as a way to reduce racial achievement gaps, but evidence about their effects in educational settings is mixed, leaving ambiguity about the likely benefits of these strategies if implemented broadly. A key limitation in interpreting these mixed results is that they come from studies conducted by different research teams with different procedures in different settings; it is therefore impossible to isolate whether different effects are the result of theorized heterogeneity, unidentified moderators, or idiosyncratic features of the different studies. We addressed this limitation by conducting a well-powered replication of self-affirmation in a setting where a previous large-scale field experiment demonstrated significant positive impacts, using the same procedures. We found no evidence of effects in this replication study and estimates were precise enough to reject benefits larger than an effect size of 0.10. These null effects were significantly different from persistent benefits in the prior study in the same setting, and extensive testing revealed that currently theorized moderators of self-affirmation effects could not explain the difference. These results highlight the potential fragility of self-affirmation in educational settings when implemented widely and the need for new theory, measures, and evidence about the necessary conditions for self-affirmation success. PMID:28450753

A Novel Consensus-Based Particle Swarm Optimization-Assisted Trust-Tech Methodology for Large-Scale Global Optimization.

PubMed

Zhang, Yong-Feng; Chiang, Hsiao-Dong

2017-09-01

A novel three-stage methodology, termed the "consensus-based particle swarm optimization (PSO)-assisted Trust-Tech methodology," to find global optimal solutions for nonlinear optimization problems is presented. It is composed of Trust-Tech methods, consensus-based PSO, and local optimization methods that are integrated to compute a set of high-quality local optimal solutions that can contain the global optimal solution. The proposed methodology compares very favorably with several recently developed PSO algorithms based on a set of small-dimension benchmark optimization problems and 20 large-dimension test functions from the CEC 2010 competition. The analytical basis for the proposed methodology is also provided. Experimental results demonstrate that the proposed methodology can rapidly obtain high-quality optimal solutions that can contain the global optimal solution. The scalability of the proposed methodology is promising.

NTS radiological assessment project: comparison of delta-surface interpolation with kriging for the Frenchman Lake region of area 5

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

Foley, T.A. Jr.

The primary objective of this report is to compare the results of delta surface interpolation with kriging on four large sets of radiological data sampled in the Frenchman Lake region at the Nevada Test Site. The results of kriging, described in Barnes, Giacomini, Reiman, and Elliott, are very similar to those using the delta surface interpolant. The other topic studied is in reducing the number of sample points and obtaining results similar to those using all of the data. The positive results here suggest that great savings of time and money can be made. Furthermore, the delta surface interpolant ismore » viewed as a contour map and as a three dimensional surface. These graphical representations help in the analysis of the large sets of radiological data.« less

In-house experiments in large space structures at the Air Force Wright Aeronautical Laboratories Flight Dynamics Laboratory

NASA Technical Reports Server (NTRS)

Gordon, Robert W.; Ozguner, Umit; Yurkovich, Steven

1989-01-01

The Flight Dynamics Laboratory is committed to an in-house, experimental investigation of several technical areas critical to the dynamic performance of future Air Force large space structures. The advanced beam experiment was successfully completed and provided much experience in the implementation of active control approaches on real hardware. A series of experiments is under way in evaluating ground test methods on the 12 meter trusses with significant passive damping. Ground simulated zero-g response data from the undamped truss will be compared directly with true zero-g flight test data. The performance of several leading active control approaches will be measured and compared on one of the trusses in the presence of significant passive damping. In the future, the PACOSS dynamic test article will be set up as a test bed for the evaluation of system identification and control techniques on a complex, representative structure with high modal density and significant passive damping.

Approximate method for calculating free vibrations of a large-wind-turbine tower structure

NASA Technical Reports Server (NTRS)

Das, S. C.; Linscott, B. S.

1977-01-01

A set of ordinary differential equations were derived for a simplified structural dynamic lumped-mass model of a typical large-wind-turbine tower structure. Dunkerley's equation was used to arrive at a solution for the fundamental natural frequencies of the tower in bending and torsion. The ERDA-NASA 100-kW wind turbine tower structure was modeled, and the fundamental frequencies were determined by the simplified method described. The approximate fundamental natural frequencies for the tower agree within 18 percent with test data and predictions analyzed.

Assessment of TD-DFT methods and of various spin scaled CIS(D) and CC2 versions for the treatment of low-lying valence excitations of large organic dyes

NASA Astrophysics Data System (ADS)

Goerigk, Lars; Grimme, Stefan

2010-05-01

We present an extension of our previously published benchmark set for low-lying valence transitions of large organic dyes [L. Goerigk et al., Phys. Chem. Chem. Phys. 11, 4611 (2009)]. The new set comprises in total 12 molecules, including two charged species and one with a clear charge-transfer transition. Our previous study on TD-DFT methods is repeated for the new test set with a larger basis set. Additionally, we want to shed light on different spin-scaled variants of the configuration interaction singles with perturbative doubles correction [CIS(D)] and the approximate coupled cluster singles and doubles method (CC2). Particularly for CIS(D) we want to clarify, which of the proposed versions can be recommended. Our results indicate that an unpublished SCS-CIS(D) variant, which is implemented into the TURBOMOLE program package, shows worse results than the original CIS(D) method, while other modified versions perform better. An SCS-CIS(D) version with a parameterization, that has already been used in an application by us recently [L. Goerigk and S. Grimme, ChemPhysChem 9, 2467 (2008)], yields the best results. Another SCS-CIS(D) version and the SOS-CIS(D) method [Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007)] perform very similar, though. For the electronic transitions considered herein, there is no improvement observed when going from the original CC2 to the SCS-CC2 method but further adjustment of the latter seems to be beneficial. Double-hybrid density functionals belong to best methods tested here. Particularly B2GP-PLYP provides uniformly good results for the complete set and is considered to be close to chemical accuracy within an ab initio theory of color. For conventional hybrid functionals, a Fock-exchange mixing parameter of about 0.4 seems to be optimum in TD-DFT treatments of large chromophores. A range-separated functional such as, e.g., CAM-B3LYP seems also to be promising.

Spinning Spacecraft Attitude Estimation Using Markley Variables: Filter Implementation And Results

NASA Technical Reports Server (NTRS)

Sedlak, Joseph E.

2005-01-01

Attitude estimation is often more difficult for spinning spacecraft than for three-axis stabilized platforms due to the need to follow rapidly-varying state vector elements and the lack of three-axis rate measurements from gyros. The estimation problem simplifies when torques are negligible and nutation has damped out, but the general case requires a sequential filter with dynamics propagation. This paper describes the implementation and test results for an extended Kalman filter for spinning spacecraft attitude and rate estimation based on a novel set of variables suggested in a paper by Markley [AAS93-3301 (referred to hereafter as Markley variables). Markley has demonstrated that the new set of variables provides a superior parameterization for numerical integration of the attitude dynamics for spinning or momentum-biased spacecraft. The advantage is that the Markley variables have fewer rapidly-varying elements than other representations such as the attitude quaternion and rate vector. A filter based on these variables was expected to show improved performance due to the more accurate numerical state propagation. However, for a variety of test cases, it has been found that the new filter, as currently implemented, does not perform significantly better than a quaternion-based filter that was developed and tested in parallel. This paper reviews the mathematical background for a filter based on Markley variables. It also describes some features of the implementation and presents test results. The test cases are based on a mission using magnetometer and Sun sensor data and gyro measurements on two axes normal to the spin axis. The orbit and attitude scenarios and spacecraft parameters are modeled after one of the THEMIS (Time History of Events and Macroscale Interactions during Substorms) probes. Several tests are presented that demonstrate the filter accuracy and convergence properties. The tests include torque-free motion with various nutation angles, large constant-torque attitude slews, sensor misalignments, large initial attitude and rate errors, and cases with low data frequency. It is found that the convergence is rapid, the radius of convergence is large, and the results are reasonably accurate even in the presence of unmodeled perturbations.

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

NASA Astrophysics Data System (ADS)

Kruse, Holger; Grimme, Stefan

2012-04-01

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.

Intelligent System Development Using a Rough Sets Methodology

NASA Technical Reports Server (NTRS)

Anderson, Gray T.; Shelton, Robert O.

1997-01-01

The purpose of this research was to examine the potential of the rough sets technique for developing intelligent models of complex systems from limited information. Rough sets a simple but promising technology to extract easily understood rules from data. The rough set methodology has been shown to perform well when used with a large set of exemplars, but its performance with sparse data sets is less certain. The difficulty is that rules will be developed based on just a few examples, each of which might have a large amount of noise associated with them. The question then becomes, what is the probability of a useful rule being developed from such limited information? One nice feature of rough sets is that in unusual situations, the technique can give an answer of 'I don't know'. That is, if a case arises that is different from the cases the rough set rules were developed on, the methodology can recognize this and alert human operators of it. It can also be trained to do this when the desired action is unknown because conflicting examples apply to the same set of inputs. This summer's project was to look at combining rough set theory with statistical theory to develop confidence limits in rules developed by rough sets. Often it is important not to make a certain type of mistake (e.g., false positives or false negatives), so the rules must be biased toward preventing a catastrophic error, rather than giving the most likely course of action. A method to determine the best course of action in the light of such constraints was examined. The resulting technique was tested with files containing electrical power line 'signatures' from the space shuttle and with decompression sickness data.

Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

PubMed Central

2012-01-01

Background Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and consider all genes that differ by more than an arbitrary cut-off value to be differentially expressed. This filtering approach is not a statistical test and there is no associated value that can indicate the level of confidence in the designation of genes as differentially expressed or not differentially expressed. At the same time the fold change by itself provide valuable information and it is important to find unambiguous ways of using this information in expression data treatment. Results A new method of finding differentially expressed genes, called distributional fold change (DFC) test is introduced. The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance. The proposed method allows one to rank each feature based on the signal-to-noise ratio and to ascertain for each feature the confidence level and power for being differentially expressed. The performance of the new method was evaluated using the total and partial area under receiver operating curves and tested on 11 data sets from Gene Omnibus Database with independently verified differentially expressed genes and compared with the t-test and shrinkage t-test. Overall the DFC test performed the best – on average it had higher sensitivity and partial AUC and its elevation was most prominent in the low range of differentially expressed features, typical for formalin-fixed paraffin-embedded sample sets. Conclusions The distributional fold change test is an effective method for finding and ranking differentially expressed probesets on microarrays. The application of this test is advantageous to data sets using formalin-fixed paraffin-embedded samples or other systems where degradation effects diminish the applicability of correlation adjusted methods to the whole feature set. PMID:23122055

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

Development and Validation of Decision Forest Model for Estrogen Receptor Binding Prediction of Chemicals Using Large Data Sets.

PubMed

Ng, Hui Wen; Doughty, Stephen W; Luo, Heng; Ye, Hao; Ge, Weigong; Tong, Weida; Hong, Huixiao

2015-12-21

Some chemicals in the environment possess the potential to interact with the endocrine system in the human body. Multiple receptors are involved in the endocrine system; estrogen receptor α (ERα) plays very important roles in endocrine activity and is the most studied receptor. Understanding and predicting estrogenic activity of chemicals facilitates the evaluation of their endocrine activity. Hence, we have developed a decision forest classification model to predict chemical binding to ERα using a large training data set of 3308 chemicals obtained from the U.S. Food and Drug Administration's Estrogenic Activity Database. We tested the model using cross validations and external data sets of 1641 chemicals obtained from the U.S. Environmental Protection Agency's ToxCast project. The model showed good performance in both internal (92% accuracy) and external validations (∼ 70-89% relative balanced accuracies), where the latter involved the validations of the model across different ER pathway-related assays in ToxCast. The important features that contribute to the prediction ability of the model were identified through informative descriptor analysis and were related to current knowledge of ER binding. Prediction confidence analysis revealed that the model had both high prediction confidence and accuracy for most predicted chemicals. The results demonstrated that the model constructed based on the large training data set is more accurate and robust for predicting ER binding of chemicals than the published models that have been developed using much smaller data sets. The model could be useful for the evaluation of ERα-mediated endocrine activity potential of environmental chemicals.

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning

NASA Astrophysics Data System (ADS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-01

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning

PubMed Central

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-01-01

Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate. PMID:28418043

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.

PubMed

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-18

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Capturing flight system test engineering expertise: Lessons learned

NASA Technical Reports Server (NTRS)

Woerner, Irene Wong

1991-01-01

Within a few years, JPL will be challenged by the most active mission set in history. Concurrently, flight systems are increasingly more complex. Presently, the knowledge to conduct integration and test of spacecraft and large instruments is held by a few key people, each with many years of experience. JPL is in danger of losing a significant amount of this critical expertise, through retirement, during a period when demand for this expertise is rapidly increasing. The most critical issue at hand is to collect and retain this expertise and develop tools that would ensure the ability to successfully perform the integration and test of future spacecraft and large instruments. The proposed solution was to capture and codity a subset of existing knowledge, and to utilize this captured expertise in knowledge-based systems. First year results and activities planned for the second year of this on-going effort are described. Topics discussed include lessons learned in knowledge acquisition and elicitation techniques, life-cycle paradigms, and rapid prototyping of a knowledge-based advisor (Spacecraft Test Assistant) and a hypermedia browser (Test Engineering Browser). The prototype Spacecraft Test Assistant supports a subset of integration and test activities for flight systems. Browser is a hypermedia tool that allows users easy perusal of spacecraft test topics. A knowledge acquisition tool called ConceptFinder which was developed to search through large volumes of data for related concepts is also described and is modified to semi-automate the process of creating hypertext links.

An experimental study of the sensitivity of helicopter rotor blade tracking to root pitch adjustment in hover

NASA Technical Reports Server (NTRS)

Wilkie, W. Keats; Langston, Chester W.; Mirick, Paul H.; Singleton, Jeffrey D.; Wilbur, Matthew L.; Yeager, William T., Jr.

1991-01-01

The sensitivity of blade tracking in hover to variations in root pitch was examined for two rotor configurations. Tests were conducted using a four bladed articulated rotor mounted on the NASA-Army aeroelastic rotor experimental system (ARES). Two rotor configurations were tested: one consisting of a blade set with flexible fiberglass spars and one with stiffer (by a factor of five in flapwise and torsional stiffnesses) aluminum spars. Both blade sets were identical in planform and airfoil distribution and were untwisted. The two configurations were ballasted to the same Lock number so that a direct comparison of the tracking sensitivity to a gross change in blade stiffness could be made. Experimental results show no large differences between the two sets of blades in the sensitivity of the blade tracking to root pitch adjustments. However, a measurable reduction in intrack coning of the fiberglass spar blades with respect to the aluminum blades is noted at higher rotor thrust conditions.

Predicting reading and mathematics from neural activity for feedback learning.

PubMed

Peters, Sabine; Van der Meulen, Mara; Zanolie, Kiki; Crone, Eveline A

2017-01-01

Although many studies use feedback learning paradigms to study the process of learning in laboratory settings, little is known about their relevance for real-world learning settings such as school. In a large developmental sample (N = 228, 8-25 years), we investigated whether performance and neural activity during a feedback learning task predicted reading and mathematics performance 2 years later. The results indicated that feedback learning performance predicted both reading and mathematics performance. Activity during feedback learning in left superior dorsolateral prefrontal cortex (DLPFC) predicted reading performance, whereas activity in presupplementary motor area/anterior cingulate cortex (pre-SMA/ACC) predicted mathematical performance. Moreover, left superior DLPFC and pre-SMA/ACC activity predicted unique variance in reading and mathematics ability over behavioral testing of feedback learning performance alone. These results provide valuable insights into the relationship between laboratory-based learning tasks and learning in school settings, and the value of neural assessments for prediction of school performance over behavioral testing alone. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The Electrolyte Genome project: A big data approach in battery materials discovery

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

Qu, Xiaohui; Jain, Anubhav; Rajput, Nav Nidhi

2015-06-01

We present a high-throughput infrastructure for the automated calculation of molecular properties with a focus on battery electrolytes. The infrastructure is largely open-source and handles both practical aspects (input file generation, output file parsing, and information management) as well as more complex problems (structure matching, salt complex generation, and failure recovery). Using this infrastructure, we have computed the ionization potential (IP) and electron affinities (EA) of 4830 molecules relevant to battery electrolytes (encompassing almost 55,000 quantum mechanics calculations) at the B3LYP/6-31+G(*) level. We describe automated workflows for computing redox potential, dissociation constant, and salt-molecule binding complex structure generation. We presentmore » routines for automatic recovery from calculation errors, which brings the failure rate from 9.2% to 0.8% for the QChem DFT code. Automated algorithms to check duplication between two arbitrary molecules and structures are described. We present benchmark data on basis sets and functionals on the G2-97 test set; one finding is that a IP/EA calculation method that combines PBE geometry optimization and B3LYP energy evaluation requires less computational cost and yields nearly identical results as compared to a full B3LYP calculation, and could be suitable for the calculation of large molecules. Our data indicates that among the 8 functionals tested, XYGJ-OS and B3LYP are the two best functionals to predict IP/EA with an RMSE of 0.12 and 0.27 eV, respectively. Application of our automated workflow to a large set of quinoxaline derivative molecules shows that functional group effect and substitution position effect can be separated for IP/EA of quinoxaline derivatives, and the most sensitive position is different for IP and EA. Published by Elsevier B.V« less

The prediction of airborne and structure-borne noise potential for a tire

NASA Astrophysics Data System (ADS)

Sakamoto, Nicholas Y.

Tire/pavement interaction noise is a major component of both exterior pass-by noise and vehicle interior noise. The current testing methods for ranking tires from loud to quiet require expensive equipment, multiple tires, and/or long experimental set-up and run times. If a laboratory based off-vehicle test could be used to identify the airborne and structure-borne potential of a tire from its dynamic characteristics, a relative ranking of a large group of tires could be performed at relatively modest expense. This would provide a smaller sample set of tires for follow-up testing and thus save expense for automobile OEMs. The focus of this research was identifying key noise features from a tire/pavement experiment. These results were compared against a stationary tire test in which the natural response of the tire to a forced input was measured. Since speed was identified as having some effect on the noise, an input function was also developed to allow the tires to be ranked at an appropriate speed. A relative noise model was used on a second sample set of tires to verify if the ranking could be used against interior vehicle measurements. While overall level analysis of the specified spectrum had mixed success, important noise generating features were identified, and the methods used could be improved to develop a standard off-vehicle test to predict a tire's noise potential.

Decentralization of CD4 testing in resource-limited settings: 7 years of experience in six African countries.

PubMed

Marinucci, F; Medina-Moreno, S; Paterniti, A D; Wattleworth, M; Redfield, R R

2011-05-01

Improving access to CD4 testing in resource-limited settings can be achieved through both centralized and decentralized testing networks. Decentralized testing models are more suitable for countries where the HIV epidemic affects a large portion of rural populations. Timely access to accurate CD4 results is crucial at the primary level of the health system. For the past 7 years, the Institute of Human Virology of the University of Maryland School of Medicine has implemented a flexible and sustainable three-phase model: (1) site assessment and improvement, (2) appropriate technology selection with capacity building through practical training and laboratory mentoring, and (3) quality management system strengthening and monitoring, to support accessibility to reliable CD4 counting at the point of service. CD4 testing capacity was established in 122 of 229 (53%) laboratories supported in Nigeria, Uganda, Kenya, Zambia, Tanzania, and Rwanda. Among those in rural settings, 46% (69/151) had CD4 testing available at site level, with a functioning flow cytometer installed at 28% (8/29) and 50% (61/122) of level 1 and level 2 sites, respectively. To strengthen local capacity, a total of 1,152 laboratory technicians were trained through 188 training sessions provided both on-site and at central locations. The overall quality of CD4 total testing procedure was assessed at 76% (92/121) of the laboratories, with 25% (23/92), 34% (31/92), and 33% (30/92) of them reporting excellent, good, and satisfactory performance. Balancing country-specific factors with the location of the clinic, number of patients, and the expected workload, was crucial in adapting this flexible model for decentralizing CD4 testing. The close collaboration with local governments and private vendors was key to successfully expanding access to CD4 testing within the framework of HIV care and treatment programs and for the sustainability of medical laboratories in resource-limited settings. Copyright © 2011 International Society for Advancement of Cytometry.

Executive functioning in healthy elderly Chinese people.

PubMed

Lin, Han; Chan, Raymond C K; Zheng, Liuning; Yang, Tianxiao; Wang, Ya

2007-05-01

This study aimed to explore the executive function of healthy elderly Chinese people. A sample of 58 healthy Chinese aged 60 and over was recruited from Guangzhou in China. They were divided into two age groups, a younger age group (aged 60-70) and an older age group (aged over 70). Executive function was measured by a battery of seven tests which were assumed to capture specific components of executive function. The tests were initiation (Hayling Sentence Completion Test (HSC)), sustained attention (Monotone Counting Test), switching and flexibility (word fluency and modified Wisconsin Card Sorting Test (WCST)), disinhibition (Modified Six Element Task (SET), Stroop Test, and HSC), attention allocation and planning (SET and modified version of WCST), and updating (Chinese Letter-Number Span). When independent neurocognitive tests were analyzed, there were significant age differences in the WCST (perseverative errors and category completed, p=0.025, 0.023) and the SET (raw score, p=0.050). The older age group tended to do worse in the total profile score of the SET and correct responses of the HSC Part A. However, when these tests were grouped into specific executive function components, a significant difference was found between the two groups in attention allocation and planning (p=0.007) and total component score (p=0.026). Regression analyses also indicated that age accounted for only very little variance of executive function in this narrow band of the elderly, whereas educational level accounted for a large part of the variance in initiation (R(2)=0.252, p<0.001), switching and flexibility (R(2)=0.211, p<0.001), and updating (R(2)=0.236, p<0.001) components of executive function. Our findings suggest that a significant decline in general executive functioning with advancing age was only evident in some putative tests in this sample. In addition, executive functions were selectively affected by older age, with attention location and planning and initiation being the components that were most affected.

Usability-driven pruning of large ontologies: the case of SNOMED CT

PubMed Central

Boeker, Martin; Illarramendi, Arantza; Schulz, Stefan

2012-01-01

Objectives To study ontology modularization techniques when applied to SNOMED CT in a scenario in which no previous corpus of information exists and to examine if frequency-based filtering using MEDLINE can reduce subset size without discarding relevant concepts. Materials and Methods Subsets were first extracted using four graph-traversal heuristics and one logic-based technique, and were subsequently filtered with frequency information from MEDLINE. Twenty manually coded discharge summaries from cardiology patients were used as signatures and test sets. The coverage, size, and precision of extracted subsets were measured. Results Graph-traversal heuristics provided high coverage (71–96% of terms in the test sets of discharge summaries) at the expense of subset size (17–51% of the size of SNOMED CT). Pre-computed subsets and logic-based techniques extracted small subsets (1%), but coverage was limited (24–55%). Filtering reduced the size of large subsets to 10% while still providing 80% coverage. Discussion Extracting subsets to annotate discharge summaries is challenging when no previous corpus exists. Ontology modularization provides valuable techniques, but the resulting modules grow as signatures spread across subhierarchies, yielding a very low precision. Conclusion Graph-traversal strategies and frequency data from an authoritative source can prune large biomedical ontologies and produce useful subsets that still exhibit acceptable coverage. However, a clinical corpus closer to the specific use case is preferred when available. PMID:22268217

Comparison of Feature Selection Techniques in Machine Learning for Anatomical Brain MRI in Dementia.

PubMed

Tohka, Jussi; Moradi, Elaheh; Huttunen, Heikki

2016-07-01

We present a comparative split-half resampling analysis of various data driven feature selection and classification methods for the whole brain voxel-based classification analysis of anatomical magnetic resonance images. We compared support vector machines (SVMs), with or without filter based feature selection, several embedded feature selection methods and stability selection. While comparisons of the accuracy of various classification methods have been reported previously, the variability of the out-of-training sample classification accuracy and the set of selected features due to independent training and test sets have not been previously addressed in a brain imaging context. We studied two classification problems: 1) Alzheimer's disease (AD) vs. normal control (NC) and 2) mild cognitive impairment (MCI) vs. NC classification. In AD vs. NC classification, the variability in the test accuracy due to the subject sample did not vary between different methods and exceeded the variability due to different classifiers. In MCI vs. NC classification, particularly with a large training set, embedded feature selection methods outperformed SVM-based ones with the difference in the test accuracy exceeding the test accuracy variability due to the subject sample. The filter and embedded methods produced divergent feature patterns for MCI vs. NC classification that suggests the utility of the embedded feature selection for this problem when linked with the good generalization performance. The stability of the feature sets was strongly correlated with the number of features selected, weakly correlated with the stability of classification accuracy, and uncorrelated with the average classification accuracy.

High-Value, Cost-Conscious Care: Iterative Systems-Based Interventions to Reduce Unnecessary Laboratory Testing.

PubMed

Sadowski, Brett W; Lane, Alison B; Wood, Shannon M; Robinson, Sara L; Kim, Chin Hee

2017-09-01

Inappropriate testing contributes to soaring healthcare costs within the United States, and teaching hospitals are vulnerable to providing care largely for academic development. Via its "Choosing Wisely" campaign, the American Board of Internal Medicine recommends avoiding repetitive testing for stable inpatients. We designed systems-based interventions to reduce laboratory orders for patients admitted to the wards at an academic facility. We identified the computer-based order entry system as an appropriate target for sustainable intervention. The admission order set had allowed multiple routine tests to be ordered repetitively each day. Our iterative study included interventions on the automated order set and cost displays at order entry. The primary outcome was number of routine tests controlled for inpatient days compared with the preceding year. Secondary outcomes included cost savings, delays in care, and adverse events. Data were collected over a 2-month period following interventions in sequential years and compared with the year prior. The first intervention led to 0.97 fewer laboratory tests per inpatient day (19.4%). The second intervention led to sustained reduction, although by less of a margin than order set modifications alone (15.3%). When extrapolating the results utilizing fees from the Centers for Medicare and Medicaid Services, there was a cost savings of $290,000 over 2 years. Qualitative survey data did not suggest an increase in care delays or near-miss events. This series of interventions targeting unnecessary testing demonstrated a sustained reduction in the number of routine tests ordered, without adverse effects on clinical care. Published by Elsevier Inc.

An artificial neural network prediction model of congenital heart disease based on risk factors: A hospital-based case-control study.

PubMed

Li, Huixia; Luo, Miyang; Zheng, Jianfei; Luo, Jiayou; Zeng, Rong; Feng, Na; Du, Qiyun; Fang, Junqun

2017-02-01

An artificial neural network (ANN) model was developed to predict the risks of congenital heart disease (CHD) in pregnant women.This hospital-based case-control study involved 119 CHD cases and 239 controls all recruited from birth defect surveillance hospitals in Hunan Province between July 2013 and June 2014. All subjects were interviewed face-to-face to fill in a questionnaire that covered 36 CHD-related variables. The 358 subjects were randomly divided into a training set and a testing set at the ratio of 85:15. The training set was used to identify the significant predictors of CHD by univariate logistic regression analyses and develop a standard feed-forward back-propagation neural network (BPNN) model for the prediction of CHD. The testing set was used to test and evaluate the performance of the ANN model. Univariate logistic regression analyses were performed on SPSS 18.0. The ANN models were developed on Matlab 7.1.The univariate logistic regression identified 15 predictors that were significantly associated with CHD, including education level (odds ratio  = 0.55), gravidity (1.95), parity (2.01), history of abnormal reproduction (2.49), family history of CHD (5.23), maternal chronic disease (4.19), maternal upper respiratory tract infection (2.08), environmental pollution around maternal dwelling place (3.63), maternal exposure to occupational hazards (3.53), maternal mental stress (2.48), paternal chronic disease (4.87), paternal exposure to occupational hazards (2.51), intake of vegetable/fruit (0.45), intake of fish/shrimp/meat/egg (0.59), and intake of milk/soymilk (0.55). After many trials, we selected a 3-layer BPNN model with 15, 12, and 1 neuron in the input, hidden, and output layers, respectively, as the best prediction model. The prediction model has accuracies of 0.91 and 0.86 on the training and testing sets, respectively. The sensitivity, specificity, and Yuden Index on the testing set (training set) are 0.78 (0.83), 0.90 (0.95), and 0.68 (0.78), respectively. The areas under the receiver operating curve on the testing and training sets are 0.87 and 0.97, respectively.This study suggests that the BPNN model could be used to predict the risk of CHD in individuals. This model should be further improved by large-sample-size research.

Evolutionary and Neural Computing Based Decision Support System for Disease Diagnosis from Clinical Data Sets in Medical Practice.

PubMed

Sudha, M

2017-09-27

As a recent trend, various computational intelligence and machine learning approaches have been used for mining inferences hidden in the large clinical databases to assist the clinician in strategic decision making. In any target data the irrelevant information may be detrimental, causing confusion for the mining algorithm and degrades the prediction outcome. To address this issue, this study attempts to identify an intelligent approach to assist disease diagnostic procedure using an optimal set of attributes instead of all attributes present in the clinical data set. In this proposed Application Specific Intelligent Computing (ASIC) decision support system, a rough set based genetic algorithm is employed in pre-processing phase and a back propagation neural network is applied in training and testing phase. ASIC has two phases, the first phase handles outliers, noisy data, and missing values to obtain a qualitative target data to generate appropriate attribute reduct sets from the input data using rough computing based genetic algorithm centred on a relative fitness function measure. The succeeding phase of this system involves both training and testing of back propagation neural network classifier on the selected reducts. The model performance is evaluated with widely adopted existing classifiers. The proposed ASIC system for clinical decision support has been tested with breast cancer, fertility diagnosis and heart disease data set from the University of California at Irvine (UCI) machine learning repository. The proposed system outperformed the existing approaches attaining the accuracy rate of 95.33%, 97.61%, and 93.04% for breast cancer, fertility issue and heart disease diagnosis.

Experimental Evaluation of Suitability of Selected Multi-Criteria Decision-Making Methods for Large-Scale Agent-Based Simulations

PubMed Central

2016-01-01

Multi-criteria decision-making (MCDM) can be formally implemented by various methods. This study compares suitability of four selected MCDM methods, namely WPM, TOPSIS, VIKOR, and PROMETHEE, for future applications in agent-based computational economic (ACE) models of larger scale (i.e., over 10 000 agents in one geographical region). These four MCDM methods were selected according to their appropriateness for computational processing in ACE applications. Tests of the selected methods were conducted on four hardware configurations. For each method, 100 tests were performed, which represented one testing iteration. With four testing iterations conducted on each hardware setting and separated testing of all configurations with the–server parameter de/activated, altogether, 12800 data points were collected and consequently analyzed. An illustrational decision-making scenario was used which allows the mutual comparison of all of the selected decision making methods. Our test results suggest that although all methods are convenient and can be used in practice, the VIKOR method accomplished the tests with the best results and thus can be recommended as the most suitable for simulations of large-scale agent-based models. PMID:27806061

OpenCL based machine learning labeling of biomedical datasets

NASA Astrophysics Data System (ADS)

Amoros, Oscar; Escalera, Sergio; Puig, Anna

2011-03-01

In this paper, we propose a two-stage labeling method of large biomedical datasets through a parallel approach in a single GPU. Diagnostic methods, structures volume measurements, and visualization systems are of major importance for surgery planning, intra-operative imaging and image-guided surgery. In all cases, to provide an automatic and interactive method to label or to tag different structures contained into input data becomes imperative. Several approaches to label or segment biomedical datasets has been proposed to discriminate different anatomical structures in an output tagged dataset. Among existing methods, supervised learning methods for segmentation have been devised to easily analyze biomedical datasets by a non-expert user. However, they still have some problems concerning practical application, such as slow learning and testing speeds. In addition, recent technological developments have led to widespread availability of multi-core CPUs and GPUs, as well as new software languages, such as NVIDIA's CUDA and OpenCL, allowing to apply parallel programming paradigms in conventional personal computers. Adaboost classifier is one of the most widely applied methods for labeling in the Machine Learning community. In a first stage, Adaboost trains a binary classifier from a set of pre-labeled samples described by a set of features. This binary classifier is defined as a weighted combination of weak classifiers. Each weak classifier is a simple decision function estimated on a single feature value. Then, at the testing stage, each weak classifier is independently applied on the features of a set of unlabeled samples. In this work, we propose an alternative representation of the Adaboost binary classifier. We use this proposed representation to define a new GPU-based parallelized Adaboost testing stage using OpenCL. We provide numerical experiments based on large available data sets and we compare our results to CPU-based strategies in terms of time and labeling speeds.

Rapid on-line detection and grading of wooden breast myopathy in chicken fillets by near-infrared spectroscopy

PubMed Central

Veiseth-Kent, Eva; Høst, Vibeke; Løvland, Atle

2017-01-01

The main objective of this work was to develop a method for rapid and non-destructive detection and grading of wooden breast (WB) syndrome in chicken breast fillets. Near-infrared (NIR) spectroscopy was chosen as detection method, and an industrial NIR scanner was applied and tested for large scale on-line detection of the syndrome. Two approaches were evaluated for discrimination of WB fillets: 1) Linear discriminant analysis based on NIR spectra only, and 2) a regression model for protein was made based on NIR spectra and the estimated concentrations of protein were used for discrimination. A sample set of 197 fillets was used for training and calibration. A test set was recorded under industrial conditions and contained spectra from 79 fillets. The classification methods obtained 99.5–100% correct classification of the calibration set and 100% correct classification of the test set. The NIR scanner was then installed in a commercial chicken processing plant and could detect incidence rates of WB in large batches of fillets. Examples of incidence are shown for three broiler flocks where a high number of fillets (9063, 6330 and 10483) were effectively measured. Prevalence of WB of 0.1%, 6.6% and 8.5% were estimated for these flocks based on the complete sample volumes. Such an on-line system can be used to alleviate the challenges WB represents to the poultry meat industry. It enables automatic quality sorting of chicken fillets to different product categories. Manual laborious grading can be avoided. Incidences of WB from different farms and flocks can be tracked and information can be used to understand and point out main causes for WB in the chicken production. This knowledge can be used to improve the production procedures and reduce today’s extensive occurrence of WB. PMID:28278170

Prospective and retrospective timing by pigeons.

PubMed

Fetterman, J Gregor; Killeen, P Richard

2010-05-01

Pigeons discriminated between two pairs of durations: a short set (2.5 and 5 sec) and a long set (5 and 10 sec). The pairs were intermixed within sessions and identified by the colors on the signal and choice keys. Once the task was learned, the pigeons experienced the following three conditions seriatim: (1) The signal key was made ambiguous about the test change, but the choice keys were informative (retrospective); (2) the signal key identified the test range, but the choice keys did not (prospective); (3) probe trials were introduced in which the color of the center key signaled one test range, but the color of the choice keys signaled the other test range (inconsistent). Accuracy of choice decreased in the retrospective condition and, returned to baseline levels, was higher under the prospective condition than under the retrospective condition. In a final condition, referred to as conflict trials, the center-key color signified one test range and the choice-key colors the other range. The results from these conflict-inconsistent tests indicate that choice behavior was largely controlled by the signal-key color and not by the choice-key color. We relate these findings to different approaches to timing in animals.

Data Acquisition System Architecture and Capabilities At NASA GRC Plum Brook Station's Space Environment Test Facilities

NASA Technical Reports Server (NTRS)

Evans, Richard K.; Hill, Gerald M.

2012-01-01

Very large space environment test facilities present unique engineering challenges in the design of facility data systems. Data systems of this scale must be versatile enough to meet the wide range of data acquisition and measurement requirements from a diverse set of customers and test programs, but also must minimize design changes to maintain reliability and serviceability. This paper presents an overview of the common architecture and capabilities of the facility data acquisition systems available at two of the world?s largest space environment test facilities located at the NASA Glenn Research Center?s Plum Brook Station in Sandusky, Ohio; namely, the Space Propulsion Research Facility (commonly known as the B-2 facility) and the Space Power Facility (SPF). The common architecture of the data systems is presented along with details on system scalability and efficient measurement systems analysis and verification. The architecture highlights a modular design, which utilizes fully-remotely managed components, enabling the data systems to be highly configurable and support multiple test locations with a wide-range of measurement types and very large system channel counts.

Data Acquisition System Architecture and Capabilities at NASA GRC Plum Brook Station's Space Environment Test Facilities

NASA Technical Reports Server (NTRS)

Evans, Richard K.; Hill, Gerald M.

2014-01-01

Very large space environment test facilities present unique engineering challenges in the design of facility data systems. Data systems of this scale must be versatile enough to meet the wide range of data acquisition and measurement requirements from a diverse set of customers and test programs, but also must minimize design changes to maintain reliability and serviceability. This paper presents an overview of the common architecture and capabilities of the facility data acquisition systems available at two of the world's largest space environment test facilities located at the NASA Glenn Research Center's Plum Brook Station in Sandusky, Ohio; namely, the Space Propulsion Research Facility (commonly known as the B-2 facility) and the Space Power Facility (SPF). The common architecture of the data systems is presented along with details on system scalability and efficient measurement systems analysis and verification. The architecture highlights a modular design, which utilizes fully-remotely managed components, enabling the data systems to be highly configurable and support multiple test locations with a wide-range of measurement types and very large system channel counts.

Cholesky-decomposed density MP2 with density fitting: Accurate MP2 and double-hybrid DFT energies for large systems

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

Maurer, Simon A.; Clin, Lucien; Ochsenfeld, Christian, E-mail: christian.ochsenfeld@uni-muenchen.de

2014-06-14

Our recently developed QQR-type integral screening is introduced in our Cholesky-decomposed pseudo-densities Møller-Plesset perturbation theory of second order (CDD-MP2) method. We use the resolution-of-the-identity (RI) approximation in combination with efficient integral transformations employing sparse matrix multiplications. The RI-CDD-MP2 method shows an asymptotic cubic scaling behavior with system size and a small prefactor that results in an early crossover to conventional methods for both small and large basis sets. We also explore the use of local fitting approximations which allow to further reduce the scaling behavior for very large systems. The reliability of our method is demonstrated on test sets formore » interaction and reaction energies of medium sized systems and on a diverse selection from our own benchmark set for total energies of larger systems. Timings on DNA systems show that fast calculations for systems with more than 500 atoms are feasible using a single processor core. Parallelization extends the range of accessible system sizes on one computing node with multiple cores to more than 1000 atoms in a double-zeta basis and more than 500 atoms in a triple-zeta basis.« less

Semi-automatic ground truth generation using unsupervised clustering and limited manual labeling: Application to handwritten character recognition

PubMed Central

Vajda, Szilárd; Rangoni, Yves; Cecotti, Hubert

2015-01-01

For training supervised classifiers to recognize different patterns, large data collections with accurate labels are necessary. In this paper, we propose a generic, semi-automatic labeling technique for large handwritten character collections. In order to speed up the creation of a large scale ground truth, the method combines unsupervised clustering and minimal expert knowledge. To exploit the potential discriminant complementarities across features, each character is projected into five different feature spaces. After clustering the images in each feature space, the human expert labels the cluster centers. Each data point inherits the label of its cluster’s center. A majority (or unanimity) vote decides the label of each character image. The amount of human involvement (labeling) is strictly controlled by the number of clusters – produced by the chosen clustering approach. To test the efficiency of the proposed approach, we have compared, and evaluated three state-of-the art clustering methods (k-means, self-organizing maps, and growing neural gas) on the MNIST digit data set, and a Lampung Indonesian character data set, respectively. Considering a k-nn classifier, we show that labeling manually only 1.3% (MNIST), and 3.2% (Lampung) of the training data, provides the same range of performance than a completely labeled data set would. PMID:25870463

A Simple but Powerful Heuristic Method for Accelerating k-Means Clustering of Large-Scale Data in Life Science.

PubMed

Ichikawa, Kazuki; Morishita, Shinichi

2014-01-01

K-means clustering has been widely used to gain insight into biological systems from large-scale life science data. To quantify the similarities among biological data sets, Pearson correlation distance and standardized Euclidean distance are used most frequently; however, optimization methods have been largely unexplored. These two distance measurements are equivalent in the sense that they yield the same k-means clustering result for identical sets of k initial centroids. Thus, an efficient algorithm used for one is applicable to the other. Several optimization methods are available for the Euclidean distance and can be used for processing the standardized Euclidean distance; however, they are not customized for this context. We instead approached the problem by studying the properties of the Pearson correlation distance, and we invented a simple but powerful heuristic method for markedly pruning unnecessary computation while retaining the final solution. Tests using real biological data sets with 50-60K vectors of dimensions 10-2001 (~400 MB in size) demonstrated marked reduction in computation time for k = 10-500 in comparison with other state-of-the-art pruning methods such as Elkan's and Hamerly's algorithms. The BoostKCP software is available at http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/boostKCP/.

Diagnostic Tests for Entering and Departing Undergraduate Students

NASA Astrophysics Data System (ADS)

Waltham, Chris; Kotlicki, A.

2006-12-01

A diagnostic test administered at the start of a class should test basic concepts which are recognized as course prerequisites. The questions should not be over-packaged: e.g. students should be required to create models, rather than this being done for them each time. Students should be allowed great latitude in their answers, so we can discover what they are thinking. When administered at the end of a class the goals should be similar: testing concepts taught in the class itself and the retention of necessary concepts from previous classes. Great care has to be taken to avoid teaching to the test. In assessing an entire program, for example an undergraduate majors degree in physics, then one looks for very general skills and knowledge not specific to any one course. The purpose of an undergraduate degree in physics (or indeed any science) is to equip the students with a set of problem-solving skills and basic knowledge which can be applied in a large variety of workplace settings and to allow that student to contribute to civic society as a science-literate person. The creator of any diagnostic test should always have these big goals in mind. We have developed a set of questions which we think fulfill these criteria, yet are not specific to any particular level of science education. They have been administered to students in secondary schools across Canada, incoming first-year science students and final-year physics students at the University of British Columbia. The results will be presented.

Estimation of the chemical-induced eye injury using a Weight-of-Evidence (WoE) battery of 21 artificial neural network (ANN) c-QSAR models (QSAR-21): part II: corrosion potential.

PubMed

Verma, Rajeshwar P; Matthews, Edwin J

2015-03-01

This is part II of an in silico investigation of chemical-induced eye injury that was conducted at FDA's CFSAN. Serious eye damage caused by chemical (eye corrosion) is assessed using the rabbit Draize test, and this endpoint is an essential part of hazard identification and labeling of industrial and consumer products to ensure occupational and consumer safety. There is an urgent need to develop an alternative to the Draize test because EU's 7th amendment to the Cosmetic Directive (EC, 2003; 76/768/EEC) and recast Regulation now bans animal testing on all cosmetic product ingredients and EU's REACH Program limits animal testing for chemicals in commerce. Although in silico methods have been reported for eye irritation (reversible damage), QSARs specific for eye corrosion (irreversible damage) have not been published. This report describes the development of 21 ANN c-QSAR models (QSAR-21) for assessing eye corrosion potential of chemicals using a large and diverse CFSAN data set of 504 chemicals, ADMET Predictor's three sensitivity analyses and ANNE classification functionalities with 20% test set selection from seven different methods. QSAR-21 models were internally and externally validated and exhibited high predictive performance: average statistics for the training, verification, and external test sets of these models were 96/96/94% sensitivity and 91/91/90% specificity. Copyright © 2014 Elsevier Inc. All rights reserved.

Uncovering the hidden risk architecture of the schizophrenias: confirmation in three independent genome-wide association studies.

PubMed

Arnedo, Javier; Svrakic, Dragan M; Del Val, Coral; Romero-Zaliz, Rocío; Hernández-Cuervo, Helena; Fanous, Ayman H; Pato, Michele T; Pato, Carlos N; de Erausquin, Gabriel A; Cloninger, C Robert; Zwir, Igor

2015-02-01

The authors sought to demonstrate that schizophrenia is a heterogeneous group of heritable disorders caused by different genotypic networks that cause distinct clinical syndromes. In a large genome-wide association study of cases with schizophrenia and controls, the authors first identified sets of interacting single-nucleotide polymorphisms (SNPs) that cluster within particular individuals (SNP sets) regardless of clinical status. Second, they examined the risk of schizophrenia for each SNP set and tested replicability in two independent samples. Third, they identified genotypic networks composed of SNP sets sharing SNPs or subjects. Fourth, they identified sets of distinct clinical features that cluster in particular cases (phenotypic sets or clinical syndromes) without regard for their genetic background. Fifth, they tested whether SNP sets were associated with distinct phenotypic sets in a replicable manner across the three studies. The authors identified 42 SNP sets associated with a 70% or greater risk of schizophrenia, and confirmed 34 (81%) or more with similar high risk of schizophrenia in two independent samples. Seventeen networks of SNP sets did not share any SNP or subject. These disjoint genotypic networks were associated with distinct gene products and clinical syndromes (i.e., the schizophrenias) varying in symptoms and severity. Associations between genotypic networks and clinical syndromes were complex, showing multifinality and equifinality. The interactive networks explained the risk of schizophrenia more than the average effects of all SNPs (24%). Schizophrenia is a group of heritable disorders caused by a moderate number of separate genotypic networks associated with several distinct clinical syndromes.

Efficacy of Cruise Control in controlling postocclusion surge with Legacy and Millennium venturi phacoemulsification machines.

PubMed

Wade, Matthew; Isom, Ryan; Georgescu, Dan; Olson, Randall J

2007-06-01

To determine the efficacy of the Cruise Control surge-limiting device (Staar Surgical) with phacoemulsification machines known to have high levels of surge. John A. Moran Eye Center Clinical Laboratories. In an in vitro study, postocclusion anterior chamber depth changes were measured in fresh phakic human eye-bank eyes using the Alcon Legacy and Bausch & Lomb Millennium venturi machines in conjunction with the Staar Cruise Control device. Both machines were tested with 19-gauge non-Aspiration Bypass System tips at high-surge settings (500 mm Hg vacuum pressure, 75 cm bottle height, 40 mL/min flow rate for the Legacy) and low-surge settings (400 mm Hg vacuum pressure, 125 cm bottle height, 40 mL/min flow rate for the Legacy). Adjusted parameters of flow, vacuum, and irrigation were used based on previous studies to create identical conditions for each device tested. The effect of the Cruise Control device on aspiration rates was also tested with both machines at the low-surge settings. At the high setting with the addition of Cruise Control, surge decreased significantly with the Legacy but was too large to measure with the Millennium venturi. At the low setting with the addition of Cruise Control, surge decreased significantly with both machines. Surge with the Millennium decreased from more than 1.0 mm to a mean of 0.21 mm +/- 0.02 (SD) (P<.0001). Surge with the Legacy decreased from a mean of 0.09 +/- 0.02 mm to 0.05 +/- 0 mm, a 42.9% decrease (P<.0001). The Millennium had the highest surge and aspiration rate before Cruise Control and the greatest percentage decrease in the surge and aspiration rates as a result of the addition of Cruise Control. In the Legacy machine, the Cruise Control device had a statistically and clinically significant effect. Cruise Control had a large effect on fluidics as well as surge amplitude with the Millennium machine. The greater the flow or greater the initial surge, the greater the impact of the Cruise Control device.

QSAR Classification of ToxCast and Tox21 Chemicals on the Basis of Estrogen Receptor Assays (FutureToxII)

EPA Science Inventory

The ToxCast and Tox21 programs have tested ~8,200 chemicals in a broad screening panel of in vitro high-throughput screening (HTS) assays for estrogen receptor (ER) agonist and antagonist activity. The present work uses this large in vitro data set to develop in silico QSAR model...

Empirical Manifestations of Power among Adult Learners in Online Discussions

ERIC Educational Resources Information Center

Jun, JuSung

2007-01-01

This study examined the nature of power manifestations in a specific online learning setting. The two online classes selected for this study were Master's level courses in a professional school at a large state university in the United States. A total of 1340 postings were made in the two classes over the span of the semester. To test the research…

Big questions, big science: meeting the challenges of global ecology

Treesearch

David Schimel; Michael Keller

2015-01-01

Ecologists are increasingly tackling questions that require significant infrastucture, large experiments, networks of observations, and complex data and computation. Key hypotheses in ecology increasingly require more investment, and larger data sets to be tested than can be collected by a single investigator’s or s group of investigator’s labs, sustained for longer...

An approach to effectiveness monitoring of floodplain channel aquatic habitat: channel condition assessment.

Treesearch

Richard D. Woodsmith; James R. Noel; Michael L. Dilger

2005-01-01

The condition of aquatic habitat and the health of species dependent on that habitat are issues of significant concern to land management agencies, other organizations, and the public at large in southeastern Alaska, as well as along much of the Pacific coastal region of North America. We develop and test a set of effectiveness monitoring procedures for measuring...

How Should Witnesses Regulate the Accuracy of Their Identification Decisions: One Step Forward, Two Steps Back?

ERIC Educational Resources Information Center

Perfect, Timothy J.; Weber, Nathan

2012-01-01

Explorations of memory accuracy control normally contrast forced-report with free-report performance across a set of items and show a trade-off between memory quantity and accuracy. However, this memory control framework has not been tested with lineup identifications that may involve rejection of all alternatives. A large-scale (N = 439) lineup…

Development of forest regeneration imputation models using permanent plots in Oregon and Washington

Treesearch

Karin Kralicek; Andrew Sánchez Meador; Leah Rathbun

2015-01-01

Imputation models were developed and tested to estimate tree regeneration on Forest Service land in Oregon and Washington. The models were based on Forest Inventory and Analysis and Pacific Northwest Regional NFS Monitoring data. The data was processed into sets of tables containing estimates of regeneration by broad plant associations and spanning a large variety in...

Horizon Detection In The Visible Spectrum

DTIC Science & Technology

2016-09-01

techniques can also recognize star patterns in star trackers for satellite attitude determination. Horizon detection in the visible spectrum was largely...discarded for attitude determination in favor of thermal imagery, due to the greater consistency of the earth’s thermal radiation. This thesis...in 85% of the tested image set. 14. SUBJECT TERMS attitude determination, machine learning, image classification, earth horizon sensor, computer

Fast Poisson noise removal by biorthogonal Haar domain hypothesis testing

NASA Astrophysics Data System (ADS)

Zhang, B.; Fadili, M. J.; Starck, J.-L.; Digel, S. W.

2008-07-01

Methods based on hypothesis tests (HTs) in the Haar domain are widely used to denoise Poisson count data. Facing large datasets or real-time applications, Haar-based denoisers have to use the decimated transform to meet limited-memory or computation-time constraints. Unfortunately, for regular underlying intensities, decimation yields discontinuous estimates and strong “staircase” artifacts. In this paper, we propose to combine the HT framework with the decimated biorthogonal Haar (Bi-Haar) transform instead of the classical Haar. The Bi-Haar filter bank is normalized such that the p-values of Bi-Haar coefficients (p) provide good approximation to those of Haar (pH) for high-intensity settings or large scales; for low-intensity settings and small scales, we show that p are essentially upper-bounded by pH. Thus, we may apply the Haar-based HTs to Bi-Haar coefficients to control a prefixed false positive rate. By doing so, we benefit from the regular Bi-Haar filter bank to gain a smooth estimate while always maintaining a low computational complexity. A Fisher-approximation-based threshold implementing the HTs is also established. The efficiency of this method is illustrated on an example of hyperspectral-source-flux estimation.

Learning to Work with Databases in Astronomy: Quantitative Analysis of Science Educators' and Students' Pre-/Post-Tests

NASA Astrophysics Data System (ADS)

Schwortz, Andria C.; Burrows, Andrea C.; Myers, Adam D.

2015-01-01

Astronomy is increasingly moving towards working with large databases, from the state-of-the-art Sloan Digital Sky Survey Data Release 10, to the historical Digital Access to a Sky Century at Harvard. Non-astronomy fields as well tend to work with large datasets, be it in the form of warehouse inventory, health trends, or the stock market. However very few fields explicitly teach students the necessary skills to analyze such data. The authors studied a matched set of 37 participants working with 200-entry databases in astronomy using Google Spreadsheets, with limited information about a random set of quasars drawn from SDSS DR5. Here the authors present the quantitative results from an eight question pre-/post-test, with questions designed to span Bloom's taxonomy, on both the topics of the skills of using spreadsheets, and the content of quasars. Participants included both Astro 101 summer students and professionals including in-service K-12 teachers and science communicators. All groups showed statistically significant gains (as per Hake, 1998), with the greatest difference between women's gains of 0.196 and men's of 0.480.

The effect of a workplace violence training program for generalist nurses in the acute hospital setting: A quasi-experimental study.

PubMed

Lamont, Scott; Brunero, Scott

2018-05-19

Workplace violence prevalence has attracted significant attention within the international nursing literature. Little attention to non-mental health settings and a lack of evaluation rigor have been identified within review literature. To examine the effects of a workplace violence training program in relation to risk assessment and management practices, de-escalation skills, breakaway techniques, and confidence levels, within an acute hospital setting. A quasi-experimental study of nurses using pretest-posttest measurements of educational objectives and confidence levels, with two week follow-up. A 440 bed metropolitan tertiary referral hospital in Sydney, Australia. Nurses working in specialties identified as a 'high risk' for violence. A pre-post-test design was used with participants attending a one day workshop. The workshop evaluation comprised the use of two validated questionnaires: the Continuing Professional Development Reaction questionnaire, and the Confidence in Coping with Patient Aggression Instrument. Descriptive and inferential statistics were calculated. The paired t-test was used to assess the statistical significance of changes in the clinical behaviour intention and confidence scores from pre- to post-intervention. Cohen's d effect sizes were calculated to determine the extent of the significant results. Seventy-eight participants completed both pre- and post-workshop evaluation questionnaires. Statistically significant increases in behaviour intention scores were found in fourteen of the fifteen constructs relating to the three broad workshop objectives, and confidence ratings, with medium to large effect sizes observed in some constructs. A significant increase in overall confidence in coping with patient aggression was also found post-test with large effect size. Positive results were observed from the workplace violence training. Training needs to be complimented by a multi-faceted organisational approach which includes governance, quality and review processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

A large-scale video codec comparison of x264, x265 and libvpx for practical VOD applications

NASA Astrophysics Data System (ADS)

De Cock, Jan; Mavlankar, Aditya; Moorthy, Anush; Aaron, Anne

2016-09-01

Over the last years, we have seen exciting improvements in video compression technology, due to the introduction of HEVC and royalty-free coding specifications such as VP9. The potential compression gains of HEVC over H.264/AVC have been demonstrated in different studies, and are usually based on the HM reference software. For VP9, substantial gains over H.264/AVC have been reported in some publications, whereas others reported less optimistic results. Differences in configurations between these publications make it more difficult to assess the true potential of VP9. Practical open-source encoder implementations such as x265 and libvpx (VP9) have matured, and are now showing high compression gains over x264. In this paper, we demonstrate the potential of these encoder imple- mentations, with settings optimized for non-real-time random access, as used in a video-on-demand encoding pipeline. We report results from a large-scale video codec comparison test, which includes x264, x265 and libvpx. A test set consisting of a variety of titles with varying spatio-temporal characteristics from our catalog is used, resulting in tens of millions of encoded frames, hence larger than test sets previously used in the literature. Re- sults are reported in terms of PSNR, SSIM, MS-SSIM, VIF and the recently introduced VMAF quality metric. BD-rate calculations show that using x265 and libvpx vs. x264 can lead to significant bitrate savings for the same quality. x265 outperforms libvpx in most cases, but the performance gap narrows (or even reverses) at the higher resolutions.

Discerning some Tylenol brands using attenuated total reflection Fourier transform infrared data and multivariate analysis techniques.

PubMed

Msimanga, Huggins Z; Ollis, Robert J

2010-06-01

Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to classify acetaminophen-containing medicines using their attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectra. Four formulations of Tylenol (Arthritis Pain Relief, Extra Strength Pain Relief, 8 Hour Pain Relief, and Extra Strength Pain Relief Rapid Release) along with 98% pure acetaminophen were selected for this study because of the similarity of their spectral features, with correlation coefficients ranging from 0.9857 to 0.9988. Before acquiring spectra for the predictor matrix, the effects on spectral precision with respect to sample particle size (determined by sieve size opening), force gauge of the ATR accessory, sample reloading, and between-tablet variation were examined. Spectra were baseline corrected and normalized to unity before multivariate analysis. Analysis of variance (ANOVA) was used to study spectral precision. The large particles (35 mesh) showed large variance between spectra, while fine particles (120 mesh) indicated good spectral precision based on the F-test. Force gauge setting did not significantly affect precision. Sample reloading using the fine particle size and a constant force gauge setting of 50 units also did not compromise precision. Based on these observations, data acquisition for the predictor matrix was carried out with the fine particles (sieve size opening of 120 mesh) at a constant force gauge setting of 50 units. After removing outliers, PCA successfully classified the five samples in the first and second components, accounting for 45.0% and 24.5% of the variances, respectively. The four-component PLS-DA model (R(2)=0.925 and Q(2)=0.906) gave good test spectra predictions with an overall average of 0.961 +/- 7.1% RSD versus the expected 1.0 prediction for the 20 test spectra used.

Wind-tunnel investigation of the powered low-speed longitudinal aerodynamics of the Vectored-Engine-Over (VEO) wing fighter configuration

NASA Technical Reports Server (NTRS)

Paulson, J. W.; Whitten, P. D.; Stumpfl, S. C.

1982-01-01

A wind-tunnel investigation incorporating both static and wind-on testing was conducted in the Langley 4- by 7-Meter Tunnel to determine the effects of vectored thrust along with spanwise blowing on the low-speed aerodynamics of an advanced fighter configuration. Data were obtained over a large range of thrust coefficients corresponding to takeoff and landing thrust settings for many nozzle configurations. The complete set of static thrust data and the complete set of longitudinal aerodynamic data obtained in the investigation are presented. These data are intended for reference purposes and, therefore, are presented without analysis or comment. The analysis of the thrust-induced effects found in the investigation are not discussed.

Improvement in Generic Problem-Solving Abilities of Students by Use of Tutor-less Problem-Based Learning in a Large Classroom Setting

PubMed Central

Klegeris, Andis; Bahniwal, Manpreet; Hurren, Heather

2013-01-01

Problem-based learning (PBL) was originally introduced in medical education programs as a form of small-group learning, but its use has now spread to large undergraduate classrooms in various other disciplines. Introduction of new teaching techniques, including PBL-based methods, needs to be justified by demonstrating the benefits of such techniques over classical teaching styles. Previously, we demonstrated that introduction of tutor-less PBL in a large third-year biochemistry undergraduate class increased student satisfaction and attendance. The current study assessed the generic problem-solving abilities of students from the same class at the beginning and end of the term, and compared student scores with similar data obtained in three classes not using PBL. Two generic problem-solving tests of equal difficulty were administered such that students took different tests at the beginning and the end of the term. Blinded marking showed a statistically significant 13% increase in the test scores of the biochemistry students exposed to PBL, while no trend toward significant change in scores was observed in any of the control groups not using PBL. Our study is among the first to demonstrate that use of tutor-less PBL in a large classroom leads to statistically significant improvement in generic problem-solving skills of students. PMID:23463230

Probabilistic hazard assessment for skin sensitization potency by dose–response modeling using feature elimination instead of quantitative structure–activity relationships

PubMed Central

McKim, James M.; Hartung, Thomas; Kleensang, Andre; Sá-Rocha, Vanessa

2016-01-01

Supervised learning methods promise to improve integrated testing strategies (ITS), but must be adjusted to handle high dimensionality and dose–response data. ITS approaches are currently fueled by the increasing mechanistic understanding of adverse outcome pathways (AOP) and the development of tests reflecting these mechanisms. Simple approaches to combine skin sensitization data sets, such as weight of evidence, fail due to problems in information redundancy and high dimension-ality. The problem is further amplified when potency information (dose/response) of hazards would be estimated. Skin sensitization currently serves as the foster child for AOP and ITS development, as legislative pressures combined with a very good mechanistic understanding of contact dermatitis have led to test development and relatively large high-quality data sets. We curated such a data set and combined a recursive variable selection algorithm to evaluate the information available through in silico, in chemico and in vitro assays. Chemical similarity alone could not cluster chemicals’ potency, and in vitro models consistently ranked high in recursive feature elimination. This allows reducing the number of tests included in an ITS. Next, we analyzed with a hidden Markov model that takes advantage of an intrinsic inter-relationship among the local lymph node assay classes, i.e. the monotonous connection between local lymph node assay and dose. The dose-informed random forest/hidden Markov model was superior to the dose-naive random forest model on all data sets. Although balanced accuracy improvement may seem small, this obscures the actual improvement in misclassifications as the dose-informed hidden Markov model strongly reduced "false-negatives" (i.e. extreme sensitizers as non-sensitizer) on all data sets. PMID:26046447

Probabilistic hazard assessment for skin sensitization potency by dose-response modeling using feature elimination instead of quantitative structure-activity relationships.

PubMed

Luechtefeld, Thomas; Maertens, Alexandra; McKim, James M; Hartung, Thomas; Kleensang, Andre; Sá-Rocha, Vanessa

2015-11-01

Supervised learning methods promise to improve integrated testing strategies (ITS), but must be adjusted to handle high dimensionality and dose-response data. ITS approaches are currently fueled by the increasing mechanistic understanding of adverse outcome pathways (AOP) and the development of tests reflecting these mechanisms. Simple approaches to combine skin sensitization data sets, such as weight of evidence, fail due to problems in information redundancy and high dimensionality. The problem is further amplified when potency information (dose/response) of hazards would be estimated. Skin sensitization currently serves as the foster child for AOP and ITS development, as legislative pressures combined with a very good mechanistic understanding of contact dermatitis have led to test development and relatively large high-quality data sets. We curated such a data set and combined a recursive variable selection algorithm to evaluate the information available through in silico, in chemico and in vitro assays. Chemical similarity alone could not cluster chemicals' potency, and in vitro models consistently ranked high in recursive feature elimination. This allows reducing the number of tests included in an ITS. Next, we analyzed with a hidden Markov model that takes advantage of an intrinsic inter-relationship among the local lymph node assay classes, i.e. the monotonous connection between local lymph node assay and dose. The dose-informed random forest/hidden Markov model was superior to the dose-naive random forest model on all data sets. Although balanced accuracy improvement may seem small, this obscures the actual improvement in misclassifications as the dose-informed hidden Markov model strongly reduced " false-negatives" (i.e. extreme sensitizers as non-sensitizer) on all data sets. Copyright © 2015 John Wiley & Sons, Ltd.

A pragmatic cluster randomised controlled trial to evaluate the safety, clinical effectiveness, cost effectiveness and satisfaction with point of care testing in a general practice setting - rationale, design and baseline characteristics.

PubMed

Laurence, Caroline; Gialamas, Angela; Yelland, Lisa; Bubner, Tanya; Ryan, Philip; Willson, Kristyn; Glastonbury, Briony; Gill, Janice; Shephard, Mark; Beilby, Justin

2008-08-06

Point of care testing (PoCT) may be a useful adjunct in the management of chronic conditions in general practice (GP). The provision of pathology test results at the time of the consultation could lead to enhanced clinical management, better health outcomes, greater convenience and satisfaction for patients and general practitioners (GPs), and savings in costs and time. It could also result in inappropriate testing, increased consultations and poor health outcomes resulting from inaccurate results. Currently there are very few randomised controlled trials (RCTs) in GP that have investigated these aspects of PoCT. The Point of Care Testing in General Practice Trial (PoCT Trial) was an Australian Government funded multi-centre, cluster randomised controlled trial to determine the safety, clinical effectiveness, cost effectiveness and satisfaction of PoCT in a GP setting.The PoCT Trial covered an 18 month period with the intervention consisting of the use of PoCT for seven tests used in the management of patients with diabetes, hyperlipidaemia and patients on anticoagulant therapy. The primary outcome measure was the proportion of patients within target range, a measure of therapeutic control. In addition, the PoCT Trial investigated the safety of PoCT, impact of PoCT on patient compliance to medication, stakeholder satisfaction, cost effectiveness of PoCT versus laboratory testing, and influence of geographic location. The paper provides an overview of the Trial Design, the rationale for the research methodology chosen and how the Trial was implemented in a GP environment. The evaluation protocol and data collection processes took into account the large number of patients, the broad range of practice types distributed over a large geographic area, and the inclusion of pathology test results from multiple pathology laboratories.The evaluation protocol developed reflects the complexity of the Trial setting, the Trial Design and the approach taken within the funding provided. The PoCT Trial is regarded as a pragmatic RCT, evaluating the effectiveness of implementing PoCT in GP and every effort was made to ensure that, in these circumstances, internal and external validity was maintained. 12612605000272695.

Assessment of thermal spray coatings for wear and abrasion resistance applications

NASA Astrophysics Data System (ADS)

Karode, Ishaan Nitin

Thermal spray cermet and metallic coatings are extensively used for wear, abrasion and corrosion control in a variety of industries. The first part of the thesis focuses mainly on testing of sand erosion resistance of thermal spray coatings on carbon composites used in the manufacture of helicopter rotor blades. The test set-up employed is a sand blasting machine and is an effort to duplicate the in-flight conditions especially those encountered in hot arid conditions. The technique adopted follows the Department of Defence test method standard. Carbon Composites have excellent stiffness, strength and low weight/density. The strength to weight ratio is high. Hence, these are used in aerospace applications to a large extent. However, the biggest problem encountered with carbon composites is its low abrasion resistance as its surface is very weak. Hence, thermal spray coatings are used to improve the surface properties of CFRP. Zinc bond coats and WC-Co coatings were tested. However, high amount of thermal stresses were developed between the substrate and the coating due to large differences in the CTE's of the both, leading to high mass losses within two minutes and just 130 grams of sand sprayed on to the coatings with the sand blasting machine built; and hence the coatings with CC as a substrate could not qualify for the application. The second part of the thesis focuses on the assessment of different thermal spray coatings used for manufacture of mechanical seals in pumps and analyze the best coating material for the wear resistance application through detail quantification of material loss by block-on-ring test set-up. A machine based on Block-on-ring test set-up following ASTM G77 (Measurement of Adhesive wear resistance of thermal spray coatings) standards was built to duplicate the pump conditions. Thermally sprayed coated materials were tested in different conditions (Load, time, abrasive). WC-Co had the highest wear resistance (lower volume losses) and proved to be the best coating amongst all the other ones followed by Cr2O3 and Al2O3 in deionized water. In the presence of abrasive alumina slurry WC-Co offered the highest abrasive resistance with the lowest volume losses followed by Al2O3 and Cr2O3. In both the testing conditions B4C coating showed lower wear/abrasion resistance giving the highest volume losses.

Machine learning of molecular properties: Locality and active learning

NASA Astrophysics Data System (ADS)

Gubaev, Konstantin; Podryabinkin, Evgeny V.; Shapeev, Alexander V.

2018-06-01

In recent years, the machine learning techniques have shown great potent1ial in various problems from a multitude of disciplines, including materials design and drug discovery. The high computational speed on the one hand and the accuracy comparable to that of density functional theory on another hand make machine learning algorithms efficient for high-throughput screening through chemical and configurational space. However, the machine learning algorithms available in the literature require large training datasets to reach the chemical accuracy and also show large errors for the so-called outliers—the out-of-sample molecules, not well-represented in the training set. In the present paper, we propose a new machine learning algorithm for predicting molecular properties that addresses these two issues: it is based on a local model of interatomic interactions providing high accuracy when trained on relatively small training sets and an active learning algorithm of optimally choosing the training set that significantly reduces the errors for the outliers. We compare our model to the other state-of-the-art algorithms from the literature on the widely used benchmark tests.

Special ergodic theorems and dynamical large deviations

NASA Astrophysics Data System (ADS)

Kleptsyn, Victor; Ryzhov, Dmitry; Minkov, Stanislav

2012-11-01

Let f : M → M be a self-map of a compact Riemannian manifold M, admitting a global SRB measure μ. For a continuous test function \\varphi\\colon M\\to R and a constant α > 0, consider the set Kφ,α of the initial points for which the Birkhoff time averages of the function φ differ from its μ-space average by at least α. As the measure μ is a global SRB one, the set Kφ,α should have zero Lebesgue measure. The special ergodic theorem, whenever it holds, claims that, moreover, this set has a Hausdorff dimension less than the dimension of M. We prove that for Lipschitz maps, the special ergodic theorem follows from the dynamical large deviations principle. We also define and prove analogous result for flows. Applying the theorems of Young and of Araújo and Pacifico, we conclude that the special ergodic theorem holds for transitive hyperbolic attractors of C2-diffeomorphisms, as well as for some other known classes of maps (including the one of partially hyperbolic non-uniformly expanding maps) and flows.

Understanding the heavy-tailed dynamics in human behavior

NASA Astrophysics Data System (ADS)

Ross, Gordon J.; Jones, Tim

2015-06-01

The recent availability of electronic data sets containing large volumes of communication data has made it possible to study human behavior on a larger scale than ever before. From this, it has been discovered that across a diverse range of data sets, the interevent times between consecutive communication events obey heavy-tailed power law dynamics. Explaining this has proved controversial, and two distinct hypotheses have emerged. The first holds that these power laws are fundamental, and arise from the mechanisms such as priority queuing that humans use to schedule tasks. The second holds that they are statistical artifacts which only occur in aggregated data when features such as circadian rhythms and burstiness are ignored. We use a large social media data set to test these hypotheses, and find that although models that incorporate circadian rhythms and burstiness do explain part of the observed heavy tails, there is residual unexplained heavy-tail behavior which suggests a more fundamental cause. Based on this, we develop a quantitative model of human behavior which improves on existing approaches and gives insight into the mechanisms underlying human interactions.

Predicting who will drop out of nursing courses: a machine learning exercise.

PubMed

Moseley, Laurence G; Mead, Donna M

2008-05-01

The concepts of causation and prediction are different, and have different implications for practice. This distinction is applied here to studies of the problem of student attrition (although it is more widely applicable). Studies of attrition from nursing courses have tended to concentrate on causation, trying, largely unsuccessfully, to elicit what causes drop out. However, the problem may more fruitfully be cast in terms of predicting who is likely to drop out. One powerful method for attempting to make predictions is rule induction. This paper reports the use of the Answer Tree package from SPSS for that purpose. The main data set consisted of 3978 records on 528 nursing students, split into a training set and a test set. The source was standard university student records. The method obtained 84% sensitivity, 70% specificity, and 94% accuracy on previously unseen cases. The method requires large amounts of high quality data. When such data are available, rule induction offers a way to reduce attrition. It would be desirable to compare its results with those of predictions made by tutors using more informal conventional methods.

Search for diphoton events with large missing transverse energy with 36 pb –1 of 7 TeV proton–proton collision data with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2011-10-05

Making use of 36 pb –1 of proton–proton collision data at √s = 7 TeV, the ATLAS Collaboration has performed a search for diphoton events with large missing transverse energy. Observing no excess of events above the Standard Model prediction, a 95% Confidence Level (CL) upper limit is set on the cross section for new physics of σ<0.38–0.65 pb in the context of a generalised model of gauge-mediated supersymmetry breaking (GGM) with a bino-like lightest neutralino, and of σ<0.18–0.23 pb in the context of a specific model with one universal extra dimension (UED). A 95% CL lower limit of 560more » GeV, for bino masses above 50 GeV, is set on the GGM gluino mass, while a lower limit of 1/ R>961 GeV is set on the UED compactification radius R. In conclusion, these limits provide the most stringent tests of these models to date.« less

HIV testing in dermatology - a national audit.

PubMed

Esson, Gavin A; Holme, S A

2018-05-01

Forty percent of individuals have late-stage HIV at the time of diagnosis, resulting in increased morbidity. Identifying key diseases which may indicate HIV infection can prompt clinicians to trigger testing, which may result in more timely diagnosis. The British HIV Association has published guidelines on such indicator diseases in dermatology. We audited the practice of HIV testing in UK dermatologists and General Practitioners (GPs) and compared results with the national guidelines. This audit showed that HIV testing in key indicator diseases remains below the standard set out by the national guidelines, and that GPs with special interest in dermatology have a lower likelihood for testing, and lower confidence when compared to consultants, registrars and associate specialists. Large proportions of respondents believed further training in HIV testing would be beneficial.

Application of physical parameter identification to finite-element models

NASA Technical Reports Server (NTRS)

Bronowicki, Allen J.; Lukich, Michael S.; Kuritz, Steven P.

1987-01-01

The time domain parameter identification method described previously is applied to TRW's Large Space Structure Truss Experiment. Only control sensors and actuators are employed in the test procedure. The fit of the linear structural model to the test data is improved by more than an order of magnitude using a physically reasonable parameter set. The electro-magnetic control actuators are found to contribute significant damping due to a combination of eddy current and back electro-motive force (EMF) effects. Uncertainties in both estimated physical parameters and modal behavior variables are given.

Development and evaluation of an automatic labeling technique for spring small grains

NASA Technical Reports Server (NTRS)

Crist, E. P.; Malila, W. A. (Principal Investigator)

1981-01-01

A labeling technique is described which seeks to associate a sampling entity with a particular crop or crop group based on similarity of growing season and temporal-spectral patterns of development. Human analyst provide contextual information, after which labeling decisions are made automatically. Results of a test of the technique on a large, multi-year data set are reported. Grain labeling accuracies are similar to those achieved by human analysis techniques, while non-grain accuracies are lower. Recommendations for improvments and implications of the test results are discussed.

Slicing of silicon into sheet material. Silicon sheet growth development for the large area silicon sheet task of the low cost silicon solar array project

NASA Technical Reports Server (NTRS)

Holden, S. C.; Fleming, J. R.

1978-01-01

Fabrication of a prototype large capacity multiple blade slurry saw is considered. Design of the bladehead which will tension up to 1000 blades, and cut a 45 cm long silicon ingot as large as 12 cm in diameter is given. The large blade tensioning force of 270,000 kg is applied through two bolts acting on a pair of scissor toggles, significantly reducing operator set-up time. Tests with an upside-down cutting technique resulted in 100% wafering yields and the highest wafer accuracy yet experienced with MS slicing. Variations in oil and abrasives resulted only in degraded slicing results. A technique of continuous abrasive slurry separation to remove silicon debris is described.

Testing the robustness of Citizen Science projects: Evaluating the results of pilot project COMBER.

PubMed

Chatzigeorgiou, Giorgos; Faulwetter, Sarah; Dailianis, Thanos; Smith, Vincent Stuart; Koulouri, Panagiota; Dounas, Costas; Arvanitidis, Christos

2016-01-01

Citizen Science (CS) as a term implies a great deal of approaches and scopes involving many different fields of science. The number of the relevant projects globally has been increased significantly in the recent years. Large scale ecological questions can be answered only through extended observation networks and CS projects can support this effort. Although the need of such projects is apparent, an important part of scientific community cast doubt on the reliability of CS data sets. The pilot CS project COMBER has been created in order to provide evidence to answer the aforementioned question in the coastal marine biodiversity monitoring. The results of the current analysis show that a carefully designed CS project with clear hypotheses, wide participation and data sets validation, can be a valuable tool for the large scale and long term changes in marine biodiversity pattern change and therefore for relevant management and conservation issues.

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

PubMed

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease

PubMed Central

Lambert, Jean-Charles; Ibrahim-Verbaas, Carla A; Harold, Denise; Naj, Adam C; Sims, Rebecca; Bellenguez, Céline; Jun, Gyungah; DeStefano, Anita L; Bis, Joshua C; Beecham, Gary W; Grenier-Boley, Benjamin; Russo, Giancarlo; Thornton-Wells, Tricia A; Jones, Nicola; Smith, Albert V; Chouraki, Vincent; Thomas, Charlene; Ikram, M Arfan; Zelenika, Diana; Vardarajan, Badri N; Kamatani, Yoichiro; Lin, Chiao-Feng; Gerrish, Amy; Schmidt, Helena; Kunkle, Brian; Dunstan, Melanie L; Ruiz, Agustin; Bihoreau, Marie-Thérèse; Choi, Seung-Hoan; Reitz, Christiane; Pasquier, Florence; Hollingworth, Paul; Ramirez, Alfredo; Hanon, Olivier; Fitzpatrick, Annette L; Buxbaum, Joseph D; Campion, Dominique; Crane, Paul K; Baldwin, Clinton; Becker, Tim; Gudnason, Vilmundur; Cruchaga, Carlos; Craig, David; Amin, Najaf; Berr, Claudine; Lopez, Oscar L; De Jager, Philip L; Deramecourt, Vincent; Johnston, Janet A; Evans, Denis; Lovestone, Simon; Letenneur, Luc; Morón, Francisco J; Rubinsztein, David C; Eiriksdottir, Gudny; Sleegers, Kristel; Goate, Alison M; Fiévet, Nathalie; Huentelman, Matthew J; Gill, Michael; Brown, Kristelle; Kamboh, M Ilyas; Keller, Lina; Barberger-Gateau, Pascale; McGuinness, Bernadette; Larson, Eric B; Green, Robert; Myers, Amanda J; Dufouil, Carole; Todd, Stephen; Wallon, David; Love, Seth; Rogaeva, Ekaterina; Gallacher, John; St George-Hyslop, Peter; Clarimon, Jordi; Lleo, Alberto; Bayer, Anthony; Tsuang, Debby W; Yu, Lei; Tsolaki, Magda; Bossù, Paola; Spalletta, Gianfranco; Proitsi, Petroula; Collinge, John; Sorbi, Sandro; Sanchez-Garcia, Florentino; Fox, Nick C; Hardy, John; Deniz Naranjo, Maria Candida; Bosco, Paolo; Clarke, Robert; Brayne, Carol; Galimberti, Daniela; Mancuso, Michelangelo; Matthews, Fiona; Moebus, Susanne; Mecocci, Patrizia; Zompo, Maria Del; Maier, Wolfgang; Hampel, Harald; Pilotto, Alberto; Bullido, Maria; Panza, Francesco; Caffarra, Paolo; Nacmias, Benedetta; Gilbert, John R; Mayhaus, Manuel; Lannfelt, Lars; Hakonarson, Hakon; Pichler, Sabrina; Carrasquillo, Minerva M; Ingelsson, Martin; Beekly, Duane; Alvarez, Victoria; Zou, Fanggeng; Valladares, Otto; Younkin, Steven G; Coto, Eliecer; Hamilton-Nelson, Kara L; Gu, Wei; Razquin, Cristina; Pastor, Pau; Mateo, Ignacio; Owen, Michael J; Faber, Kelley M; Jonsson, Palmi V; Combarros, Onofre; O’Donovan, Michael C; Cantwell, Laura B; Soininen, Hilkka; Blacker, Deborah; Mead, Simon; Mosley, Thomas H; Bennett, David A; Harris, Tamara B; Fratiglioni, Laura; Holmes, Clive; de Bruijn, Renee F A G; Passmore, Peter; Montine, Thomas J; Bettens, Karolien; Rotter, Jerome I; Brice, Alexis; Morgan, Kevin; Foroud, Tatiana M; Kukull, Walter A; Hannequin, Didier; Powell, John F; Nalls, Michael A; Ritchie, Karen; Lunetta, Kathryn L; Kauwe, John S K; Boerwinkle, Eric; Riemenschneider, Matthias; Boada, Mercè; Hiltunen, Mikko; Martin, Eden R; Schmidt, Reinhold; Rujescu, Dan; Wang, Li-san; Dartigues, Jean-François; Mayeux, Richard; Tzourio, Christophe; Hofman, Albert; Nöthen, Markus M; Graff, Caroline; Psaty, Bruce M; Jones, Lesley; Haines, Jonathan L; Holmans, Peter A; Lathrop, Mark; Pericak-Vance, Margaret A; Launer, Lenore J; Farrer, Lindsay A; van Duijn, Cornelia M; Van Broeckhoven, Christine; Moskvina, Valentina; Seshadri, Sudha; Williams, Julie; Schellenberg, Gerard D; Amouyel, Philippe

2013-01-01

Eleven susceptibility loci for late-onset Alzheimer’s disease (LOAD) were identified by previous studies; however, a large portion of the genetic risk for this disease remains unexplained. We conducted a large, two-stage meta-analysis of genome-wide association studies (GWAS) in individuals of European ancestry. In stage 1, we used genotyped and imputed data (7,055,881 SNPs) to perform meta-analysis on 4 previously published GWAS data sets consisting of 17,008 Alzheimer’s disease cases and 37,154 controls. In stage 2,11,632 SNPs were genotyped and tested for association in an independent set of 8,572 Alzheimer’s disease cases and 11,312 controls. In addition to the APOE locus (encoding apolipoprotein E), 19 loci reached genome-wide significance (P < 5 × 10−8) in the combined stage 1 and stage 2 analysis, of which 11 are newly associated with Alzheimer’s disease. PMID:24162737

Incremental wind tunnel testing of high lift systems

NASA Astrophysics Data System (ADS)

Victor, Pricop Mihai; Mircea, Boscoianu; Daniel-Eugeniu, Crunteanu

2016-06-01

Efficiency of trailing edge high lift systems is essential for long range future transport aircrafts evolving in the direction of laminar wings, because they have to compensate for the low performance of the leading edge devices. Modern high lift systems are subject of high performance requirements and constrained to simple actuation, combined with a reduced number of aerodynamic elements. Passive or active flow control is thus required for the performance enhancement. An experimental investigation of reduced kinematics flap combined with passive flow control took place in a low speed wind tunnel. The most important features of the experimental setup are the relatively large size, corresponding to a Reynolds number of about 2 Million, the sweep angle of 30 degrees corresponding to long range airliners with high sweep angle wings and the large number of flap settings and mechanical vortex generators. The model description, flap settings, methodology and results are presented.

A new parallel algorithm of MP2 energy calculations.

PubMed

Ishimura, Kazuya; Pulay, Peter; Nagase, Shigeru

2006-03-01

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

A multilayer membrane amperometric glucose sensor fabricated using planar techniques for large-scale production.

PubMed

Matsumoto, T; Saito, S; Ikeda, S

2006-03-23

This paper reports on a multilayer membrane amperometric glucose sensor fabricated using planar techniques. It is characterized by good reproducibility and suitable for large-scale production. The glucose sensor has 82 electrode sets formed on a single glass substrate, each with a platinum working electrode (WE), a platinum counter electrode (CE) and an Ag/AgCl reference electrode (RE). The electrode sets are coated with a membrane consisting of five layers: gamma-aminopropyltriethoxysilane (gamma-APTES), Nafion, glucose oxidase (GOX), gamma-APTES and perfluorocarbon polymer (PFCP), in that order. Tests have shown that the sensor has acceptably low dispersion (relative standard deviation, R.S.D.=42.9%, n=82), a wide measurement range (1.11-111 mM) and measurement stability over a 27-day period. Measurements of the glucose concentration in a control human urine sample demonstrated that the sensor has very low dispersion (R.S.D.=2.49%, n=10).

Using Browser Notebooks to Analyse Big Atmospheric Data-sets in the Cloud

NASA Astrophysics Data System (ADS)

Robinson, N.; Tomlinson, J.; Arribas, A.; Prudden, R.

2016-12-01

We are presenting an account of our experience building an ecosystem for the analysis of big atmospheric data-sets. By using modern technologies we have developed a prototype platform which is scaleable and capable of analysing very large atmospheric datasets. We tested different big-data ecosystems such as Hadoop MapReduce, Spark and Dask, in order to find the one which was best suited for analysis of multidimensional binary data such as NetCDF. We make extensive use of infrastructure-as-code and containerisation to provide a platform which is reusable, and which can scale to accommodate changes in demand. We make this platform readily accessible using browser based notebooks. As a result, analysts with minimal technology experience can, in tens of lines of Python, make interactive data-visualisation web pages, which can analyse very large amounts of data using cutting edge big-data technology

Development and Validation of Various Phenotyping Algorithms for Diabetes Mellitus Using Data from Electronic Health Records.

PubMed

Esteban, Santiago; Rodríguez Tablado, Manuel; Peper, Francisco; Mahumud, Yamila S; Ricci, Ricardo I; Kopitowski, Karin; Terrasa, Sergio

2017-01-01

Precision medicine requires extremely large samples. Electronic health records (EHR) are thought to be a cost-effective source of data for that purpose. Phenotyping algorithms help reduce classification errors, making EHR a more reliable source of information for research. Four algorithm development strategies for classifying patients according to their diabetes status (diabetics; non-diabetics; inconclusive) were tested (one codes-only algorithm; one boolean algorithm, four statistical learning algorithms and six stacked generalization meta-learners). The best performing algorithms within each strategy were tested on the validation set. The stacked generalization algorithm yielded the highest Kappa coefficient value in the validation set (0.95 95% CI 0.91, 0.98). The implementation of these algorithms allows for the exploitation of data from thousands of patients accurately, greatly reducing the costs of constructing retrospective cohorts for research.

Contextual classification on the massively parallel processor

NASA Technical Reports Server (NTRS)

Tilton, James C.

1987-01-01

Classifiers are often used to produce land cover maps from multispectral Earth observation imagery. Conventionally, these classifiers have been designed to exploit the spectral information contained in the imagery. Very few classifiers exploit the spatial information content of the imagery, and the few that do rarely exploit spatial information content in conjunction with spectral and/or temporal information. A contextual classifier that exploits spatial and spectral information in combination through a general statistical approach was studied. Early test results obtained from an implementation of the classifier on a VAX-11/780 minicomputer were encouraging, but they are of limited meaning because they were produced from small data sets. An implementation of the contextual classifier is presented on the Massively Parallel Processor (MPP) at Goddard that for the first time makes feasible the testing of the classifier on large data sets.

Energetics and dynamics of simple impulsive solar flares

NASA Technical Reports Server (NTRS)

Starr, R.; Heindl, W. A.; Crannell, C. J.; Thomas, R. J.; Batchelor, D. A.; Magun, A.

1987-01-01

Flare energetics and dynamics were studied using observations of simple impulsive spike bursts. A large, homogeneous set of events was selected to enable the most definite tests possible of competing flare models, in the absence of spatially resolved observations. The emission mechanisms and specific flare models that were considered in this investigation are described, and the derivations of the parameters that were tested are presented. Results of the correlation analysis between soft and hard X-ray energetics are also presented. The ion conduction front model and tests of that model with the well-observed spike bursts are described. Finally, conclusions drawn from this investigation and suggestions for future studies are discussed.

Are there two processes in reasoning? The dimensionality of inductive and deductive inferences.

PubMed

Stephens, Rachel G; Dunn, John C; Hayes, Brett K

2018-03-01

Single-process accounts of reasoning propose that the same cognitive mechanisms underlie inductive and deductive inferences. In contrast, dual-process accounts propose that these inferences depend upon 2 qualitatively different mechanisms. To distinguish between these accounts, we derived a set of single-process and dual-process models based on an overarching signal detection framework. We then used signed difference analysis to test each model against data from an argument evaluation task, in which induction and deduction judgments are elicited for sets of valid and invalid arguments. Three data sets were analyzed: data from Singmann and Klauer (2011), a database of argument evaluation studies, and the results of an experiment designed to test model predictions. Of the large set of testable models, we found that almost all could be rejected, including all 2-dimensional models. The only testable model able to account for all 3 data sets was a model with 1 dimension of argument strength and independent decision criteria for induction and deduction judgments. We conclude that despite the popularity of dual-process accounts, current results from the argument evaluation task are best explained by a single-process account that incorporates separate decision thresholds for inductive and deductive inferences. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The limitations of simple gene set enrichment analysis assuming gene independence.

PubMed

Tamayo, Pablo; Steinhardt, George; Liberzon, Arthur; Mesirov, Jill P

2016-02-01

Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods. © The Author(s) 2012.

Experimental and numerical investigation of the nonlinear dynamics of compliant mechanisms for deployable structures

NASA Astrophysics Data System (ADS)

Dewalque, Florence; Schwartz, Cédric; Denoël, Vincent; Croisier, Jean-Louis; Forthomme, Bénédicte; Brüls, Olivier

2018-02-01

This paper studies the dynamics of tape springs which are characterised by a highly geometrical nonlinear behaviour including buckling, the formation of folds and hysteresis. An experimental set-up is designed to capture these complex nonlinear phenomena. The experimental data are acquired by the means of a 3D motion analysis system combined with a synchronised force plate. Deployment tests show that the motion can be divided into three phases characterised by different types of folds, frequencies of oscillation and damping behaviours. Furthermore, the reproducibility quality of the dynamic and quasi-static results is validated by performing a large number of tests. In parallel, a nonlinear finite element model is developed. The required model parameters are identified based on simple experimental tests such as static deformed configurations and small amplitude vibration tests. In the end, the model proves to be well correlated with the experimental results in opposite sense bending, while in equal sense, both the experimental set-up and the numerical model are particularly sensitive to the initial conditions.

Establishing a successful HIV counseling and testing service. A blueprint for preventing pediatric HIV infections and translating research into clinical practice.

PubMed

Rips, J

1997-12-01

The findings of ACTG 076 have already resulted in local, state, and federal legislative initiatives targeted at pregnant and post-partum women and their newborns. This article advises clinicians and administrations on setting up successful voluntary prenatal HIV counseling and testing programs for early detection of HIV infection, and complying with the burgeoning array of legislative directives. Over the past several years their have been attempts to optimize and evaluate testing programs--perinatal ZDV counseling and administration of ZDV--and to link HIV-infected women with care in academic, community, and municipal hospitals. The suggestions are, therefore, broad enough to be applicable to a full array of clinical practices, from a private single provider office to a large hospital-based prenatal clinic. It is hoped that the models presented in this article can be replicated in diverse settings, and that readers can avoid the pitfalls and barriers sometimes encountered.

Aerodynamics of an Axisymmetric Missile Concept Having Cruciform Strakes and In-Line Tail Fins From Mach 0.60 to 4.63

NASA Technical Reports Server (NTRS)

Allen, Jerry M.

2005-01-01

An experimental study has been performed to develop a large force and moment aerodynamic data set on a slender axisymmetric missile configuration having cruciform strakes and in-line control tail fins. The data include six-component balance measurements of the configuration aerodynamics and three-component measurements on all four tail fins. The test variables include angle of attack, roll angle, Mach number, model buildup, strake length, nose size, and tail fin deflection angles to provide pitch, yaw, and roll control. Test Mach numbers ranged from 0.60 to 4.63. The entire data set is presented on a CD-ROM that is attached to this paper. The CD-ROM also includes extensive plots of both the six-component configuration data and the three-component tail fin data. Selected samples of these plots are presented in this paper to illustrate the features of the data and to investigate the effects of the test variables.

Aerodynamics of an Axisymmetric Missile Concept Having Cruciform Strakes and In-Line Tail Fins From Mach 0.60 to 4.63, Supplement

NASA Technical Reports Server (NTRS)

Allen, Jerry M.

2005-01-01

An experimental study has been performed to develop a large force and moment aerodynamic data set on a slender axisymmetric missile configuration having cruciform strakes and in-line control tail fins. The data include six-component balance measurements of the configuration aerodynamics and three-component measurements on all four tail fins. The test variables include angle of attack, roll angle, Mach number, model buildup, strake length, nose size, and tail fin deflection angles to provide pitch, yaw, and roll control. Test Mach numbers ranged from 0.60 to 4.63. The entire data set is presented on a CD-ROM that is attached to this paper. The CD-ROM also includes extensive plots of both the six-component configuration data and the three-component tail fin data. Selected samples of these plots are presented in this paper to illustrate the features of the data and to investigate the effects of the test variables.

Platelet Aggregometry Testing: Molecular Mechanisms, Techniques and Clinical Implications

PubMed Central

Koltai, Katalin; Kesmarky, Gabor; Feher, Gergely; Tibold, Antal

2017-01-01

Platelets play a fundamental role in normal hemostasis, while their inherited or acquired dysfunctions are involved in a variety of bleeding disorders or thrombotic events. Several laboratory methodologies or point-of-care testing methods are currently available for clinical and experimental settings. These methods describe different aspects of platelet function based on platelet aggregation, platelet adhesion, the viscoelastic properties during clot formation, the evaluation of thromboxane metabolism or certain flow cytometry techniques. Platelet aggregometry is applied in different clinical settings as monitoring response to antiplatelet therapies, the assessment of perioperative bleeding risk, the diagnosis of inherited bleeding disorders or in transfusion medicine. The rationale for platelet function-driven antiplatelet therapy was based on the result of several studies on patients undergoing percutaneous coronary intervention (PCI), where an association between high platelet reactivity despite P2Y12 inhibition and ischemic events as stent thrombosis or cardiovascular death was found. However, recent large scale randomized, controlled trials have consistently failed to demonstrate a benefit of personalised antiplatelet therapy based on platelet function testing. PMID:28820484

A regional test of global models for flow, rheology, and seismic anisotropy at the base of the mantle

NASA Astrophysics Data System (ADS)

Ford, Heather A.; Long, Maureen D.

2015-08-01

The study of flow patterns and seismic anisotropy in the lowermost mantle is fraught with uncertainties, given the limitations in our understanding of the physical properties of the lowermost mantle and the relationships between deformation and anisotropy. Here we use a set of SKS, SKKS, and ScS splitting measurements that sample the eastern edge of the African Large Low Shear Velocity Province to test predictions of seismic anisotropy derived from previously published 3D global mantle flow models and anisotropy modeling (Walker et al., 2011). The observations can be fit by a model that invokes flow directed to the southwest with a component of downwelling in our study region, and slip that occurs along the (0 1 0) plane of post-perovskite. Most importantly, we demonstrate the ability of a regional shear wave splitting data set to test the robustness of models for flow and deformation in the lowermost mantle.

Combining deep learning and level set for the automated segmentation of the left ventricle of the heart from cardiac cine magnetic resonance.

PubMed

Ngo, Tuan Anh; Lu, Zhi; Carneiro, Gustavo

2017-01-01

We introduce a new methodology that combines deep learning and level set for the automated segmentation of the left ventricle of the heart from cardiac cine magnetic resonance (MR) data. This combination is relevant for segmentation problems, where the visual object of interest presents large shape and appearance variations, but the annotated training set is small, which is the case for various medical image analysis applications, including the one considered in this paper. In particular, level set methods are based on shape and appearance terms that use small training sets, but present limitations for modelling the visual object variations. Deep learning methods can model such variations using relatively small amounts of annotated training, but they often need to be regularised to produce good generalisation. Therefore, the combination of these methods brings together the advantages of both approaches, producing a methodology that needs small training sets and produces accurate segmentation results. We test our methodology on the MICCAI 2009 left ventricle segmentation challenge database (containing 15 sequences for training, 15 for validation and 15 for testing), where our approach achieves the most accurate results in the semi-automated problem and state-of-the-art results for the fully automated challenge. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Scanning electron microscope comparative surface evaluation of glazed-lithium disilicate ceramics under different irradiation settings of Nd:YAG and Er:YAG lasers.

PubMed

Viskic, Josko; Jokic, Drazen; Jakovljevic, Suzana; Bergman, Lana; Ortolan, Sladana Milardovic; Mestrovic, Senka; Mehulic, Ketij

2018-01-01

To evaluate the surface of glazed lithium disilicate dental ceramics after irradiation under different irradiation settings of Nd:YAG and Er:YAG lasers using a scanning electron microscope (SEM). Three glazed-press lithium disilicate ceramic discs were treated with HF, Er:YAG, and Nd:YAG, respectively. The laser-setting variables tested were laser mode, repetition rate (Hz), power (W), time of exposure (seconds), and laser energy (mJ). Sixteen different variable settings were tested for each laser type, and all the samples were analyzed by SEM at 500× and 1000× magnification. Surface analysis of the HF-treated sample showed a typical surface texture with a homogenously rough pattern and exposed ceramic crystals. Er:YAG showed no effect on the surface under any irradiation setting. The surface of Nd:YAG-irradiated samples showed cracking, melting, and resolidifying of the ceramic glaze. These changes became more pronounced as the power increased. At the highest power setting (2.25 W), craters on the surface with large areas of melted or resolidified glaze surrounded by globules were visible. However, there was little to no exposure of ceramic crystals or visible regular surface roughening. Neither Er:YAG nor Nd:YAG dental lasers exhibited adequate surface modification for bonding of orthodontic brackets on glazed lithium disilicate ceramics compared with the control treated with 9.5% HF.

Scramjet test flow reconstruction for a large-scale expansion tube, Part 2: axisymmetric CFD analysis

NASA Astrophysics Data System (ADS)

Gildfind, D. E.; Jacobs, P. A.; Morgan, R. G.; Chan, W. Y. K.; Gollan, R. J.

2018-07-01

This paper presents the second part of a study aiming to accurately characterise a Mach 10 scramjet test flow generated using a large free-piston-driven expansion tube. Part 1 described the experimental set-up, the quasi-one-dimensional simulation of the full facility, and the hybrid analysis technique used to compute the nozzle exit test flow properties. The second stage of the hybrid analysis applies the computed 1-D shock tube flow history as an inflow to a high-fidelity two-dimensional-axisymmetric analysis of the acceleration tube. The acceleration tube exit flow history is then applied as an inflow to a further refined axisymmetric nozzle model, providing the final nozzle exit test flow properties and thereby completing the analysis. This paper presents the results of the axisymmetric analyses. These simulations are shown to closely reproduce experimentally measured shock speeds and acceleration tube static pressure histories, as well as nozzle centreline static and impact pressure histories. The hybrid scheme less successfully predicts the diameter of the core test flow; however, this property is readily measured through experimental pitot surveys. In combination, the full test flow history can be accurately determined.

Scramjet test flow reconstruction for a large-scale expansion tube, Part 2: axisymmetric CFD analysis

NASA Astrophysics Data System (ADS)

Gildfind, D. E.; Jacobs, P. A.; Morgan, R. G.; Chan, W. Y. K.; Gollan, R. J.

2017-11-01

This paper presents the second part of a study aiming to accurately characterise a Mach 10 scramjet test flow generated using a large free-piston-driven expansion tube. Part 1 described the experimental set-up, the quasi-one-dimensional simulation of the full facility, and the hybrid analysis technique used to compute the nozzle exit test flow properties. The second stage of the hybrid analysis applies the computed 1-D shock tube flow history as an inflow to a high-fidelity two-dimensional-axisymmetric analysis of the acceleration tube. The acceleration tube exit flow history is then applied as an inflow to a further refined axisymmetric nozzle model, providing the final nozzle exit test flow properties and thereby completing the analysis. This paper presents the results of the axisymmetric analyses. These simulations are shown to closely reproduce experimentally measured shock speeds and acceleration tube static pressure histories, as well as nozzle centreline static and impact pressure histories. The hybrid scheme less successfully predicts the diameter of the core test flow; however, this property is readily measured through experimental pitot surveys. In combination, the full test flow history can be accurately determined.

Statistical Searches for Microlensing Events in Large, Non-uniformly Sampled Time-Domain Surveys: A Test Using Palomar Transient Factory Data

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.; Agüeros, Marcel A.; Fournier, Amanda P.; Street, Rachel; Ofek, Eran O.; Covey, Kevin R.; Levitan, David; Laher, Russ R.; Sesar, Branimir; Surace, Jason

2014-01-01

Many photometric time-domain surveys are driven by specific goals, such as searches for supernovae or transiting exoplanets, which set the cadence with which fields are re-imaged. In the case of the Palomar Transient Factory (PTF), several sub-surveys are conducted in parallel, leading to non-uniform sampling over its ~20,000 deg2 footprint. While the median 7.26 deg2 PTF field has been imaged ~40 times in the R band, ~2300 deg2 have been observed >100 times. We use PTF data to study the trade off between searching for microlensing events in a survey whose footprint is much larger than that of typical microlensing searches, but with far-from-optimal time sampling. To examine the probability that microlensing events can be recovered in these data, we test statistics used on uniformly sampled data to identify variables and transients. We find that the von Neumann ratio performs best for identifying simulated microlensing events in our data. We develop a selection method using this statistic and apply it to data from fields with >10 R-band observations, 1.1 × 109 light curves, uncovering three candidate microlensing events. We lack simultaneous, multi-color photometry to confirm these as microlensing events. However, their number is consistent with predictions for the event rate in the PTF footprint over the survey's three years of operations, as estimated from near-field microlensing models. This work can help constrain all-sky event rate predictions and tests microlensing signal recovery in large data sets, which will be useful to future time-domain surveys, such as that planned with the Large Synoptic Survey Telescope.

Large Scale Flame Spread Environmental Characterization Testing

NASA Technical Reports Server (NTRS)

Clayman, Lauren K.; Olson, Sandra L.; Gokoghi, Suleyman A.; Brooker, John E.; Ferkul, Paul V.; Kacher, Henry F.

2013-01-01

Under the Advanced Exploration Systems (AES) Spacecraft Fire Safety Demonstration Project (SFSDP), as a risk mitigation activity in support of the development of a large-scale fire demonstration experiment in microgravity, flame-spread tests were conducted in normal gravity on thin, cellulose-based fuels in a sealed chamber. The primary objective of the tests was to measure pressure rise in a chamber as sample material, burning direction (upward/downward), total heat release, heat release rate, and heat loss mechanisms were varied between tests. A Design of Experiments (DOE) method was imposed to produce an array of tests from a fixed set of constraints and a coupled response model was developed. Supplementary tests were run without experimental design to additionally vary select parameters such as initial chamber pressure. The starting chamber pressure for each test was set below atmospheric to prevent chamber overpressure. Bottom ignition, or upward propagating burns, produced rapid acceleratory turbulent flame spread. Pressure rise in the chamber increases as the amount of fuel burned increases mainly because of the larger amount of heat generation and, to a much smaller extent, due to the increase in gaseous number of moles. Top ignition, or downward propagating burns, produced a steady flame spread with a very small flat flame across the burning edge. Steady-state pressure is achieved during downward flame spread as the pressure rises and plateaus. This indicates that the heat generation by the flame matches the heat loss to surroundings during the longer, slower downward burns. One heat loss mechanism included mounting a heat exchanger directly above the burning sample in the path of the plume to act as a heat sink and more efficiently dissipate the heat due to the combustion event. This proved an effective means for chamber overpressure mitigation for those tests producing the most total heat release and thusly was determined to be a feasible mitigation strategy to incorporate into the microgravity experiment.

A hard-to-read font reduces the framing effect in a large sample.

PubMed

Korn, Christoph W; Ries, Juliane; Schalk, Lennart; Oganian, Yulia; Saalbach, Henrik

2018-04-01

How can apparent decision biases, such as the framing effect, be reduced? Intriguing findings within recent years indicate that foreign language settings reduce framing effects, which has been explained in terms of deeper cognitive processing. Because hard-to-read fonts have been argued to trigger deeper cognitive processing, so-called cognitive disfluency, we tested whether hard-to-read fonts reduce framing effects. We found no reliable evidence for an effect of hard-to-read fonts on four framing scenarios in a laboratory (final N = 158) and an online study (N = 271). However, in a preregistered online study with a rather large sample (N = 732), a hard-to-read font reduced the framing effect in the classic "Asian disease" scenario (in a one-sided test). This suggests that hard-read-fonts can modulate decision biases-albeit with rather small effect sizes. Overall, our findings stress the importance of large samples for the reliability and replicability of modulations of decision biases.

MEGARA: large pupil element tests and performance

NASA Astrophysics Data System (ADS)

Martínez-Delgado, I.; Sánchez-Blanco, E.; Pérez-Calpena, A.; García-Vargas, M. L.; Maldonado, X. M.; Gil de Paz, A.; Carrasco, E.; Gallego, J.; Iglesias-Páramo, J.; Sánchez-Moreno, F. M.

2016-07-01

MEGARA is a third generation spectrograph for the Spanish 10.4m telescope (GTC) providing two observing modes: a large central Integral Field Unit (IFU), called the Large Compact Bundle (LCB), covering a FOV of 12.5 × 11.3 arcsec2, and a Multi-Object Spectrograph (MOS) with a FOV of 3.5 × 3.5 arcmin2. MEGARA will observe the whole visible range from 3650A to 10000A allowing different spectral resolutions (low, medium and high) with R = 6000, 11000 and 18000 respectively. The dispersive elements are placed at the spectrograph pupil position in the path of the collimated beam and they are composed of a set of volume phase hologram gratings (VPHs) sandwiched between two flat windows and coupled in addition to two prisms in the case of the medium- and high-resolution units. We will describe the tests and setups developed to check the requirements of all units, as well as the obtained performance at laboratory

Fabrication of the HIAD Large-Scale Demonstration Assembly and Upcoming Mission Applications

NASA Technical Reports Server (NTRS)

Swanson, G. T.; Johnson, R. K.; Hughes, S. J.; Dinonno, J. M.; Cheatwood, F M.

2017-01-01

Over a decade of work has been conducted in the development of NASAs Hypersonic Inflatable Aerodynamic Decelerator (HIAD) technology. This effort has included multiple ground test campaigns and flight tests culminating in the HIAD projects second generation (Gen-2) deployable aeroshell system and associated analytical tools. NASAs HIAD project team has developed, fabricated, and tested inflatable structures (IS) integrated with flexible thermal protection system (F-TPS), ranging in diameters from 3-6m, with cone angles of 60 and 70 deg.In 2015, United Launch Alliance (ULA) announced that they will use a HIAD (10-12m) as part of their Sensible, Modular, Autonomous Return Technology (SMART) for their upcoming Vulcan rocket. ULA expects SMART reusability, coupled with other advancements for Vulcan, will substantially reduce the cost of access to space. The first booster engine recovery via HIAD is scheduled for 2024. To meet this near-term need, as well as future NASA applications, the HIAD team is investigating taking the technology to the 10-15m diameter scale.In the last year, many significant development and fabrication efforts have been accomplished, culminating in the construction of a large-scale inflatable structure demonstration assembly. This assembly incorporated the first three tori for a 12m Mars Human-Scale Pathfinder HIAD conceptual design that was constructed with the current state of the art material set. Numerous design trades and torus fabrication demonstrations preceded this effort. In 2016, three large-scale tori (0.61m cross-section) and six subscale tori (0.25m cross-section) were manufactured to demonstrate fabrication techniques using the newest candidate material sets. These tori were tested to evaluate durability and load capacity. This work led to the selection of the inflatable structures third generation (Gen-3) structural liner. In late 2016, the three tori required for the large-scale demonstration assembly were fabricated, and then integrated in early 2017. The design includes provisions to add the remaining four tori necessary to complete the assembly of the 12m Human-Scale Pathfinder HIAD in the event future project funding becomes available.This presentation will discuss the HIAD large-scale demonstration assembly design and fabrication per-formed in the last year including the precursor tori development and the partial-stack fabrication. Potential near-term and future 10-15m HIAD applications will also be discussed.

Fabrication of the HIAD Large-Scale Demonstration Assembly

NASA Technical Reports Server (NTRS)

Swanson, G. T.; Johnson, R. K.; Hughes, S. J.; DiNonno, J. M.; Cheatwood, F. M.

2017-01-01

Over a decade of work has been conducted in the development of NASA's Hypersonic Inflatable Aerodynamic Decelerator (HIAD) technology. This effort has included multiple ground test campaigns and flight tests culminating in the HIAD projects second generation (Gen-2) deployable aeroshell system and associated analytical tools. NASAs HIAD project team has developed, fabricated, and tested inflatable structures (IS) integrated with flexible thermal protection system (F-TPS), ranging in diameters from 3-6m, with cone angles of 60 and 70 deg.In 2015, United Launch Alliance (ULA) announced that they will use a HIAD (10-12m) as part of their Sensible, Modular, Autonomous Return Technology (SMART) for their upcoming Vulcan rocket. ULA expects SMART reusability, coupled with other advancements for Vulcan, will substantially reduce the cost of access to space. The first booster engine recovery via HIAD is scheduled for 2024. To meet this near-term need, as well as future NASA applications, the HIAD team is investigating taking the technology to the 10-15m diameter scale. In the last year, many significant development and fabrication efforts have been accomplished, culminating in the construction of a large-scale inflatable structure demonstration assembly. This assembly incorporated the first three tori for a 12m Mars Human-Scale Pathfinder HIAD conceptual design that was constructed with the current state of the art material set. Numerous design trades and torus fabrication demonstrations preceded this effort. In 2016, three large-scale tori (0.61m cross-section) and six subscale tori (0.25m cross-section) were manufactured to demonstrate fabrication techniques using the newest candidate material sets. These tori were tested to evaluate durability and load capacity. This work led to the selection of the inflatable structures third generation (Gen-3) structural liner. In late 2016, the three tori required for the large-scale demonstration assembly were fabricated, and then integrated in early 2017. The design includes provisions to add the remaining four tori necessary to complete the assembly of the 12m Human-Scale Pathfinder HIAD in the event future project funding becomes available.This presentation will discuss the HIAD large-scale demonstration assembly design and fabrication per-formed in the last year including the precursor tori development and the partial-stack fabrication. Potential near-term and future 10-15m HIAD applications will also be discussed.

Steel Rack Connections: Identification of Most Influential Factors and a Comparison of Stiffness Design Methods.

PubMed

Shah, S N R; Sulong, N H Ramli; Shariati, Mahdi; Jumaat, M Z

2015-01-01

Steel pallet rack (SPR) beam-to-column connections (BCCs) are largely responsible to avoid the sway failure of frames in the down-aisle direction. The overall geometry of beam end connectors commercially used in SPR BCCs is different and does not allow a generalized analytic approach for all types of beam end connectors; however, identifying the effects of the configuration, profile and sizes of the connection components could be the suitable approach for the practical design engineers in order to predict the generalized behavior of any SPR BCC. This paper describes the experimental behavior of SPR BCCs tested using a double cantilever test set-up. Eight sets of specimens were identified based on the variation in column thickness, beam depth and number of tabs in the beam end connector in order to investigate the most influential factors affecting the connection performance. Four tests were repeatedly performed for each set to bring uniformity to the results taking the total number of tests to thirty-two. The moment-rotation (M-θ) behavior, load-strain relationship, major failure modes and the influence of selected parameters on connection performance were investigated. A comparative study to calculate the connection stiffness was carried out using the initial stiffness method, the slope to half-ultimate moment method and the equal area method. In order to find out the more appropriate method, the mean stiffness of all the tested connections and the variance in values of mean stiffness according to all three methods were calculated. The calculation of connection stiffness by means of the initial stiffness method is considered to overestimate the values when compared to the other two methods. The equal area method provided more consistent values of stiffness and lowest variance in the data set as compared to the other two methods.

How one might miss early warning signals of critical transitions in time series data: A systematic study of two major currency pairs

PubMed Central

Ciamarra, Massimo Pica; Cheong, Siew Ann

2018-01-01

There is growing interest in the use of critical slowing down and critical fluctuations as early warning signals for critical transitions in different complex systems. However, while some studies found them effective, others found the opposite. In this paper, we investigated why this might be so, by testing three commonly used indicators: lag-1 autocorrelation, variance, and low-frequency power spectrum at anticipating critical transitions in the very-high-frequency time series data of the Australian Dollar-Japanese Yen and Swiss Franc-Japanese Yen exchange rates. Besides testing rising trends in these indicators at a strict level of confidence using the Kendall-tau test, we also required statistically significant early warning signals to be concurrent in the three indicators, which must rise to appreciable values. We then found for our data set the optimum parameters for discovering critical transitions, and showed that the set of critical transitions found is generally insensitive to variations in the parameters. Suspecting that negative results in the literature are the results of low data frequencies, we created time series with time intervals over three orders of magnitude from the raw data, and tested them for early warning signals. Early warning signals can be reliably found only if the time interval of the data is shorter than the time scale of critical transitions in our complex system of interest. Finally, we compared the set of time windows with statistically significant early warning signals with the set of time windows followed by large movements, to conclude that the early warning signals indeed provide reliable information on impending critical transitions. This reliability becomes more compelling statistically the more events we test. PMID:29538373

How one might miss early warning signals of critical transitions in time series data: A systematic study of two major currency pairs.

PubMed

Wen, Haoyu; Ciamarra, Massimo Pica; Cheong, Siew Ann

2018-01-01

There is growing interest in the use of critical slowing down and critical fluctuations as early warning signals for critical transitions in different complex systems. However, while some studies found them effective, others found the opposite. In this paper, we investigated why this might be so, by testing three commonly used indicators: lag-1 autocorrelation, variance, and low-frequency power spectrum at anticipating critical transitions in the very-high-frequency time series data of the Australian Dollar-Japanese Yen and Swiss Franc-Japanese Yen exchange rates. Besides testing rising trends in these indicators at a strict level of confidence using the Kendall-tau test, we also required statistically significant early warning signals to be concurrent in the three indicators, which must rise to appreciable values. We then found for our data set the optimum parameters for discovering critical transitions, and showed that the set of critical transitions found is generally insensitive to variations in the parameters. Suspecting that negative results in the literature are the results of low data frequencies, we created time series with time intervals over three orders of magnitude from the raw data, and tested them for early warning signals. Early warning signals can be reliably found only if the time interval of the data is shorter than the time scale of critical transitions in our complex system of interest. Finally, we compared the set of time windows with statistically significant early warning signals with the set of time windows followed by large movements, to conclude that the early warning signals indeed provide reliable information on impending critical transitions. This reliability becomes more compelling statistically the more events we test.

Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV).

PubMed

Piette, Elizabeth R; Moore, Jason H

2018-01-01

Machine learning methods and conventions are increasingly employed for the analysis of large, complex biomedical data sets, including genome-wide association studies (GWAS). Reproducibility of machine learning analyses of GWAS can be hampered by biological and statistical factors, particularly so for the investigation of non-additive genetic interactions. Application of traditional cross validation to a GWAS data set may result in poor consistency between the training and testing data set splits due to an imbalance of the interaction genotypes relative to the data as a whole. We propose a new cross validation method, proportional instance cross validation (PICV), that preserves the original distribution of an independent variable when splitting the data set into training and testing partitions. We apply PICV to simulated GWAS data with epistatic interactions of varying minor allele frequencies and prevalences and compare performance to that of a traditional cross validation procedure in which individuals are randomly allocated to training and testing partitions. Sensitivity and positive predictive value are significantly improved across all tested scenarios for PICV compared to traditional cross validation. We also apply PICV to GWAS data from a study of primary open-angle glaucoma to investigate a previously-reported interaction, which fails to significantly replicate; PICV however improves the consistency of testing and training results. Application of traditional machine learning procedures to biomedical data may require modifications to better suit intrinsic characteristics of the data, such as the potential for highly imbalanced genotype distributions in the case of epistasis detection. The reproducibility of genetic interaction findings can be improved by considering this variable imbalance in cross validation implementation, such as with PICV. This approach may be extended to problems in other domains in which imbalanced variable distributions are a concern.

Heavy Tail Behavior of Rainfall Extremes across Germany

NASA Astrophysics Data System (ADS)

Castellarin, A.; Kreibich, H.; Vorogushyn, S.; Merz, B.

2017-12-01

Distributions are termed heavy-tailed if extreme values are more likely than would be predicted by probability distributions that have exponential asymptotic behavior. Heavy-tail behavior often leads to surprise, because historical observations can be a poor guide for the future. Heavy-tail behavior seems to be widespread for hydro-meteorological extremes, such as extreme rainfall and flood events. To date there have been only vague hints to explain under which conditions these extremes show heavy-tail behavior. We use an observational data set consisting of 11 climate variables at 1440 stations across Germany. This homogenized, gap-free data set covers 110 years (1901-2010) at daily resolution. We estimate the upper tail behavior, including its uncertainty interval, of daily precipitation extremes for the 1,440 stations at the annual and seasonal time scales. Different tail indicators are tested, including the shape parameter of the Generalized Extreme Value distribution, the upper tail ratio and the obesity index. In a further step, we explore to which extent the tail behavior can be explained by geographical and climate factors. A large number of characteristics is derived, such as station elevation, degree of continentality, aridity, measures for quantifying the variability of humidity and wind velocity, or event-triggering large-scale atmospheric situation. The link between the upper tail behavior and these characteristics is investigated via data mining methods capable of detecting non-linear relationships in large data sets. This exceptionally rich observational data set, in terms of number of stations, length of time series and number of explaining variables, allows insights into the upper tail behavior which is rarely possible given the typical observational data sets available.

Hints on the nature of dark matter from the properties of Milky Way satellites

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

Anderhalden, Donnino; Diemand, Juerg; Schneider, Aurel

2013-03-01

The nature of dark matter is still unknown and one of the most fundamental scientific mysteries. Although successfully describing large scales, the standard cold dark matter model (CDM) exhibits possible shortcomings on galactic and sub-galactic scales. It is exactly at these highly non-linear scales where strong astrophysical constraints can be set on the nature of the dark matter particle. While observations of the Lyman-α forest probe the matter power spectrum in the mildly non-linear regime, satellite galaxies of the Milky Way provide an excellent laboratory as a test of the underlying cosmology on much smaller scales. Here we present resultsmore » from a set of high resolution simulations of a Milky Way sized dark matter halo in eight distinct cosmologies: CDM, warm dark matter (WDM) with a particle mass of 2 keV and six different cold plus warm dark matter (C+WDM) models, varying the fraction, f{sub wdm}, and the mass, m{sub wdm}, of the warm component. We used three different observational tests based on Milky Way satellite observations: the total satellite abundance, their radial distribution and their mass profile. We show that the requirement of simultaneously satisfying all three constraints sets very strong limits on the nature of dark matter. This shows the power of a multi-dimensional small scale approach in ruling out models which would be still allowed by large scale observations.« less

Working outside of the box: how HIV counselors in Sub-Saharan Africa adapt Western HIV testing norms.

PubMed

Angotti, Nicole

2010-09-01

The delivery of HIV counseling and testing programs throughout Sub-Saharan Africa relies on the work performed by trained HIV counselors. These individuals occupy a critical position: they are intermediaries between the rule-making of international and national policymakers, and the norms of the communities in which they live and work. This paper explains when, how and why HIV counselors adapt Western testing guidelines (the "3Cs"--consent, confidentiality and counseling) to local concerns, attempting to maintain the fidelity of testing principles, while reducing the harm they perceive may arise as a consequence of strict adherence to them. Data for this study come from Malawi: a poor, largely rural African country, where HIV prevalence is ranked 9th highest in the world. The analysis is based on 25 interviews with HIV counselors and a unique set of field journals, and captures local experiences and the moral quandaries that counselors in rural Sub-Saharan Africa face. The findings of this inquiry provide new insights into the implementation of HIV testing in rural African settings, insights that may guide HIV prevention policy. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

An optimized proportional-derivative controller for the human upper extremity with gravity.

PubMed

Jagodnik, Kathleen M; Blana, Dimitra; van den Bogert, Antonie J; Kirsch, Robert F

2015-10-15

When Functional Electrical Stimulation (FES) is used to restore movement in subjects with spinal cord injury (SCI), muscle stimulation patterns should be selected to generate accurate and efficient movements. Ideally, the controller for such a neuroprosthesis will have the simplest architecture possible, to facilitate translation into a clinical setting. In this study, we used the simulated annealing algorithm to optimize two proportional-derivative (PD) feedback controller gain sets for a 3-dimensional arm model that includes musculoskeletal dynamics and has 5 degrees of freedom and 22 muscles, performing goal-oriented reaching movements. Controller gains were optimized by minimizing a weighted sum of position errors, orientation errors, and muscle activations. After optimization, gain performance was evaluated on the basis of accuracy and efficiency of reaching movements, along with three other benchmark gain sets not optimized for our system, on a large set of dynamic reaching movements for which the controllers had not been optimized, to test ability to generalize. Robustness in the presence of weakened muscles was also tested. The two optimized gain sets were found to have very similar performance to each other on all metrics, and to exhibit significantly better accuracy, compared with the three standard gain sets. All gain sets investigated used physiologically acceptable amounts of muscular activation. It was concluded that optimization can yield significant improvements in controller performance while still maintaining muscular efficiency, and that optimization should be considered as a strategy for future neuroprosthesis controller design. Published by Elsevier Ltd.

Building Large Collections of Chinese and English Medical Terms from Semi-Structured and Encyclopedia Websites

PubMed Central

Xu, Yan; Wang, Yining; Sun, Jian-Tao; Zhang, Jianwen; Tsujii, Junichi; Chang, Eric

2013-01-01

To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (), Object Recall (), and Surface Head recall (). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available. PMID:23874426

Building large collections of Chinese and English medical terms from semi-structured and encyclopedia websites.

PubMed

Xu, Yan; Wang, Yining; Sun, Jian-Tao; Zhang, Jianwen; Tsujii, Junichi; Chang, Eric

2013-01-01

To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (R(S)), Object Recall (R(O)), and Surface Head recall (R(H)). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available.

Index Blood Tests and National Early Warning Scores within 24 Hours of Emergency Admission Can Predict the Risk of In-Hospital Mortality: A Model Development and Validation Study

PubMed Central

Mohammed, Mohammed A.; Rudge, Gavin; Watson, Duncan; Wood, Gordon; Smith, Gary B.; Prytherch, David R.; Girling, Alan; Stevens, Andrew

2013-01-01

Background We explored the use of routine blood tests and national early warning scores (NEWS) reported within ±24 hours of admission to predict in-hospital mortality in emergency admissions, using empirical decision Tree models because they are intuitive and may ultimately be used to support clinical decision making. Methodology A retrospective analysis of adult emergency admissions to a large acute hospital during April 2009 to March 2010 in the West Midlands, England, with a full set of index blood tests results (albumin, creatinine, haemoglobin, potassium, sodium, urea, white cell count and an index NEWS undertaken within ±24 hours of admission). We developed a Tree model by randomly splitting the admissions into a training (50%) and validation dataset (50%) and assessed its accuracy using the concordance (c-) statistic. Emergency admissions (about 30%) did not have a full set of index blood tests and/or NEWS and so were not included in our analysis. Results There were 23248 emergency admissions with a full set of blood tests and NEWS with an in-hospital mortality of 5.69%. The Tree model identified age, NEWS, albumin, sodium, white cell count and urea as significant (p<0.001) predictors of death, which described 17 homogeneous subgroups of admissions with mortality ranging from 0.2% to 60%. The c-statistic for the training model was 0.864 (95%CI 0.852 to 0.87) and when applied to the testing data set this was 0.853 (95%CI 0.840 to 0.866). Conclusions An easy to interpret validated risk adjustment Tree model using blood test and NEWS taken within ±24 hours of admission provides good discrimination and offers a novel approach to risk adjustment which may potentially support clinical decision making. Given the nature of the clinical data, the results are likely to be generalisable but further research is required to investigate this promising approach. PMID:23734195

Physician consideration of patients' out-of-pocket costs in making common clinical decisions.

PubMed

Pham, Hoangmai H; Alexander, G Caleb; O'Malley, Ann S

2007-04-09

Patients face growing cost-sharing through higher deductibles and other out-of-pocket (OP) expenses, with uncertain effects on clinical decision making. We analyzed data on 6628 respondents to the nationally representative 2004-2005 Community Tracking Study Physician Survey to examine how frequently physicians report considering their insured patients' OP expenses when prescribing drugs, selecting diagnostic tests, and choosing inpatient vs outpatient care settings. Responses were dichotomized as always/usually vs sometimes/rarely/never. In separate multivariate logistic regressions, we examined associations between physicians' reported frequency of considering OP costs for each type of decision and characteristics of individual physicians and their practices. Seventy-eight percent of physicians reported routinely considering OP costs when prescribing drugs, while 51.2% reported doing so when selecting care settings, and 40.2% when selecting diagnostic tests. In adjusted analyses, primary care physicians were more likely than medical specialists to consider patients' OP costs in choosing prescription drugs (85.3% vs 74.5%) (P<.001), care settings (53.9% vs 43.1%) (P<.001), and diagnostic tests (46.3% vs 29.9%) (P<.001). Physicians working in large groups or health maintenance organizations were more likely to consider OP costs in prescribing generic drugs (P<.001 for comparisons with solo and 2-person practices), but those in solo or 2-person practices were more likely to do so in choosing tests and care settings (P<.05 for all comparisons with other practice types). Physicians providing at least 10 hours of charity care a month were more likely than those not providing any to consider OP costs in both diagnostic testing (40.7% vs 35.8%) (P<.001) and care setting decisions (51.4% vs 47.6%) (P<.005). Cost-sharing arrangements targeting patients are likely to have limited effects in safely reducing health care spending because physicians do not routinely consider patients' OP costs when making decisions regarding more expensive medical services.

Testing of the BipiColombo Antenna Pointing Mechanism

NASA Astrophysics Data System (ADS)

Campo, Pablo; Barrio, Aingeru; Martin, Fernando

2015-09-01

BepiColombo is an ESA mission to Mercury, its planetary orbiter (MPO) has two antenna pointing mechanism, High gain antenna (HGA) pointing mechanism steers and points a large reflector which is integrated at system level by TAS-I Rome. Medium gain antenna (MGA) APM points a 1.5 m boom with a horn antenna. Both radiating elements are exposed to sun fluxes as high as 10 solar constants without protections.A previous paper [1] described the design and development process to solve the challenges of performing in harsh environment.. Current paper is focused on the testing process of the qualification units. Testing performance of antenna pointing mechanism in its specific environmental conditions has required special set-up and techniques. The process has provided valuable feedback on the design and the testing methods which have been included in the PFM design and tests.Some of the technologies and components were developed on dedicated items priort to EQM, but once integrated, test behaviour had relevant differences.Some of the major concerns for the APM testing are:- Create during the thermal vacuum testing the qualification temperature map with gradients along the APM. From of 200oC to 70oC.- Test in that conditions the radio frequency and pointing performances adding also high RF power to check the power handling and self-heating of the rotary joint.- Test in life up to 12000 equivalent APM revolutions, that is 14.3 million motor revolutions in different thermal conditions.- Measure low thermal distortion of the mechanical chain, being at the same time insulated from external environment and interfaces (55 arcsec pointing error)- Perform deployment of large items guaranteeing during the process low humidity, below 5% to protect dry lubrication- Verify stability with representative inertia of large boom or reflector 20 Kgm2.

Improving Bayesian credibility intervals for classifier error rates using maximum entropy empirical priors.

PubMed

Gustafsson, Mats G; Wallman, Mikael; Wickenberg Bolin, Ulrika; Göransson, Hanna; Fryknäs, M; Andersson, Claes R; Isaksson, Anders

2010-06-01

Successful use of classifiers that learn to make decisions from a set of patient examples require robust methods for performance estimation. Recently many promising approaches for determination of an upper bound for the error rate of a single classifier have been reported but the Bayesian credibility interval (CI) obtained from a conventional holdout test still delivers one of the tightest bounds. The conventional Bayesian CI becomes unacceptably large in real world applications where the test set sizes are less than a few hundred. The source of this problem is that fact that the CI is determined exclusively by the result on the test examples. In other words, there is no information at all provided by the uniform prior density distribution employed which reflects complete lack of prior knowledge about the unknown error rate. Therefore, the aim of the study reported here was to study a maximum entropy (ME) based approach to improved prior knowledge and Bayesian CIs, demonstrating its relevance for biomedical research and clinical practice. It is demonstrated how a refined non-uniform prior density distribution can be obtained by means of the ME principle using empirical results from a few designs and tests using non-overlapping sets of examples. Experimental results show that ME based priors improve the CIs when employed to four quite different simulated and two real world data sets. An empirically derived ME prior seems promising for improving the Bayesian CI for the unknown error rate of a designed classifier. Copyright 2010 Elsevier B.V. All rights reserved.

Production of primary mirror segments for the Giant Magellan Telescope

NASA Astrophysics Data System (ADS)

Martin, H. M.; Allen, R. G.; Burge, J. H.; Davis, J. M.; Davison, W. B.; Johns, M.; Kim, D. W.; Kingsley, J. S.; Law, K.; Lutz, R. D.; Strittmatter, P. A.; Su, P.; Tuell, M. T.; West, S. C.; Zhou, P.

2014-07-01

Segment production for the Giant Magellan Telescope is well underway, with the off-axis Segment 1 completed, off-axis Segments 2 and 3 already cast, and mold construction in progress for the casting of Segment 4, the center segment. All equipment and techniques required for segment fabrication and testing have been demonstrated in the manufacture of Segment 1. The equipment includes a 28 m test tower that incorporates four independent measurements of the segment's figure and geometry. The interferometric test uses a large asymmetric null corrector with three elements including a 3.75 m spherical mirror and a computer-generated hologram. For independent verification of the large-scale segment shape, we use a scanning pentaprism test that exploits the natural geometry of the telescope to focus collimated light to a point. The Software Configurable Optical Test System, loosely based on the Hartmann test, measures slope errors to submicroradian accuracy at high resolution over the full aperture. An enhanced laser tracker system guides the figuring through grinding and initial polishing. All measurements agree within the expected uncertainties, including three independent measurements of radius of curvature that agree within 0.3 mm. Segment 1 was polished using a 1.2 m stressed lap for smoothing and large-scale figuring, and a set of smaller passive rigid-conformal laps on an orbital polisher for deterministic small-scale figuring. For the remaining segments, the Mirror Lab is building a smaller, orbital stressed lap to combine the smoothing capability with deterministic figuring.

Large-Scale Assessment of Language Proficiency: Theoretical and Pedagogical Reflections on the Use of Multiple-Choice Tests

ERIC Educational Resources Information Center

Argüelles Álvarez, Irina

2013-01-01

The new requirement placed on students in tertiary settings in Spain to demonstrate a B1 or a B2 proficiency level of English, in accordance with the Common European Framework of Reference for Languages (CEFRL), has led most Spanish universities to develop a program of certification or accreditation of the required level. The first part of this…

Stability and Change in Interests: A Longitudinal Study of Adolescents from Grades 8 through 12

ERIC Educational Resources Information Center

Tracey, Terence J. G.; Robbins, Steven B.; Hofsess, Christy D.

2005-01-01

The pattern of RIASEC interests and academic skills were assessed longitudinally from a large-scale national database at three time points: eight grade, 10th grade, and 12th grade. Validation and cross-validation samples of 1000 males and 1000 females in each set were used to test the pattern of these scores over time relative to mean changes,…

OTSEGO COUNTY EXPERIMENTAL PROGRAM FOR TESTING METHODS OF FORMING FARM MANAGEMENT STUDY GROUPS, A PROGRESS REPORT. EXTENSION STUDY, NUMBER 8.

ERIC Educational Resources Information Center

LONGEST, JAMES W.; GENGENBACK, WILLIAM H.

THE MOST FREQUENT METHOD OF GROUP FORMATION FOR INTENSIVE FARM MANAGEMENT PROGRAMS IN NEW YORK STATE HAS BEEN TO COMBINE ALL INTERESTED FARMERS IN LARGE GROUPS AT THE COUNTY EXTENSION HEADQUARTERS. THIS EXPERIMENT WAS SET UP TO STUDY THE EFFECTIVENESS OF TWO METHODS OF FORMING SMALL GROUPS--BY SOCIOMETRIC CHOICE OR SIMILAR CHARACTERISTICS. ALL…

An intelligent system based on fuzzy probabilities for medical diagnosis– a study in aphasia diagnosis*

PubMed Central

Moshtagh-Khorasani, Majid; Akbarzadeh-T, Mohammad-R; Jahangiri, Nader; Khoobdel, Mehdi

2009-01-01

BACKGROUND: Aphasia diagnosis is particularly challenging due to the linguistic uncertainty and vagueness, inconsistencies in the definition of aphasic syndromes, large number of measurements with imprecision, natural diversity and subjectivity in test objects as well as in opinions of experts who diagnose the disease. METHODS: Fuzzy probability is proposed here as the basic framework for handling the uncertainties in medical diagnosis and particularly aphasia diagnosis. To efficiently construct this fuzzy probabilistic mapping, statistical analysis is performed that constructs input membership functions as well as determines an effective set of input features. RESULTS: Considering the high sensitivity of performance measures to different distribution of testing/training sets, a statistical t-test of significance is applied to compare fuzzy approach results with NN results as well as author's earlier work using fuzzy logic. The proposed fuzzy probability estimator approach clearly provides better diagnosis for both classes of data sets. Specifically, for the first and second type of fuzzy probability classifiers, i.e. spontaneous speech and comprehensive model, P-values are 2.24E-08 and 0.0059, respectively, strongly rejecting the null hypothesis. CONCLUSIONS: The technique is applied and compared on both comprehensive and spontaneous speech test data for diagnosis of four Aphasia types: Anomic, Broca, Global and Wernicke. Statistical analysis confirms that the proposed approach can significantly improve accuracy using fewer Aphasia features. PMID:21772867

Validating the use of Hospital Episode Statistics data and comparison of costing methodologies for economic evaluation: an end-of-life case study from the Cluster randomised triAl of PSA testing for Prostate cancer (CAP)

PubMed Central

Thorn, Joanna C; Turner, Emma L; Hounsome, Luke; Walsh, Eleanor; Down, Liz; Verne, Julia; Donovan, Jenny L; Neal, David E; Hamdy, Freddie C; Martin, Richard M; Noble, Sian M

2016-01-01

Objectives To evaluate the accuracy of routine data for costing inpatient resource use in a large clinical trial and to investigate costing methodologies. Design Final-year inpatient cost profiles were derived using (1) data extracted from medical records mapped to the National Health Service (NHS) reference costs via service codes and (2) Hospital Episode Statistics (HES) data using NHS reference costs. Trust finance departments were consulted to obtain costs for comparison purposes. Setting 7 UK secondary care centres. Population A subsample of 292 men identified as having died at least a year after being diagnosed with prostate cancer in Cluster randomised triAl of PSA testing for Prostate cancer (CAP), a long-running trial to evaluate the effectiveness and cost-effectiveness of prostate-specific antigen (PSA) testing. Results Both inpatient cost profiles showed a rise in costs in the months leading up to death, and were broadly similar. The difference in mean inpatient costs was £899, with HES data yielding ∼8% lower costs than medical record data (differences compatible with chance, p=0.3). Events were missing from both data sets. 11 men (3.8%) had events identified in HES that were all missing from medical record review, while 7 men (2.4%) had events identified in medical record review that were all missing from HES. The response from finance departments to requests for cost data was poor: only 3 of 7 departments returned adequate data sets within 6 months. Conclusions Using HES routine data coupled with NHS reference costs resulted in mean annual inpatient costs that were very similar to those derived via medical record review; therefore, routinely available data can be used as the primary method of costing resource use in large clinical trials. Neither HES nor medical record review represent gold standards of data collection. Requesting cost data from finance departments is impractical for large clinical trials. Trial registration number ISRCTN92187251; Pre-results. PMID:27130167

Utilizing the ultrasensitive Schistosoma up-converting phosphor lateral flow circulating anodic antigen (UCP-LF CAA) assay for sample pooling-strategies.

PubMed

Corstjens, Paul L A M; Hoekstra, Pytsje T; de Dood, Claudia J; van Dam, Govert J

2017-11-01

Methodological applications of the high sensitivity genus-specific Schistosoma CAA strip test, allowing detection of single worm active infections (ultimate sensitivity), are discussed for efficient utilization in sample pooling strategies. Besides relevant cost reduction, pooling of samples rather than individual testing can provide valuable data for large scale mapping, surveillance, and monitoring. The laboratory-based CAA strip test utilizes luminescent quantitative up-converting phosphor (UCP) reporter particles and a rapid user-friendly lateral flow (LF) assay format. The test includes a sample preparation step that permits virtually unlimited sample concentration with urine, reaching ultimate sensitivity (single worm detection) at 100% specificity. This facilitates testing large urine pools from many individuals with minimal loss of sensitivity and specificity. The test determines the average CAA level of the individuals in the pool thus indicating overall worm burden and prevalence. When requiring test results at the individual level, smaller pools need to be analysed with the pool-size based on expected prevalence or when unknown, on the average CAA level of a larger group; CAA negative pools do not require individual test results and thus reduce the number of tests. Straightforward pooling strategies indicate that at sub-population level the CAA strip test is an efficient assay for general mapping, identification of hotspots, determination of stratified infection levels, and accurate monitoring of mass drug administrations (MDA). At the individual level, the number of tests can be reduced i.e. in low endemic settings as the pool size can be increased as opposed to prevalence decrease. At the sub-population level, average CAA concentrations determined in urine pools can be an appropriate measure indicating worm burden. Pooling strategies allowing this type of large scale testing are feasible with the various CAA strip test formats and do not affect sensitivity and specificity. It allows cost efficient stratified testing and monitoring of worm burden at the sub-population level, ideally for large-scale surveillance generating hard data for performance of MDA programs and strategic planning when moving towards transmission-stop and elimination.

Associations between basal cortisol levels and memory retrieval in healthy young individuals.

PubMed

Ackermann, Sandra; Hartmann, Francina; Papassotiropoulos, Andreas; de Quervain, Dominique J F; Rasch, Björn

2013-11-01

Cortisol is known to affect memory processes. On the one hand, stress-induced or pharmacologically induced elevations of cortisol levels enhance memory consolidation. On the other hand, such experimentally induced elevations of cortisol levels have been shown to impair memory retrieval. However, the effects of individual differences in basal cortisol levels on memory processes remain largely unknown. Here we tested whether individual differences in cortisol levels predict picture learning and recall in a large sample. A total of 1225 healthy young women and men viewed two different sets of emotional and neutral pictures on two consecutive days. Both sets were recalled after a short delay (10 min). On Day 2, the pictures seen on Day 1 were additionally recalled, resulting in a long-delay (20 hr) recall condition. Cortisol levels were measured three times on Days 1 and 2 via saliva samples before encoding, between encoding and recall as well as after recall testing. We show that stronger decreases in cortisol levels during retrieval testing were associated with better recall performance of pictures, regardless of emotional valence of the pictures or length of the retention interval (i.e., 10 min vs. 20 hr). In contrast, average cortisol levels during retrieval were not related to picture recall. Remarkably during encoding, individual differences in average cortisol levels as well as changes in cortisol did not predict memory recall. Our results support previous findings indicating that higher cortisol levels during retrieval testing hinders recall of episodic memories and extend this view onto interindividual changes in basal cortisol levels.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

PubMed

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

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

Lopez, Jesse E.; Baptista, António M.

A sediment model coupled to the hydrodynamic model SELFE is validated against a benchmark combining a set of idealized tests and an application to a field-data rich energetic estuary. After sensitivity studies, model results for the idealized tests largely agree with previously reported results from other models in addition to analytical, semi-analytical, or laboratory results. Results of suspended sediment in an open channel test with fixed bottom are sensitive to turbulence closure and treatment for hydrodynamic bottom boundary. Results for the migration of a trench are very sensitive to critical stress and erosion rate, but largely insensitive to turbulence closure.more » The model is able to qualitatively represent sediment dynamics associated with estuarine turbidity maxima in an idealized estuary. Applied to the Columbia River estuary, the model qualitatively captures sediment dynamics observed by fixed stations and shipborne profiles. Representation of the vertical structure of suspended sediment degrades when stratification is underpredicted. Across all tests, skill metrics of suspended sediments lag those of hydrodynamics even when qualitatively representing dynamics. The benchmark is fully documented in an openly available repository to encourage unambiguous comparisons against other models.« less

Multilocus Association Mapping Using Variable-Length Markov Chains

PubMed Central

Browning, Sharon R.

2006-01-01

I propose a new method for association-based gene mapping that makes powerful use of multilocus data, is computationally efficient, and is straightforward to apply over large genomic regions. The approach is based on the fitting of variable-length Markov chain models, which automatically adapt to the degree of linkage disequilibrium (LD) between markers to create a parsimonious model for the LD structure. Edges of the fitted graph are tested for association with trait status. This approach can be thought of as haplotype testing with sophisticated windowing that accounts for extent of LD to reduce degrees of freedom and number of tests while maximizing information. I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests. PMID:16685642

Multilocus association mapping using variable-length Markov chains.

PubMed

Browning, Sharon R

2006-06-01

I propose a new method for association-based gene mapping that makes powerful use of multilocus data, is computationally efficient, and is straightforward to apply over large genomic regions. The approach is based on the fitting of variable-length Markov chain models, which automatically adapt to the degree of linkage disequilibrium (LD) between markers to create a parsimonious model for the LD structure. Edges of the fitted graph are tested for association with trait status. This approach can be thought of as haplotype testing with sophisticated windowing that accounts for extent of LD to reduce degrees of freedom and number of tests while maximizing information. I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests.

Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor.

PubMed

Saha, Arjun; Raghavachari, Krishnan

2015-05-12

We have investigated the performance of two classes of fragmentation methods developed in our group (Molecules-in-Molecules (MIM) and Many-Overlapping-Body (MOB) expansion), to reproduce the unfragmented MP2 energies on a test set composed of 10 small to large biomolecules. They have also been assessed to recover the relative energies of different motifs of the acetyl(ala)18NH2 system. Performance of different bond-cutting environments and the use of Hartree-Fock and different density functionals (as a low level of theory) in conjunction with the fragmentation strategies have been analyzed. Our investigation shows that while a low level of theory (for recovering long-range interactions) may not be necessary for small peptides, it provides a very effective strategy to accurately reproduce the total and relative energies of larger peptides such as the different motifs of the acetyl(ala)18NH2 system. Employing M06-2X as the low level of theory, the calculated mean total energy deviation (maximum deviation) in the total MP2 energies for the 10 molecules in the test set at MIM(d=3.5Å), MIM(η=9), and MOB(d=5Å) are 1.16 (2.31), 0.72 (1.87), and 0.43 (2.02) kcal/mol, respectively. The excellent performance suggests that such fragment-based methods should be of general use for the computation of accurate energies of large biomolecular systems.

A cis-regulatory logic simulator.

PubMed

Zeigler, Robert D; Gertz, Jason; Cohen, Barak A

2007-07-27

A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence. We developed a gene expression simulator which generates expression data using user-defined interactions between cis-regulatory sites. The simulator can incorporate additive, cooperative, competitive, and synergistic interactions between regulatory elements. Constraints on the spacing, distance, and orientation of regulatory elements and their interactions may also be defined and Gaussian noise can be added to the expression values. The simulator allows for a data transformation that simulates the sigmoid shape of expression levels from real promoters. We found good agreement between sets of simulated promoters and predicted regulatory modules from real expression data. We present several data sets that may be useful for testing new methodologies for predicting gene expression from promoter sequence. We developed a flexible gene expression simulator that rapidly generates large numbers of simulated promoters and their corresponding transcriptional output based on specified interactions between cis-regulatory sites. When appropriate rule sets are used, the data generated by our simulator faithfully reproduces experimentally derived data sets. We anticipate that using simulated gene expression data sets will facilitate the direct comparison of computational strategies to predict gene expression from promoter sequence. The source code is available online and as additional material. The test sets are available as additional material.

A microprocessor-based automation test system for the experiment of the multi-stage compressor

NASA Astrophysics Data System (ADS)

Zhang, Huisheng; Lin, Chongping

1991-08-01

An automation test system that is controlled by the microprocessor and used in the multistage compressor experiment is described. Based on the analysis of the compressor experiment performances, a complete hardware system structure is set up. It is composed of a IBM PC/XT computer, a large scale sampled data system, the moving machine with three directions, the scanners, the digital instrumentation and some output devices. A program structure of real-time software system is described. The testing results show that this test system can take the measure of many parameter magnitudes in the blade row places and on a boundary layer in different states. The automatic extent and the accuracy of experiment is increased and the experimental cost is reduced.

DDS-Suite - A Dynamic Data Acquisition, Processing, and Analysis System for Wind Tunnel Testing

NASA Technical Reports Server (NTRS)

Burnside, Jathan J.

2012-01-01

Wind Tunnels have optimized their steady-state data systems for acquisition and analysis and even implemented large dynamic-data acquisition systems, however development of near real-time processing and analysis tools for dynamic-data have lagged. DDS-Suite is a set of tools used to acquire, process, and analyze large amounts of dynamic data. Each phase of the testing process: acquisition, processing, and analysis are handled by separate components so that bottlenecks in one phase of the process do not affect the other, leading to a robust system. DDS-Suite is capable of acquiring 672 channels of dynamic data at rate of 275 MB / s. More than 300 channels of the system use 24-bit analog-to-digital cards and are capable of producing data with less than 0.01 of phase difference at 1 kHz. System architecture, design philosophy, and examples of use during NASA Constellation and Fundamental Aerodynamic tests are discussed.

Joint mouse–human phenome-wide association to test gene function and disease risk

DOE PAGES

Wang, Xusheng; Pandey, Ashutosh K.; Mulligan, Megan K.; ...

2016-02-02

Phenome-wide association is a novel reverse genetic strategy to analyze genome-to-phenome relations in human clinical cohorts. Here we test this approach using a large murine population segregating for ~5 million sequence variants, and we compare our results to those extracted from a matched analysis of gene variants in a large human cohort. For the mouse cohort, we amassed a deep and broad open-access phenome consisting of ~4,500 metabolic, physiological, pharmacological and behavioural traits, and more than 90 independent expression quantitative trait locus (QTL), transcriptome, proteome, metagenome and metabolome data sets-by far the largest coherent phenome for any experimental cohort (www.genenetwork.org).more » Here, we tested downstream effects of subsets of variants and discovered several novel associations, including a missense mutation in fumarate hydratase that controls variation in the mitochondrial unfolded protein response in both mouse and Caenorhabditis elegans, and missense mutations in Col6a5 that underlies variation in bone mineral density in both mouse and human.« less

Safety modelling and testing of lithium-ion batteries in electrified vehicles

NASA Astrophysics Data System (ADS)

Deng, Jie; Bae, Chulheung; Marcicki, James; Masias, Alvaro; Miller, Theodore

2018-04-01

To optimize the safety of batteries, it is important to understand their behaviours when subjected to abuse conditions. Most early efforts in battery safety modelling focused on either one battery cell or a single field of interest such as mechanical or thermal failure. These efforts may not completely reflect the failure of batteries in automotive applications, where various physical processes can take place in a large number of cells simultaneously. In this Perspective, we review modelling and testing approaches for battery safety under abuse conditions. We then propose a general framework for large-scale multi-physics modelling and experimental work to address safety issues of automotive batteries in real-world applications. In particular, we consider modelling coupled mechanical, electrical, electrochemical and thermal behaviours of batteries, and explore strategies to extend simulations to the battery module and pack level. Moreover, we evaluate safety test approaches for an entire range of automotive hardware sets from cell to pack. We also discuss challenges in building this framework and directions for its future development.

[The effect of magnetotherapy on the immunobiochemical indices of subjects with diseases of the periodontal tissues and joints].

PubMed

Samoĭlovich, V A

1999-01-01

Kept under medical surveillance in a health resort setting were 52 patients with disorders of the parodontium and large joints. All patients were given a complex therapy involving dietotherapy, therapeutic exercise, hydrotherapy, mud-treatment. Those patients having parodontium diseases were also prescribed topical treatment (chloride-sodium mouth baths and mud applications to the gingiva area). The main group subjects were also exposed to VMF using the unit for low-frequency therapy "Gradient-1". Laboratory means were also made use of, as a complex of biochemical tests characterizing changes in lipid metabolism. The level of the natural bodily resistance was determined by nitroblue tetrazolium test (NBT-test). The condition of the parodontium was evaluated by the Loë-Silness index. Adaptive reactions were studied by the lymphocytes-to-segmented neutrophils ratio. Adoption of therapy involving physiobalneofactors in patients with afflictions of the parodontium tissues and large joints makes for development of favourable in prognostic respect adaptive reactions.

Heavy Analysis and Light Virtualization of Water Use Data with Python

NASA Astrophysics Data System (ADS)

Kim, H.; Bijoor, N.; Famiglietti, J. S.

2014-12-01

Water utilities possess a large amount of water data that could be used to inform urban ecohydrology, management decisions, and conservation policies, but such data are rarely analyzed owing to difficulty in analyzation, visualization, and interpretion. We have developed a high performance computing resource for this purpose. We partnered with 6 water agencies in Orange County who provided 10 years of parcel-level monthly water use billing data for a pilot study. The first challenge that we overcame was to refine all human errors and unify the many different formats of data over all agencies. Second, we tested and applied experimental approaches to the data, including complex calculations, with high efficiency. Third, we developed a method to refine the data so it can be browsed along a time series index and/or geo-spatial queries with high efficiency, no matter how large the data. Python scientific libraries were the best match to handle arbitrary data sets in our environment. Further milestones include agency entry, sets of formulae, and maintaining 15M rows X 70 columns of data with high performance of cpu-bound processes. To deal with billions of rows, we performed an analysis virtualization stack by leveraging iPython parallel computing. With this architecture, one agency could be considered one computing node or virtual machine that maintains its own data sets respectively. For example, a big agency could use a large node, and a small agency could use a micro node. Under the minimum required raw data specs, more agencies could be analyzed. The program developed in this study simplifies data analysis, visualization, and interpretation of large water datasets, and can be used to analyze large data volumes from water agencies nationally or worldwide.

Automatic food detection in egocentric images using artificial intelligence technology.

PubMed

Jia, Wenyan; Li, Yuecheng; Qu, Ruowei; Baranowski, Thomas; Burke, Lora E; Zhang, Hong; Bai, Yicheng; Mancino, Juliet M; Xu, Guizhi; Mao, Zhi-Hong; Sun, Mingui

2018-03-26

To develop an artificial intelligence (AI)-based algorithm which can automatically detect food items from images acquired by an egocentric wearable camera for dietary assessment. To study human diet and lifestyle, large sets of egocentric images were acquired using a wearable device, called eButton, from free-living individuals. Three thousand nine hundred images containing real-world activities, which formed eButton data set 1, were manually selected from thirty subjects. eButton data set 2 contained 29 515 images acquired from a research participant in a week-long unrestricted recording. They included both food- and non-food-related real-life activities, such as dining at both home and restaurants, cooking, shopping, gardening, housekeeping chores, taking classes, gym exercise, etc. All images in these data sets were classified as food/non-food images based on their tags generated by a convolutional neural network. A cross data-set test was conducted on eButton data set 1. The overall accuracy of food detection was 91·5 and 86·4 %, respectively, when one-half of data set 1 was used for training and the other half for testing. For eButton data set 2, 74·0 % sensitivity and 87·0 % specificity were obtained if both 'food' and 'drink' were considered as food images. Alternatively, if only 'food' items were considered, the sensitivity and specificity reached 85·0 and 85·8 %, respectively. The AI technology can automatically detect foods from low-quality, wearable camera-acquired real-world egocentric images with reasonable accuracy, reducing both the burden of data processing and privacy concerns.

Set shifting and working memory in adults with attention-deficit/hyperactivity disorder.

PubMed

Rohlf, Helena; Jucksch, Viola; Gawrilow, Caterina; Huss, Michael; Hein, Jakob; Lehmkuhl, Ulrike; Salbach-Andrae, Harriet

2012-01-01

Compared to the high number of studies that investigated executive functions (EF) in children with attention-deficit/hyperactivity disorder (ADHD), a little is known about the EF performance of adults with ADHD. This study compared 37 adults with ADHD (ADHD(total)) and 32 control participants who were equivalent in age, intelligence quotient (IQ), sex, and years of education, in two domains of EF--set shifting and working memory. Additionally, the ADHD(total) group was subdivided into two subgroups: ADHD patients without comorbidity (ADHD(-), n = 19) and patients with at least one comorbid disorder (ADHD(+), n = 18). Participants fulfilled two measures for set shifting (i.e., the trail making test, TMT and a computerized card sorting test, CKV) and one measure for working memory (i.e., digit span test, DS). Compared to the control group the ADHD(total) group displayed deficits in set shifting and working memory. The differences between the groups were of medium-to-large effect size (TMT: d = 0.48; DS: d = 0.51; CKV: d = 0.74). The subgroup comparison of the ADHD(+) group and the ADHD(-) group revealed a poorer performance in general information processing speed for the ADHD(+) group. With regard to set shifting and working memory, no significant differences could be found between the two subgroups. These results suggest that the deficits of the ADHD(total) group are attributable to ADHD rather than to comorbidity. An influence of comorbidity, however, could not be completely ruled out as there was a trend of a poorer performance in the ADHD(+) group on some of the outcome measures.

Do regional methods really help reduce uncertainties in flood frequency analyses?

NASA Astrophysics Data System (ADS)

Cong Nguyen, Chi; Payrastre, Olivier; Gaume, Eric

2013-04-01

Flood frequency analyses are often based on continuous measured series at gauge sites. However, the length of the available data sets is usually too short to provide reliable estimates of extreme design floods. To reduce the estimation uncertainties, the analyzed data sets have to be extended either in time, making use of historical and paleoflood data, or in space, merging data sets considered as statistically homogeneous to build large regional data samples. Nevertheless, the advantage of the regional analyses, the important increase of the size of the studied data sets, may be counterbalanced by the possible heterogeneities of the merged sets. The application and comparison of four different flood frequency analysis methods to two regions affected by flash floods in the south of France (Ardèche and Var) illustrates how this balance between the number of records and possible heterogeneities plays in real-world applications. The four tested methods are: (1) a local statistical analysis based on the existing series of measured discharges, (2) a local analysis valuating the existing information on historical floods, (3) a standard regional flood frequency analysis based on existing measured series at gauged sites and (4) a modified regional analysis including estimated extreme peak discharges at ungauged sites. Monte Carlo simulations are conducted to simulate a large number of discharge series with characteristics similar to the observed ones (type of statistical distributions, number of sites and records) to evaluate to which extent the results obtained on these case studies can be generalized. These two case studies indicate that even small statistical heterogeneities, which are not detected by the standard homogeneity tests implemented in regional flood frequency studies, may drastically limit the usefulness of such approaches. On the other hand, these result show that the valuation of information on extreme events, either historical flood events at gauged sites or estimated extremes at ungauged sites in the considered region, is an efficient way to reduce uncertainties in flood frequency studies.

Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges.

PubMed

Lessells, Richard J; Stott, Katharine E; Manasa, Justen; Naidu, Kevindra K; Skingsley, Andrew; Rossouw, Theresa; de Oliveira, Tulio

2014-03-07

Antiretroviral drug resistance is becoming increasingly common with the expansion of human immunodeficiency virus (HIV) treatment programmes in high prevalence settings. Genotypic resistance testing could have benefit in guiding individual-level treatment decisions but successful models for delivering resistance testing in low- and middle-income countries have not been reported. An HIV Treatment Failure Clinic model was implemented within a large primary health care HIV treatment programme in northern KwaZulu-Natal, South Africa. Genotypic resistance testing was offered to adults (≥16 years) with virological failure on first-line antiretroviral therapy (one viral load >1000 copies/ml after at least 12 months on a standard first-line regimen). A genotypic resistance test report was generated with treatment recommendations from a specialist HIV clinician and sent to medical officers at the clinics who were responsible for patient management. A quantitative process evaluation was conducted to determine how the model was implemented and to provide feedback regarding barriers and challenges to delivery. A total of 508 specimens were submitted for genotyping between 8 April 2011 and 31 January 2013; in 438 cases (86.2%) a complete genotype report with recommendations from the specialist clinician was sent to the medical officer. The median turnaround time from specimen collection to receipt of final report was 18 days (interquartile range (IQR) 13-29). In 114 (26.0%) cases the recommended treatment differed from what would be given in the absence of drug resistance testing. In the majority of cases (n = 315, 71.9%), the subsequent treatment prescribed was in line with the recommendations of the report. Genotypic resistance testing was successfully implemented in this large primary health care HIV programme and the system functioned well enough for the results to influence clinical management decisions in real time. Further research will explore the impact and cost-effectiveness of different implementation models in different settings.

A systematic review of emergency department based HIV testing and linkage to care initiatives in low resource settings.

PubMed

Hansoti, Bhakti; Kelen, Gabor D; Quinn, Thomas C; Whalen, Madeleine M; DesRosiers, Taylor T; Reynolds, Steven J; Redd, Andrew; Rothman, Richard E

2017-01-01

Only 45% of people currently living with HIV infection in sub-Saharan Africa are aware of their HIV status. Unmet testing needs may be addressed by utilizing the Emergency Department (ED) as an innovative testing venue in low and middle-income countries (LMICs). The purpose of this review is to examine the burden of HIV infection described in EDs in LMICs, with a focus on summarizing the implementation of various ED-based HIV testing strategies. We performed a systematic review of Pubmed, Embase, Scopus, Web of Science and the Cochrane Library on June 12, 2016. A three-concept search was employed with emergency medicine (e.g., Emergency department, emergency medical services), HIV/AIDS (e.g., human immunodeficiency virus, acquired immunodeficiency syndrome), and LMIC terms (e.g., developing country, under developed countries, specific country names). The search returned 2026 unique articles. Of these, thirteen met inclusion criteria and were included in the final review. There was a large variation in the reported prevalence of HIV infection in the ED population ranging from to 2.14% in India to 43.3% in Uganda. The proportion HIV positive patients with previously undiagnosed infection ranged from 90% to 65.22%. In the United States ED-based HIV testing strategies have been front and center at curbing the HIV epidemic. The limited number of ED-based studies we observed in this study may represent the paucity of HIV testing in this venue in LMICs. All of the studies in this review demonstrated a high prevalence of HIV infection in the ED and an extraordinarily high percentage of previously undiagnosed HIV infection. Although the numbers of published reports are few, these diverse studies imply that in HIV endemic low resource settings EDs carry a large burden of undiagnosed HIV infections and may offer a unique testing venue.

A Step Towards Electric Propulsion Testing Standards: Pressure Measurements and Effective Pumping Speeds

NASA Technical Reports Server (NTRS)

Dankanich, John W.; Swiatek, Michael W.; Yim, John T.

2012-01-01

The electric propulsion community has been implored to establish and implement a set of universally applicable test standards during the research, development, and qualification of electric propulsion systems. Existing practices are fallible and result in testing variations which leads to suspicious results, large margins in application, or aversion to mission infusion. Performance measurements and life testing under appropriate conditions can be costly and lengthy. Measurement practices must be consistent, accurate, and repeatable. Additionally, the measurements must be universally transportable across facilities throughout the development, qualification, spacecraft integration and on-orbit performance. A preliminary step to progress towards universally applicable testing standards is outlined for facility pressure measurements and effective pumping speed calculations. The standard has been applied to multiple facilities at the NASA Glenn Research Center. Test results and analyses of universality of measurements are presented herein.

Performance evaluation of Space Shuttle SRB parachutes from air drop and scaled model wind tunnel tests. [Solid Rocket Booster recovery system

NASA Technical Reports Server (NTRS)

Moog, R. D.; Bacchus, D. L.; Utreja, L. R.

1979-01-01

The aerodynamic performance characteristics have been determined for the Space Shuttle Solid Rocket Booster drogue, main, and pilot parachutes. The performance evaluation on the 20-degree conical ribbon parachutes is based primarily on air drop tests of full scale prototype parachutes. In addition, parametric wind tunnel tests were performed and used in parachute configuration development and preliminary performance assessments. The wind tunnel test data are compared to the drop test results and both sets of data are used to determine the predicted performance of the Solid Rocket Booster flight parachutes. Data from other drop tests of large ribbon parachutes are also compared with the Solid Rocket Booster parachute performance characteristics. Parameters assessed include full open terminal drag coefficients, reefed drag area, opening characteristics, clustering effects, and forebody interference.

MANUSCRIPT IN PRESS: DEMENTIA & GERIATRIC COGNITIVE DISORDERS

PubMed Central

O’Bryant, Sid E.; Xiao, Guanghua; Barber, Robert; Cullum, C. Munro; Weiner, Myron; Hall, James; Edwards, Melissa; Grammas, Paula; Wilhelmsen, Kirk; Doody, Rachelle; Diaz-Arrastia, Ramon

2015-01-01

Background Prior work on the link between blood-based biomarkers and cognitive status has largely been based on dichotomous classifications rather than detailed neuropsychological functioning. The current project was designed to create serum-based biomarker algorithms that predict neuropsychological test performance. Methods A battery of neuropsychological measures was administered. Random forest analyses were utilized to create neuropsychological test-specific biomarker risk scores in a training set that were entered into linear regression models predicting the respective test scores in the test set. Serum multiplex biomarker data were analyzed on 108 proteins from 395 participants (197 AD cases and 198 controls) from the Texas Alzheimer’s Research and Care Consortium. Results The biomarker risk scores were significant predictors (p<0.05) of scores on all neuropsychological tests. With the exception of premorbid intellectual status (6.6%), the biomarker risk scores alone accounted for a minimum of 12.9% of the variance in neuropsychological scores. Biomarker algorithms (biomarker risk scores + demographics) accounted for substantially more variance in scores. Review of the variable importance plots indicated differential patterns of biomarker significance for each test, suggesting the possibility of domain-specific biomarker algorithms. Conclusions Our findings provide proof-of-concept for a novel area of scientific discovery, which we term “molecular neuropsychology.” PMID:24107792

Performances of a HGCDTE APD Based Detector with Electric Cooling for 2-μm DIAL/IPDA Applications

NASA Astrophysics Data System (ADS)

Dumas, A.; Rothman, J.; Gibert, F.; Lasfargues, G.; Zanatta, J.-P.; Edouart, D.

2016-06-01

In this work we report on design and testing of an HgCdTe Avalanche Photodiode (APD) detector assembly for lidar applications in the Short Wavelength Infrared Region (SWIR : 1,5 - 2 μm). This detector consists in a set of diodes set in parallel -making a 200 μm large sensitive area- and connected to a custom high gain TransImpedance Amplifier (TIA). A commercial four stages Peltier cooler is used to reach an operating temperature of 185K. Crucial performances for lidar use are investigated : linearity, dynamic range, spatial homogeneity, noise and resistance to intense illumination.

Taming parallel I/O complexity with auto-tuning

DOE PAGES

Behzad, Babak; Luu, Huong Vu Thanh; Huchette, Joseph; ...

2013-11-17

We present an auto-tuning system for optimizing I/O performance of HDF5 applications and demonstrate its value across platforms, applications, and at scale. The system uses a genetic algorithm to search a large space of tunable parameters and to identify effective settings at all layers of the parallel I/O stack. The parameter settings are applied transparently by the auto-tuning system via dynamically intercepted HDF5 calls. To validate our auto-tuning system, we applied it to three I/O benchmarks (VPIC, VORPAL, and GCRM) that replicate the I/O activity of their respective applications. We tested the system with different weak-scaling configurations (128, 2048, andmore » 4096 CPU cores) that generate 30 GB to 1 TB of data, and executed these configurations on diverse HPC platforms (Cray XE6, IBM BG/P, and Dell Cluster). In all cases, the auto-tuning framework identified tunable parameters that substantially improved write performance over default system settings. In conclusion, we consistently demonstrate I/O write speedups between 2x and 100x for test configurations.« less

Diagnosing breast cancer using Raman spectroscopy: prospective analysis

NASA Astrophysics Data System (ADS)

Haka, Abigail S.; Volynskaya, Zoya; Gardecki, Joseph A.; Nazemi, Jon; Shenk, Robert; Wang, Nancy; Dasari, Ramachandra R.; Fitzmaurice, Maryann; Feld, Michael S.

2009-09-01

We present the first prospective test of Raman spectroscopy in diagnosing normal, benign, and malignant human breast tissues. Prospective testing of spectral diagnostic algorithms allows clinicians to accurately assess the diagnostic information contained in, and any bias of, the spectroscopic measurement. In previous work, we developed an accurate, internally validated algorithm for breast cancer diagnosis based on analysis of Raman spectra acquired from fresh-frozen in vitro tissue samples. We currently evaluate the performance of this algorithm prospectively on a large ex vivo clinical data set that closely mimics the in vivo environment. Spectroscopic data were collected from freshly excised surgical specimens, and 129 tissue sites from 21 patients were examined. Prospective application of the algorithm to the clinical data set resulted in a sensitivity of 83%, a specificity of 93%, a positive predictive value of 36%, and a negative predictive value of 99% for distinguishing cancerous from normal and benign tissues. The performance of the algorithm in different patient populations is discussed. Sources of bias in the in vitro calibration and ex vivo prospective data sets, including disease prevalence and disease spectrum, are examined and analytical methods for comparison provided.

A Mine of Information: Can Sports Analytics Provide Wisdom From Your Data?

PubMed

Passfield, Louis; Hopker, James G

2017-08-01

This paper explores the notion that the availability and analysis of large data sets have the capacity to improve practice and change the nature of science in the sport and exercise setting. The increasing use of data and information technology in sport is giving rise to this change. Web sites hold large data repositories, and the development of wearable technology, mobile phone applications, and related instruments for monitoring physical activity, training, and competition provide large data sets of extensive and detailed measurements. Innovative approaches conceived to more fully exploit these large data sets could provide a basis for more objective evaluation of coaching strategies and new approaches to how science is conducted. An emerging discipline, sports analytics, could help overcome some of the challenges involved in obtaining knowledge and wisdom from these large data sets. Examples of where large data sets have been analyzed, to evaluate the career development of elite cyclists and to characterize and optimize the training load of well-trained runners, are discussed. Careful verification of large data sets is time consuming and imperative before useful conclusions can be drawn. Consequently, it is recommended that prospective studies be preferred over retrospective analyses of data. It is concluded that rigorous analysis of large data sets could enhance our knowledge in the sport and exercise sciences, inform competitive strategies, and allow innovative new research and findings.

Very large eddy simulation of the Red Sea overflow

NASA Astrophysics Data System (ADS)

Ilıcak, Mehmet; Özgökmen, Tamay M.; Peters, Hartmut; Baumert, Helmut Z.; Iskandarani, Mohamed

Mixing between overflows and ambient water masses is a critical problem of deep-water mass formation in the downwelling branch of the meridional overturning circulation of the ocean. Modeling approaches that have been tested so far rely either on algebraic parameterizations in hydrostatic ocean circulation models, or on large eddy simulations that resolve most of the mixing using nonhydrostatic models. In this study, we examine the performance of a set of turbulence closures, that have not been tested in comparison to observational data for overflows before. We employ the so-called very large eddy simulation (VLES) technique, which allows the use of k-ɛ models in nonhydrostatic models. This is done by applying a dynamic spatial filtering to the k-ɛ equations. To our knowledge, this is the first time that the VLES approach is adopted for an ocean modeling problem. The performance of k-ɛ and VLES models are evaluated by conducting numerical simulations of the Red Sea overflow and comparing them to observations from the Red Sea Outflow Experiment (REDSOX). The computations are constrained to one of the main channels transporting the overflow, which is narrow enough to permit the use of a two-dimensional (and nonhydrostatic) model. A large set of experiments are conducted using different closure models, Reynolds numbers and spatial resolutions. It is found that, when no turbulence closure is used, the basic structure of the overflow, consisting of a well-mixed bottom layer (BL) and entraining interfacial layer (IL), cannot be reproduced. The k-ɛ model leads to unrealistic thicknesses for both BL and IL, while VLES results in the most realistic reproduction of the REDSOX observations.

Estimation of maximal oxygen uptake via submaximal exercise testing in sports, clinical, and home settings.

PubMed

Sartor, Francesco; Vernillo, Gianluca; de Morree, Helma M; Bonomi, Alberto G; La Torre, Antonio; Kubis, Hans-Peter; Veicsteinas, Arsenio

2013-09-01

Assessment of the functional capacity of the cardiovascular system is essential in sports medicine. For athletes, the maximal oxygen uptake [Formula: see text] provides valuable information about their aerobic power. In the clinical setting, the (VO(2max)) provides important diagnostic and prognostic information in several clinical populations, such as patients with coronary artery disease or heart failure. Likewise, VO(2max) assessment can be very important to evaluate fitness in asymptomatic adults. Although direct determination of [VO(2max) is the most accurate method, it requires a maximal level of exertion, which brings a higher risk of adverse events in individuals with an intermediate to high risk of cardiovascular problems. Estimation of VO(2max) during submaximal exercise testing can offer a precious alternative. Over the past decades, many protocols have been developed for this purpose. The present review gives an overview of these submaximal protocols and aims to facilitate appropriate test selection in sports, clinical, and home settings. Several factors must be considered when selecting a protocol: (i) The population being tested and its specific needs in terms of safety, supervision, and accuracy and repeatability of the VO(2max) estimation. (ii) The parameters upon which the prediction is based (e.g. heart rate, power output, rating of perceived exertion [RPE]), as well as the need for additional clinically relevant parameters (e.g. blood pressure, ECG). (iii) The appropriate test modality that should meet the above-mentioned requirements should also be in line with the functional mobility of the target population, and depends on the available equipment. In the sports setting, high repeatability is crucial to track training-induced seasonal changes. In the clinical setting, special attention must be paid to the test modality, because multiple physiological parameters often need to be measured during test execution. When estimating VO(2max), one has to be aware of the effects of medication on heart rate-based submaximal protocols. In the home setting, the submaximal protocols need to be accessible to users with a broad range of characteristics in terms of age, equipment, time available, and an absence of supervision. In this setting, the smart use of sensors such as accelerometers and heart rate monitors will result in protocol-free VO(2max) assessments. In conclusion, the need for a low-risk, low-cost, low-supervision, and objective evaluation of VO(2max) has brought about the development and the validation of a large number of submaximal exercise tests. It is of paramount importance to use these tests in the right context (sports, clinical, home), to consider the population in which they were developed, and to be aware of their limitations.

Investigations of detail design issues for the high speed acoustic wind tunnel using a 60th scale model tunnel. Part 2: Tests with the closed circuit

NASA Technical Reports Server (NTRS)

Barna, P. Stephen

1991-01-01

This report summarizes the tests on the 1:60 scale model of the High Speed Acoustic Wind Tunnel (HSAWT) performed during the period June - August 1991. Throughout the testing the tunnel was operated in the 'closed circuit mode,' that is when the airflow was set up by an axial flow fan, which was located inside the tunnel circuit and was directly driven by a motor. The tests were first performed with the closed test section and were subsequently repeated with the open test section, the latter operating with the nozzle-diffuser at its optimum setting. On this subject, reference is made to the report (1) issued January 1991, under contract 17-GFY900125, which summarizes the result obtained with the tunnel operating in the 'open circuit mode.' The tests confirmed the viability of the tunnel design, and the flow distributions in most of the tunnel components were considered acceptable. There were found, however, some locations where the flow distribution requires improvement. This applies to the flow upstream of the fan where the flow was found skewed, thus affecting the flow downstream. As a result of this, the flow appeared separated at the end of the large diffuser at the outer side. All tests were performed at NASA LaRC.

Testing for post-copulatory selection for major histocompatibility complex genotype in a semi-free-ranging primate population.

PubMed

Setchell, Joanna M; Abbott, Kristin M; Gonzalez, Jean-Paul; Knapp, Leslie A

2013-10-01

A large body of evidence suggests that major histocompatibility complex (MHC) genotype influences mate choice. However, few studies have investigated MHC-mediated post-copulatory mate choice under natural, or even semi-natural, conditions. We set out to explore this question in a large semi-free-ranging population of mandrills (Mandrillus sphinx) using MHC-DRB genotypes for 127 parent-offspring triads. First, we showed that offspring MHC heterozygosity correlates positively with parental MHC dissimilarity suggesting that mating among MHC dissimilar mates is efficient in increasing offspring MHC diversity. Second, we compared the haplotypes of the parental dyad with those of the offspring to test whether post-copulatory sexual selection favored offspring with two different MHC haplotypes, more diverse gamete combinations, or greater within-haplotype diversity. Limited statistical power meant that we could only detect medium or large effect sizes. Nevertheless, we found no evidence for selection for heterozygous offspring when parents share a haplotype (large effect size), genetic dissimilarity between parental haplotypes (we could detect an odds ratio of ≥1.86), or within-haplotype diversity (medium-large effect). These findings suggest that comparing parental and offspring haplotypes may be a useful approach to test for post-copulatory selection when matings cannot be observed, as is the case in many study systems. However, it will be extremely difficult to determine conclusively whether post-copulatory selection mechanisms for MHC genotype exist, particularly if the effect sizes are small, due to the difficulty in obtaining a sufficiently large sample. © 2013 Wiley Periodicals, Inc.

Vibrational entropy of a protein: large differences between distinct conformations.

PubMed

Goethe, Martin; Fita, Ignacio; Rubi, J Miguel

2015-01-13

In this article, it is investigated whether vibrational entropy (VE) is an important contribution to the free energy of globular proteins at ambient conditions. VE represents the major configurational-entropy contribution of these proteins. By definition, it is an average of the configurational entropies of the protein within single minima of the energy landscape, weighted by their occupation probabilities. Its large part originates from thermal motion of flexible torsion angles giving rise to the finite peak widths observed in torsion angle distributions. While VE may affect the equilibrium properties of proteins, it is usually neglected in numerical calculations as its consideration is difficult. Moreover, it is sometimes believed that all well-packed conformations of a globular protein have similar VE anyway. Here, we measure explicitly the VE for six different conformations from simulation data of a test protein. Estimates are obtained using the quasi-harmonic approximation for three coordinate sets, Cartesian, bond-angle-torsion (BAT), and a new set termed rotamer-degeneracy lifted BAT coordinates by us. The new set gives improved estimates as it overcomes a known shortcoming of the quasi-harmonic approximation caused by multiply populated rotamer states, and it may serve for VE estimation of macromolecules in a very general context. The obtained VE values depend considerably on the type of coordinates used. However, for all coordinate sets we find large entropy differences between the conformations, of the order of the overall stability of the protein. This result may have important implications on the choice of free energy expressions used in software for protein structure prediction, protein design, and NMR refinement.

Comparison of the applicability domain of a quantitative structure-activity relationship for estrogenicity with a large chemical inventory.

PubMed

Netzeva, Tatiana I; Gallegos Saliner, Ana; Worth, Andrew P

2006-05-01

The aim of the present study was to illustrate that it is possible and relatively straightforward to compare the domain of applicability of a quantitative structure-activity relationship (QSAR) model in terms of its physicochemical descriptors with a large inventory of chemicals. A training set of 105 chemicals with data for relative estrogenic gene activation, obtained in a recombinant yeast assay, was used to develop the QSAR. A binary classification model for predicting active versus inactive chemicals was developed using classification tree analysis and two descriptors with a clear physicochemical meaning (octanol-water partition coefficient, or log Kow, and the number of hydrogen bond donors, or n(Hdon)). The model demonstrated a high overall accuracy (90.5%), with a sensitivity of 95.9% and a specificity of 78.1%. The robustness of the model was evaluated using the leave-many-out cross-validation technique, whereas the predictivity was assessed using an artificial external test set composed of 12 compounds. The domain of the QSAR training set was compared with the chemical space covered by the European Inventory of Existing Commercial Chemical Substances (EINECS), as incorporated in the CDB-EC software, in the log Kow / n(Hdon) plane. The results showed that the training set and, therefore, the applicability domain of the QSAR model covers a small part of the physicochemical domain of the inventory, even though a simple method for defining the applicability domain (ranges in the descriptor space) was used. However, a large number of compounds are located within the narrow descriptor window.

Expanded image database of pistachio x-ray images and classification by conventional methods

NASA Astrophysics Data System (ADS)

Keagy, Pamela M.; Schatzki, Thomas F.; Le, Lan Chau; Casasent, David P.; Weber, David

1996-12-01

In order to develop sorting methods for insect damaged pistachio nuts, a large data set of pistachio x-ray images (6,759 nuts) was created. Both film and linescan sensor images were acquired, nuts dissected and internal conditions coded using the U.S. Grade standards and definitions for pistachios. A subset of 1199 good and 686 insect damaged nuts was used to calculate and test discriminant functions. Statistical parameters of image histograms were evaluated for inclusion by forward stepwise discrimination. Using three variables in the discriminant function, 89% of test set nuts were correctly identified. Comparable data for 6 human subjects ranged from 67 to 92%. If the loss of good nuts is held to 1% by requiring a high probability to discard a nut as insect damaged, approximately half of the insect damage present in clean pistachio nuts may be detected and removed by x-ray inspection.

Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.

PubMed

Kupas, Katrin; Ultsch, Alfred; Klebe, Gerhard

2008-05-15

A new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent-accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape, as they have the great advantage of allowing a comparison at different resolutions. The number of coefficients to describe the wavelets can be chosen with respect to the size of the considered data set. The physicochemical characteristics of the patches are described by the assignment of the exposed amino acid residues to one or more of five different properties determinant for molecular recognition. A self-organizing neural network is used to project the high-dimensional feature vectors onto a two-dimensional layer of neurons, called a map. To find similarities between the binding pockets, in both geometrical and physicochemical features, a clustering of the projected feature vector is performed using an automatic distance- and density-based clustering algorithm. The method was validated with a small training data set of 109 binding cavities originating from a set of enzymes covering 12 different EC numbers. A second test data set of 1378 binding cavities, extracted from enzymes of 13 different EC numbers, was then used to prove the discriminating power of the algorithm and to demonstrate its applicability to large scale analyses. In all cases, members of the data set with the same EC number were placed into coherent regions on the map, with small distances between them. Different EC numbers are separated by large distances between the feature vectors. A third data set comprising three subfamilies of endopeptidases is used to demonstrate the ability of the algorithm to detect similar substructures between functionally related active sites. The algorithm can also be used to predict the function of novel proteins not considered in training data set. 2007 Wiley-Liss, Inc.

Reducing inpatient heritable thrombophilia testing using a clinical decision-making tool.

PubMed

Smith, Tyler W; Pi, David; Hudoba, Monika; Lee, Agnes Y Y

2014-04-01

To evaluate the impact of a clinical decision-making tool, designed to educate physicians regarding heritable thrombophilia (HT) testing, on the volume of testing in hospitalised patients in the tertiary care setting. We performed a retrospective cohort study over a 6-year period (2007-2012) at a single tertiary care centre intervention site and two regional control sites. In January 2010, the intervention site instituted a policy change whereby physicians ordering HT testing on inpatients needed to complete a pre-preprinted order (PPO) form that outlined the limitations of HT testing in the hospitalised setting. Failure to complete the PPO within 24 h resulted in test cancellation. Our main outcome measure was the volume of HT testing performed at the three study sites. Introduction of the PPO resulted in a 79.4% (95% CI 71.2% to 87.6%) reduction in factor V Leiden (FVL) testing at the intervention site. This decrease was significantly greater compared with those in the two control teaching hospitals over the same time periods (33.7% and 43.6%; both p<0.001). Reductions in FVL testing postintervention were observed among all ordering specialists. Similar postintervention reductions in testing volumes were observed for antithrombin (57.4%), protein C (61.9%) and protein S (62.2%) activity assays. In a large tertiary care hospital, the introduction of a clinical decision-making tool significantly reduced HT testing in inpatients across clinical specialties. The impact on patient outcome should be assessed in further studies.

Differential relationships between set-shifting abilities and dimensions of insight in schizophrenia.

PubMed

Diez-Martin, J; Moreno-Ortega, M; Bagney, A; Rodriguez-Jimenez, R; Padilla-Torres, D; Sanchez-Morla, E M; Santos, J L; Palomo, T; Jimenez-Arriero, M A

2014-01-01

To assess insight in a large sample of patients with schizophrenia and to study its relationship with set shifting as an executive function. The insight of a sample of 161 clinically stable, community-dwelling patients with schizophrenia was evaluated by means of the Scale to Assess Unawareness of Mental Disorder (SUMD). Set shifting was measured using the Trail-Making Test time required to complete part B minus the time required to complete part A (TMT B-A). Linear regression analyses were performed to investigate the relationships of TMT B-A with different dimensions of general insight. Regression analyses revealed a significant association between TMT B-A and two of the SUMD general components: 'awareness of mental disorder' and 'awareness of the efficacy of treatment'. The 'awareness of social consequences' component was not significantly associated with set shifting. Our results show a significant relation between set shifting and insight, but not in the same manner for the different components of the SUMD general score. Copyright © 2013 S. Karger AG, Basel.

Using Functional or Structural Magnetic Resonance Images and Personal Characteristic Data to Identify ADHD and Autism

PubMed Central

Ghiassian, Sina; Greiner, Russell; Jin, Ping; Brown, Matthew R. G.

2016-01-01

A clinical tool that can diagnose psychiatric illness using functional or structural magnetic resonance (MR) brain images has the potential to greatly assist physicians and improve treatment efficacy. Working toward the goal of automated diagnosis, we propose an approach for automated classification of ADHD and autism based on histogram of oriented gradients (HOG) features extracted from MR brain images, as well as personal characteristic data features. We describe a learning algorithm that can produce effective classifiers for ADHD and autism when run on two large public datasets. The algorithm is able to distinguish ADHD from control with hold-out accuracy of 69.6% (over baseline 55.0%) using personal characteristics and structural brain scan features when trained on the ADHD-200 dataset (769 participants in training set, 171 in test set). It is able to distinguish autism from control with hold-out accuracy of 65.0% (over baseline 51.6%) using functional images with personal characteristic data when trained on the Autism Brain Imaging Data Exchange (ABIDE) dataset (889 participants in training set, 222 in test set). These results outperform all previously presented methods on both datasets. To our knowledge, this is the first demonstration of a single automated learning process that can produce classifiers for distinguishing patients vs. controls from brain imaging data with above-chance accuracy on large datasets for two different psychiatric illnesses (ADHD and autism). Working toward clinical applications requires robustness against real-world conditions, including the substantial variability that often exists among data collected at different institutions. It is therefore important that our algorithm was successful with the large ADHD-200 and ABIDE datasets, which include data from hundreds of participants collected at multiple institutions. While the resulting classifiers are not yet clinically relevant, this work shows that there is a signal in the (f)MRI data that a learning algorithm is able to find. We anticipate this will lead to yet more accurate classifiers, over these and other psychiatric disorders, working toward the goal of a clinical tool for high accuracy differential diagnosis. PMID:28030565

Robust Machine Learning-Based Correction on Automatic Segmentation of the Cerebellum and Brainstem.

PubMed

Wang, Jun Yi; Ngo, Michael M; Hessl, David; Hagerman, Randi J; Rivera, Susan M

2016-01-01

Automated segmentation is a useful method for studying large brain structures such as the cerebellum and brainstem. However, automated segmentation may lead to inaccuracy and/or undesirable boundary. The goal of the present study was to investigate whether SegAdapter, a machine learning-based method, is useful for automatically correcting large segmentation errors and disagreement in anatomical definition. We further assessed the robustness of the method in handling size of training set, differences in head coil usage, and amount of brain atrophy. High resolution T1-weighted images were acquired from 30 healthy controls scanned with either an 8-channel or 32-channel head coil. Ten patients, who suffered from brain atrophy because of fragile X-associated tremor/ataxia syndrome, were scanned using the 32-channel head coil. The initial segmentations of the cerebellum and brainstem were generated automatically using Freesurfer. Subsequently, Freesurfer's segmentations were both manually corrected to serve as the gold standard and automatically corrected by SegAdapter. Using only 5 scans in the training set, spatial overlap with manual segmentation in Dice coefficient improved significantly from 0.956 (for Freesurfer segmentation) to 0.978 (for SegAdapter-corrected segmentation) for the cerebellum and from 0.821 to 0.954 for the brainstem. Reducing the training set size to 2 scans only decreased the Dice coefficient ≤0.002 for the cerebellum and ≤ 0.005 for the brainstem compared to the use of training set size of 5 scans in corrective learning. The method was also robust in handling differences between the training set and the test set in head coil usage and the amount of brain atrophy, which reduced spatial overlap only by <0.01. These results suggest that the combination of automated segmentation and corrective learning provides a valuable method for accurate and efficient segmentation of the cerebellum and brainstem, particularly in large-scale neuroimaging studies, and potentially for segmenting other neural regions as well.

Robust Machine Learning-Based Correction on Automatic Segmentation of the Cerebellum and Brainstem

PubMed Central

Wang, Jun Yi; Ngo, Michael M.; Hessl, David; Hagerman, Randi J.; Rivera, Susan M.

2016-01-01

Automated segmentation is a useful method for studying large brain structures such as the cerebellum and brainstem. However, automated segmentation may lead to inaccuracy and/or undesirable boundary. The goal of the present study was to investigate whether SegAdapter, a machine learning-based method, is useful for automatically correcting large segmentation errors and disagreement in anatomical definition. We further assessed the robustness of the method in handling size of training set, differences in head coil usage, and amount of brain atrophy. High resolution T1-weighted images were acquired from 30 healthy controls scanned with either an 8-channel or 32-channel head coil. Ten patients, who suffered from brain atrophy because of fragile X-associated tremor/ataxia syndrome, were scanned using the 32-channel head coil. The initial segmentations of the cerebellum and brainstem were generated automatically using Freesurfer. Subsequently, Freesurfer’s segmentations were both manually corrected to serve as the gold standard and automatically corrected by SegAdapter. Using only 5 scans in the training set, spatial overlap with manual segmentation in Dice coefficient improved significantly from 0.956 (for Freesurfer segmentation) to 0.978 (for SegAdapter-corrected segmentation) for the cerebellum and from 0.821 to 0.954 for the brainstem. Reducing the training set size to 2 scans only decreased the Dice coefficient ≤0.002 for the cerebellum and ≤ 0.005 for the brainstem compared to the use of training set size of 5 scans in corrective learning. The method was also robust in handling differences between the training set and the test set in head coil usage and the amount of brain atrophy, which reduced spatial overlap only by <0.01. These results suggest that the combination of automated segmentation and corrective learning provides a valuable method for accurate and efficient segmentation of the cerebellum and brainstem, particularly in large-scale neuroimaging studies, and potentially for segmenting other neural regions as well. PMID:27213683

Rotavirus vaccine effectiveness in low-income settings: An evaluation of the test-negative design.

PubMed

Schwartz, Lauren M; Halloran, M Elizabeth; Rowhani-Rahbar, Ali; Neuzil, Kathleen M; Victor, John C

2017-01-03

The test-negative design (TND), an epidemiologic method currently used to measure rotavirus vaccine (RV) effectiveness, compares the vaccination status of rotavirus-positive cases and rotavirus-negative controls meeting a pre-defined case definition for acute gastroenteritis. Despite the use of this study design in low-income settings, the TND has not been evaluated to measure rotavirus vaccine effectiveness. This study builds upon prior methods to evaluate the use of the TND for influenza vaccine using a randomized controlled clinical trial database. Test-negative vaccine effectiveness (VE-TND) estimates were derived from three large randomized placebo-controlled trials (RCTs) of monovalent (RV1) and pentavalent (RV5) rotavirus vaccines in sub-Saharan Africa and Asia. Derived VE-TND estimates were compared to the original RCT vaccine efficacy estimates (VE-RCTs). The core assumption of the TND (i.e., rotavirus vaccine has no effect on rotavirus-negative diarrhea) was also assessed. TND vaccine effectiveness estimates were nearly equivalent to original RCT vaccine efficacy estimates. Neither RV had a substantial effect on rotavirus-negative diarrhea. This study supports the TND as an appropriate epidemiologic study design to measure rotavirus vaccine effectiveness in low-income settings. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

CERAPP: Collaborative Estrogen Receptor Activity Prediction ...

EPA Pesticide Factsheets

Humans potentially are exposed to thousands of man-made chemicals in the environment. Some chemicals mimic natural endocrine hormones and, thus, have the potential to be endocrine disruptors. Many of these chemicals never have been tested for their ability to interact with the estrogen receptor (ER). Risk assessors need tools to prioritize chemicals for assessment in costly in vivo tests, for instance, within the EPA Endocrine Disruptor Screening Program. Here, we describe a large-scale modeling project called CERAPP (Collaborative Estrogen Receptor Activity Prediction Project) demonstrating the efficacy of using predictive computational models on high-throughput screening data to screen thousands of chemicals against the ER. CERAPP combined multiple models developed in collaboration among 17 groups in the United States and Europe to predict ER activity of a common set of 32,464 chemical structures. Quantitative structure-activity relationship models and docking approaches were employed, mostly using a common training set of 1677 compounds provided by EPA, to build a total of 40 categorical and 8 continuous models for binding, agonist, and antagonist ER activity. All predictions were tested using an evaluation set of 7522 chemicals collected from the literature. To overcome the limitations of single models, a consensus was built weighting models using a scoring function (0 to 1) based on their accuracies. Individual model scores ranged from 0.69 to 0.85, showing

Learning and liking an artificial musical system: Effects of set size and repeated exposure

PubMed Central

Loui, Psyche; Wessel, David

2009-01-01

We report an investigation of humans' musical learning ability using a novel musical system. We designed an artificial musical system based on the Bohlen-Pierce scale, a scale very different from Western music. Melodies were composed from chord progressions in the new scale by applying the rules of a finite-state grammar. After exposing participants to sets of melodies, we conducted listening tests to assess learning, including recognition tests, generalization tests, and subjective preference ratings. In Experiment 1, participants were presented with 15 melodies 27 times each. Forced choice results showed that participants were able to recognize previously encountered melodies and generalize their knowledge to new melodies, suggesting internalization of the musical grammar. Preference ratings showed no differentiation among familiar, new, and ungrammatical melodies. In Experiment 2, participants were given 10 melodies 40 times each. Results showed superior recognition but unsuccessful generalization. Additionally, preference ratings were significantly higher for familiar melodies. Results from the two experiments suggest that humans can internalize the grammatical structure of a new musical system following exposure to a sufficiently large set size of melodies, but musical preference results from repeated exposure to a small number of items. This dissociation between grammar learning and preference will be further discussed. PMID:20151034

Learning and liking an artificial musical system: Effects of set size and repeated exposure.

PubMed

Loui, Psyche; Wessel, David

2008-10-01

We report an investigation of humans' musical learning ability using a novel musical system. We designed an artificial musical system based on the Bohlen-Pierce scale, a scale very different from Western music. Melodies were composed from chord progressions in the new scale by applying the rules of a finite-state grammar. After exposing participants to sets of melodies, we conducted listening tests to assess learning, including recognition tests, generalization tests, and subjective preference ratings. In Experiment 1, participants were presented with 15 melodies 27 times each. Forced choice results showed that participants were able to recognize previously encountered melodies and generalize their knowledge to new melodies, suggesting internalization of the musical grammar.Preference ratings showed no differentiation among familiar, new, and ungrammatical melodies. In Experiment 2, participants were given 10 melodies 40 times each. Results showed superior recognition but unsuccessful generalization. Additionally, preference ratings were significantly higher for familiar melodies. Results from the two experiments suggest that humans can internalize the grammatical structure of a new musical system following exposure to a sufficiently large set size of melodies, but musical preference results from repeated exposure to a small number of items. This dissociation between grammar learning and preference will be further discussed.

Rapid detection of frozen-then-thawed minced beef using multispectral imaging and Fourier transform infrared spectroscopy.

PubMed

Ropodi, Athina I; Panagou, Efstathios Z; Nychas, George-John E

2018-01-01

In recent years, fraud detection has become a major priority for food authorities, as fraudulent practices can have various economic and safety consequences. This work explores ways of identifying frozen-then-thawed minced beef labeled as fresh in a rapid, large-scale and cost-effective way. For this reason, freshly-ground beef was purchased from seven separate shops at different times, divided in fifteen portions and placed in Petri dishes. Multi-spectral images and FTIR spectra of the first five were immediately acquired while the remaining were frozen (-20°C) and stored for 7 and 32days (5 samples for each time interval). Samples were thawed and subsequently subjected to similar data acquisition. In total, 105 multispectral images and FTIR spectra were collected which were further analyzed using partial least-squares discriminant analysis and support vector machines. Two meat batches (30 samples) were reserved for independent validation and the remaining five batches were divided in training and test set (75 samples). Results showed 100% overall correct classification for test and external validation MSI data, while FTIR data yielded 93.3 and 96.7% overall correct classification for FTIR test set and external validation set respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Collection of quantitative chemical release field data.

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

Demirgian, J.; Macha, S.; Loyola Univ.

1999-01-01

Detection and quantitation of chemicals in the environment requires Fourier-transform infrared (FTIR) instruments that are properly calibrated and tested. This calibration and testing requires field testing using matrices that are representative of actual instrument use conditions. Three methods commonly used for developing calibration files and training sets in the field are a closed optical cell or chamber, a large-scale chemical release, and a small-scale chemical release. There is no best method. The advantages and limitations of each method should be considered in evaluating field results. Proper calibration characterizes the sensitivity of an instrument, its ability to detect a component inmore » different matrices, and the quantitative accuracy and precision of the results.« less

Moisture content and gas sampling device

NASA Technical Reports Server (NTRS)

Krieg, H. C., Jr. (Inventor)

1985-01-01

An apparatus is described for measuring minute quantities of moisture and other contaminants within sealed enclosures such as electronic assemblies which may be subject to large external atmospheric pressure variations. An array of vacuum quality valves is arranged to permit cleansing of the test apparatus of residual atmospheric components from a vacuum source. This purging operation evacuates a gas sample bottle, which is then connected by valve settings to provide the drive for withdrawing a gas sample from the sealed enclosure under test into the sample bottle through a colometric detector tube (Drager tube) which indicates moisture content. The sample bottle may be disconnected and its contents (drawn from the test enclosure) separately subjected to mass spectrograph analysis.

Recommended Practice for Pressure Measurements and Calculation of Effective Pumping Speeds During Electric Propulsion Testing

NASA Technical Reports Server (NTRS)

Dankanich, John W.; Walker, Mitchell; Swiatek, Michael W.; Yim, John T.

2013-01-01

The electric propulsion community has been implored to establish and implement a set of universally applicable test standards during the research, development, and qualification of electric propulsion systems. Variability between facility-to-facility and more importantly ground-to-flight performance can result in large margins in application or aversion to mission infusion. Performance measurements and life testing under appropriate conditions can be costly and lengthy. Measurement practices must be consistent, accurate, and repeatable. Additionally, the measurements must be universally transportable across facilities throughout the development, qualification, spacecraft integration, and on-orbit performance. A recommended practice for making pressure measurements, pressure diagnostics, and calculating effective pumping speeds with justification is presented.

A computer system for processing data from routine pulmonary function tests.

PubMed Central

Pack, A I; McCusker, R; Moran, F

1977-01-01

In larger pulmonary function laboratories there is a need for computerised techniques of data processing. A flexible computer system, which is used routinely, is described. The system processes data from a relatively large range of tests. Two types of output are produced--one for laboratory purposes, and one for return to the referring physician. The system adds an automatic interpretative report for each set of results. In developing the interpretative system it has been necessary to utilise a number of arbitrary definitions. The present terminology for reporting pulmonary function tests has limitations. The computer interpretation system affords the opportunity to take account of known interaction between measurements of function and different pathological states. Images PMID:329462

Testing the Hydrological Coherence of High-Resolution Gridded Precipitation and Temperature Data Sets

NASA Astrophysics Data System (ADS)

Laiti, L.; Mallucci, S.; Piccolroaz, S.; Bellin, A.; Zardi, D.; Fiori, A.; Nikulin, G.; Majone, B.

2018-03-01

Assessing the accuracy of gridded climate data sets is highly relevant to climate change impact studies, since evaluation, bias correction, and statistical downscaling of climate models commonly use these products as reference. Among all impact studies those addressing hydrological fluxes are the most affected by errors and biases plaguing these data. This paper introduces a framework, coined Hydrological Coherence Test (HyCoT), for assessing the hydrological coherence of gridded data sets with hydrological observations. HyCoT provides a framework for excluding meteorological forcing data sets not complying with observations, as function of the particular goal at hand. The proposed methodology allows falsifying the hypothesis that a given data set is coherent with hydrological observations on the basis of the performance of hydrological modeling measured by a metric selected by the modeler. HyCoT is demonstrated in the Adige catchment (southeastern Alps, Italy) for streamflow analysis, using a distributed hydrological model. The comparison covers the period 1989-2008 and includes five gridded daily meteorological data sets: E-OBS, MSWEP, MESAN, APGD, and ADIGE. The analysis highlights that APGD and ADIGE, the data sets with highest effective resolution, display similar spatiotemporal precipitation patterns and produce the largest hydrological efficiency indices. Lower performances are observed for E-OBS, MESAN, and MSWEP, especially in small catchments. HyCoT reveals deficiencies in the representation of spatiotemporal patterns of gridded climate data sets, which cannot be corrected by simply rescaling the meteorological forcing fields, as often done in bias correction of climate model outputs. We recommend this framework to assess the hydrological coherence of gridded data sets to be used in large-scale hydroclimatic studies.

The effects of an educational meeting and subsequent computer reminders on the ordering of laboratory tests by rheumatologists: an interrupted time series analysis.

PubMed

Lesuis, Nienke; den Broeder, Nathan; Boers, Nadine; Piek, Ester; Teerenstra, Steven; Hulscher, Marlies; van Vollenhoven, Ronald; den Broeder, Alfons A

2017-01-01

To examine the effects of an educational meeting and subsequent computer reminders on the number of ordered laboratory tests. Using interrupted time series analysis we assessed whether trends in the number of laboratory tests ordered by rheumatologists between September 2012 and September 2015 at the Sint Maartenskliniek (the Netherlands) changed following an educational meeting (September 2013) and the introduction of computer reminders into the Computerised Physician Order Entry System (July 2014). The analyses were done for the set of tests on which both interventions had focussed (intervention tests; complement, cryoglobulins, immunoglobins, myeloma protein) and a set of control tests unrelated to the interventions (alanine transferase, anti-cyclic citrullinated peptide, C-reactive protein, creatine, haemoglobin, leukocytes, mean corpuscular volume, rheumatoid factor and thrombocytes). At the start of the study, 101 intervention tests and 7660 control tests were ordered per month by the rheumatologists. After the educational meeting, both the level and trend of ordered intervention and control tests did not change significantly. After implementation of the reminders, the level of ordered intervention tests decreased by 85.0 tests (95%-CI -133.3 to -36.8, p<0.01), the level of control tests did not change following the introduction of reminders. In summary, an educational meeting alone was not effective in decreasing the number of ordered intervention tests, but the combination with computer reminders did result in a large decrease of those tests. Therefore, we recommend using computer reminders in addition to education if reduction of inappropriate test use is aimed for.

Mapping the integrated Sachs-Wolfe effect

NASA Astrophysics Data System (ADS)

Manzotti, A.; Dodelson, S.

2014-12-01

On large scales, the anisotropies in the cosmic microwave background (CMB) reflect not only the primordial density field but also the energy gain when photons traverse decaying gravitational potentials of large scale structure, what is called the integrated Sachs-Wolfe (ISW) effect. Decomposing the anisotropy signal into a primordial piece and an ISW component, the main secondary effect on large scales, is more urgent than ever as cosmologists strive to understand the Universe on those scales. We present a likelihood technique for extracting the ISW signal combining measurements of the CMB, the distribution of galaxies, and maps of gravitational lensing. We test this technique with simulated data showing that we can successfully reconstruct the ISW map using all the data sets together. Then we present the ISW map obtained from a combination of real data: the NRAO VLA sky survey (NVSS) galaxy survey, temperature anisotropies, and lensing maps made by the Planck satellite. This map shows that, with the data sets used and assuming linear physics, there is no evidence, from the reconstructed ISW signal in the Cold Spot region, for an entirely ISW origin of this large scale anomaly in the CMB. However a large scale structure origin from low redshift voids outside the NVSS redshift range is still possible. Finally we show that future surveys, thanks to a better large scale lensing reconstruction will be able to improve the reconstruction signal to noise which is now mainly coming from galaxy surveys.

Deep learning with non-medical training used for chest pathology identification

NASA Astrophysics Data System (ADS)

Bar, Yaniv; Diamant, Idit; Wolf, Lior; Greenspan, Hayit

2015-03-01

In this work, we examine the strength of deep learning approaches for pathology detection in chest radiograph data. Convolutional neural networks (CNN) deep architecture classification approaches have gained popularity due to their ability to learn mid and high level image representations. We explore the ability of a CNN to identify different types of pathologies in chest x-ray images. Moreover, since very large training sets are generally not available in the medical domain, we explore the feasibility of using a deep learning approach based on non-medical learning. We tested our algorithm on a dataset of 93 images. We use a CNN that was trained with ImageNet, a well-known large scale nonmedical image database. The best performance was achieved using a combination of features extracted from the CNN and a set of low-level features. We obtained an area under curve (AUC) of 0.93 for Right Pleural Effusion detection, 0.89 for Enlarged heart detection and 0.79 for classification between healthy and abnormal chest x-ray, where all pathologies are combined into one large class. This is a first-of-its-kind experiment that shows that deep learning with large scale non-medical image databases may be sufficient for general medical image recognition tasks.

Large-scale road safety programmes in low- and middle-income countries: an opportunity to generate evidence.

PubMed

Hyder, Adnan A; Allen, Katharine A; Peters, David H; Chandran, Aruna; Bishai, David

2013-01-01

The growing burden of road traffic injuries, which kill over 1.2 million people yearly, falls mostly on low- and middle-income countries (LMICs). Despite this, evidence generation on the effectiveness of road safety interventions in LMIC settings remains scarce. This paper explores a scientific approach for evaluating road safety programmes in LMICs and introduces such a road safety multi-country initiative, the Road Safety in 10 Countries Project (RS-10). By building on existing evaluation frameworks, we develop a scientific approach for evaluating large-scale road safety programmes in LMIC settings. This also draws on '13 lessons' of large-scale programme evaluation: defining the evaluation scope; selecting study sites; maintaining objectivity; developing an impact model; utilising multiple data sources; using multiple analytic techniques; maximising external validity; ensuring an appropriate time frame; the importance of flexibility and a stepwise approach; continuous monitoring; providing feedback to implementers, policy-makers; promoting the uptake of evaluation results; and understanding evaluation costs. The use of relatively new approaches for evaluation of real-world programmes allows for the production of relevant knowledge. The RS-10 project affords an important opportunity to scientifically test these approaches for a real-world, large-scale road safety evaluation and generate new knowledge for the field of road safety.

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

PubMed Central

Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

2012-01-01

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

Spacecraft Data Simulator for the test of level zero processing systems

NASA Technical Reports Server (NTRS)

Shi, Jeff; Gordon, Julie; Mirchandani, Chandru; Nguyen, Diem

1994-01-01

The Microelectronic Systems Branch (MSB) at Goddard Space Flight Center (GSFC) has developed a Spacecraft Data Simulator (SDS) to support the development, test, and verification of prototype and production Level Zero Processing (LZP) systems. Based on a disk array system, the SDS is capable of generating large test data sets up to 5 Gigabytes and outputting serial test data at rates up to 80 Mbps. The SDS supports data formats including NASA Communication (Nascom) blocks, Consultative Committee for Space Data System (CCSDS) Version 1 & 2 frames and packets, and all the Advanced Orbiting Systems (AOS) services. The capability to simulate both sequential and non-sequential time-ordered downlink data streams with errors and gaps is crucial to test LZP systems. This paper describes the system architecture, hardware and software designs, and test data designs. Examples of test data designs are included to illustrate the application of the SDS.

Wind tunnel pressurization and recovery system

NASA Technical Reports Server (NTRS)

Pejack, Edwin R.; Meick, Joseph; Ahmad, Adnan; Lateh, Nordin; Sadeq, Omar

1988-01-01

The high density, low toxicity characteristics of refrigerant-12 (dichlorofluoromethane) make it an ideal gas for wind tunnel testing. Present limitations on R-12 emissions, set to slow the rate of ozone deterioration, pose a difficult problem in recovery and handling of large quantities of R-12. This preliminary design is a possible solution to the problem of R-12 handling in wind tunnel testing. The design incorporates cold temperature condensation with secondary purification of the R-12/air mixture by adsorption. Also discussed is the use of Freon-22 as a suitable refrigerant for the 12 foot wind tunnel.

Achieving ultra-high temperatures with a resistive emitter array

NASA Astrophysics Data System (ADS)

Danielson, Tom; Franks, Greg; Holmes, Nicholas; LaVeigne, Joe; Matis, Greg; McHugh, Steve; Norton, Dennis; Vengel, Tony; Lannon, John; Goodwin, Scott

2016-05-01

The rapid development of very-large format infrared detector arrays has challenged the IR scene projector community to also develop larger-format infrared emitter arrays to support the testing of systems incorporating these detectors. In addition to larger formats, many scene projector users require much higher simulated temperatures than can be generated with current technology in order to fully evaluate the performance of their systems and associated processing algorithms. Under the Ultra High Temperature (UHT) development program, Santa Barbara Infrared Inc. (SBIR) is developing a new infrared scene projector architecture capable of producing both very large format (>1024 x 1024) resistive emitter arrays and improved emitter pixel technology capable of simulating very high apparent temperatures. During earlier phases of the program, SBIR demonstrated materials with MWIR apparent temperatures in excess of 1400 K. New emitter materials have subsequently been selected to produce pixels that achieve even higher apparent temperatures. Test results from pixels fabricated using the new material set will be presented and discussed. A 'scalable' Read In Integrated Circuit (RIIC) is also being developed under the same UHT program to drive the high temperature pixels. This RIIC will utilize through-silicon via (TSV) and Quilt Packaging (QP) technologies to allow seamless tiling of multiple chips to fabricate very large arrays, and thus overcome the yield limitations inherent in large-scale integrated circuits. Results of design verification testing of the completed RIIC will be presented and discussed.

Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering.

PubMed

Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan

2017-03-01

Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2016, The International Biometric Society.

A Psychoevolutionary Approach to Identifying Preferred Nature Scenes With Potential to Provide Restoration From Stress.

PubMed

Thake, Carol L; Bambling, Matthew; Edirippulige, Sisira; Marx, Eric

2017-10-01

Research supports therapeutic use of nature scenes in healthcare settings, particularly to reduce stress. However, limited literature is available to provide a cohesive guide for selecting scenes that may provide optimal therapeutic effect. This study produced and tested a replicable process for selecting nature scenes with therapeutic potential. Psychoevolutionary theory informed the construction of the Importance for Survival Scale (IFSS), and its usefulness for identifying scenes that people generally prefer to view and that hold potential to reduce stress was tested. Relationships between Importance for Survival (IFS), preference, and restoration were tested. General community participants ( N = 20 males, 20 females; M age = 48 years) Q-sorted sets of landscape photographs (preranked by the researcher in terms of IFS using the IFSS) from most to least preferred, and then completed the Short-Version Revised Restoration Scale in response to viewing a selection of the scenes. Results showed significant positive relationships between IFS and each of scene preference (large effect), and restoration potential (medium effect), as well as between scene preference and restoration potential across the levels of IFS (medium effect), and for individual participants and scenes (large effect). IFS was supported as a framework for identifying nature scenes that people will generally prefer to view and that hold potential for restoration from emotional distress; however, greater therapeutic potential may be expected when people can choose which of the scenes they would prefer to view. Evidence for the effectiveness of the IFSS was produced.

Study of chromatic adaptation using memory color matches, Part II: colored illuminants.

PubMed

Smet, Kevin A G; Zhai, Qiyan; Luo, Ming R; Hanselaer, Peter

2017-04-03

In a previous paper, 12 corresponding color data sets were derived for 4 neutral illuminants using the long-term memory colours of five familiar objects. The data were used to test several linear (one-step and two-step von Kries, RLAB) and nonlinear (Hunt and Nayatani) chromatic adaptation transforms (CAT). This paper extends that study to a total of 156 corresponding color sets by including 9 more colored illuminants: 2 with low and 2 with high correlated color temperatures as well as 5 representing high chroma adaptive conditions. As in the previous study, a two-step von Kries transform whereby the degree of adaptation D is optimized to minimize the DEu'v' prediction errors outperformed all other tested models for both memory color and literature corresponding color sets, whereby prediction errors were lower for the memory color set. Most of the transforms tested, except the two- and one-step von Kries models with optimized D, showed large errors for corresponding color subsets that contained non-neutral adaptive conditions as all of them tended to overestimate the effective degree of adaptation in this study. An analysis of the impact of the sensor space primaries in which the adaptation is performed was found to have little impact compared to that of model choice. Finally, the effective degree of adaptation for the 13 illumination conditions (4 neutral + 9 colored) was successfully modelled using a bivariate Gaussian in a Macleod-Boyton like chromaticity diagram.

VO2 responses to intermittent swimming sets at velocity associated with VO2max.

PubMed

Libicz, Sebastien; Roels, Belle; Millet, Gregoire P

2005-10-01

While the physiological adaptations following endurance training are relatively well understood, in swimming there is a dearth of knowledge regarding the metabolic responses to interval training (IT). The hypothesis tested predicted that two different endurance swimming IT sets would induce differences in the total time the subjects swam at a high percentage of maximal oxygen consumption (VO(2)max). Ten trained triathletes underwent an incremental test to exhaustion in swimming so that the swimming velocity associated with VO(2)max (vVO(2)max) could be determined. This was followed by a maximal 400-m test and two intermittent sets at vVO(2)max: (a) 16 x 50 m with 15-s rest (IT(50)); (b) 8 x 100 m with 30-s rest (IT(100)). The times sustained above 95% VO(2)max (68.50 +/- 62.69 vs. 145.01 +/- 165.91 sec) and 95% HRmax (146.67 +/- 131.99 vs. 169.78 +/- 203.45 sec, p = 0.54) did not differ between IT(50) and IT(100)(values are mean +/- SD). In conclusion, swimming IT sets of equal time duration at vVO(2)max but of differing work-interval durations led to slightly different VO(2)and HR responses. The time spent above 95% of VO(2)max was twice as long in IT(100) as in IT (50), and a large variability between mean VO(2)and HR values was also observed.

Does Regular Online Testing Enhance Student Learning in the Numerical Sciences? Robust Evidence from a Large Data Set

ERIC Educational Resources Information Center

Angus, Simon D.; Watson, Judith

2009-01-01

While a number of studies have been conducted on the impact of online assessment and teaching methods on student learning, the field does not seem settled around the promised benefits of such approaches. It is argued that the reason for this state of affairs is that few studies have been able to control for a number of confounding factors in…

Robotic Range Clearance Competition (R2C2)

DTIC Science & Technology

2011-10-01

unexploded ordnance (UXO). A large part of the debris field consists of ferrous metal objects that magnetic 39 Distribution A: Approved for public...was set at 7 degrees above horizontal based on terrain around the Base station. We used the BSUBR file for all fields except the Subsurface...and subsurface clearance test areas had numerous pieces of simulated unexploded ordinance (SUXO) buried at random locations around the field . These

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.

PubMed

Reboiro-Jato, Miguel; Arrais, Joel P; Oliveira, José Luis; Fdez-Riverola, Florentino

2014-01-30

The diagnosis and prognosis of several diseases can be shortened through the use of different large-scale genome experiments. In this context, microarrays can generate expression data for a huge set of genes. However, to obtain solid statistical evidence from the resulting data, it is necessary to train and to validate many classification techniques in order to find the best discriminative method. This is a time-consuming process that normally depends on intricate statistical tools. geneCommittee is a web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. Provided with a straightforward and intuitive interface, geneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. geneCommittee allows the enrichment of microarrays raw data with gene functional annotations, producing integrated datasets that simplify the construction of better discriminative hypothesis, and allows the creation of a set of complementary classifiers. The trained committees can then be used for clinical research and diagnosis. Full documentation including common use cases and guided analysis workflows is freely available at http://sing.ei.uvigo.es/GC/.

Reducing computational costs in large scale 3D EIT by using a sparse Jacobian matrix with block-wise CGLS reconstruction.

PubMed

Yang, C L; Wei, H Y; Adler, A; Soleimani, M

2013-06-01

Electrical impedance tomography (EIT) is a fast and cost-effective technique to provide a tomographic conductivity image of a subject from boundary current-voltage data. This paper proposes a time and memory efficient method for solving a large scale 3D EIT inverse problem using a parallel conjugate gradient (CG) algorithm. The 3D EIT system with a large number of measurement data can produce a large size of Jacobian matrix; this could cause difficulties in computer storage and the inversion process. One of challenges in 3D EIT is to decrease the reconstruction time and memory usage, at the same time retaining the image quality. Firstly, a sparse matrix reduction technique is proposed using thresholding to set very small values of the Jacobian matrix to zero. By adjusting the Jacobian matrix into a sparse format, the element with zeros would be eliminated, which results in a saving of memory requirement. Secondly, a block-wise CG method for parallel reconstruction has been developed. The proposed method has been tested using simulated data as well as experimental test samples. Sparse Jacobian with a block-wise CG enables the large scale EIT problem to be solved efficiently. Image quality measures are presented to quantify the effect of sparse matrix reduction in reconstruction results.

Identifiability in N-mixture models: a large-scale screening test with bird data.

PubMed

Kéry, Marc

2018-02-01

Binomial N-mixture models have proven very useful in ecology, conservation, and monitoring: they allow estimation and modeling of abundance separately from detection probability using simple counts. Recently, doubts about parameter identifiability have been voiced. I conducted a large-scale screening test with 137 bird data sets from 2,037 sites. I found virtually no identifiability problems for Poisson and zero-inflated Poisson (ZIP) binomial N-mixture models, but negative-binomial (NB) models had problems in 25% of all data sets. The corresponding multinomial N-mixture models had no problems. Parameter estimates under Poisson and ZIP binomial and multinomial N-mixture models were extremely similar. Identifiability problems became a little more frequent with smaller sample sizes (267 and 50 sites), but were unaffected by whether the models did or did not include covariates. Hence, binomial N-mixture model parameters with Poisson and ZIP mixtures typically appeared identifiable. In contrast, NB mixtures were often unidentifiable, which is worrying since these were often selected by Akaike's information criterion. Identifiability of binomial N-mixture models should always be checked. If problems are found, simpler models, integrated models that combine different observation models or the use of external information via informative priors or penalized likelihoods, may help. © 2017 by the Ecological Society of America.

Automation of processing and photometric data analysis for transiting exoplanets observed with ESO NIR instrument HAWK-I

NASA Astrophysics Data System (ADS)

Blažek, M.; Kabáth, P.; Klocová, T.; Skarka, M.

2018-04-01

Nowadays, when amount of data still increases, it is necessary to automatise their processing. State-of-the-art instruments are capable to produce even tens of thousands of images during a single night. One of them is HAWK-I that is a part of Very Large Telescope of European Southern Observatory. This instrument works in near-infrared band. In my Master thesis, I dealt with developing a pipeline to process data obtained by the instrument. It is written in Python programming language using commands of IRAF astronomical software and it is developed directly for "Fast Photometry Mode" of HAWK-I. In this mode, a large number of data has been obtained during secondary eclipses of exoplanets by their host star. The pipeline was tested by a data set from sorting of the images to making a light curve. The data of WASP-18 system contained almost 40 000 images observed by using a filter centered at 2.09 μm wavelength and there is a plan to process other data sets. A goal of processing of WASP-18 and the other data sets is consecutive analysis of exoplanetary atmospheres of the observed systems.

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems.

PubMed

Lê Cao, Kim-Anh; Boitard, Simon; Besse, Philippe

2011-06-22

Variable selection on high throughput biological data, such as gene expression or single nucleotide polymorphisms (SNPs), becomes inevitable to select relevant information and, therefore, to better characterize diseases or assess genetic structure. There are different ways to perform variable selection in large data sets. Statistical tests are commonly used to identify differentially expressed features for explanatory purposes, whereas Machine Learning wrapper approaches can be used for predictive purposes. In the case of multiple highly correlated variables, another option is to use multivariate exploratory approaches to give more insight into cell biology, biological pathways or complex traits. A simple extension of a sparse PLS exploratory approach is proposed to perform variable selection in a multiclass classification framework. sPLS-DA has a classification performance similar to other wrapper or sparse discriminant analysis approaches on public microarray and SNP data sets. More importantly, sPLS-DA is clearly competitive in terms of computational efficiency and superior in terms of interpretability of the results via valuable graphical outputs. sPLS-DA is available in the R package mixOmics, which is dedicated to the analysis of large biological data sets.

Investigation into the efficacy of generating synthetic pathological oscillations for domain adaptation

NASA Astrophysics Data System (ADS)

Lewis, Rory; Ellenberger, James; Williams, Colton; White, Andrew M.

2013-11-01

In the ongoing investigation of integrating Knowledge Discovery in Databases (KDD) into neuroscience, we present a paper that facilitates overcoming the two challenges preventing this integration. Pathological oscillations found in the human brain are difficult to evaluate because 1) there is often no time to learn and train off of the same distribution in the fatally sick, and 2) sinusoidal signals found in the human brain are complex and transient in nature requiring large data sets to work with which are costly and often very expensive or impossible to acquire. Overcoming these challenges in today's neuro-intensive-care unit (ICU) requires insurmountable resources. For these reasons, optimizing KDD for pathological oscillations so machine learning systems can predict neuropathological states would be of immense value. Domain adaptation, which allows a way of predicting on a separate set of data than the training data, can theoretically overcome the first challenge. However, the challenge of acquiring large data sets that show whether domain adaptation is a good candidate to test in a live neuro ICU remains a challenge. To solve this conundrum, we present a methodology for generating synthesized neuropathological oscillations for domain adaptation.

Current developments in optical engineering and commercial optics; Proceedings of the Meeting, San Diego, CA, Aug. 7-11, 1989

NASA Technical Reports Server (NTRS)

Fischer, Robert E. (Editor); Pollicove, Harvey M. (Editor); Smith, Warren J. (Editor)

1989-01-01

Various papers on current developments in optical engineering and commercial optics are presented. Individual topics addressed include: large optics fabrication technology drivers and new manufacturing techniques, new technology for beryllium mirror production, design examples of hybrid refractive-diffractive lenses, optical sensor designs for detecting cracks in optical materials, retroreflector field-of-view properties for open and solid cube corners, correction of misalignment-dependent aberrations of the HST via phase retrieval, basic radiometry review for seeker test set, radiation effects on visible optical elements, and nonlinear simulation of efficiency for large-orbit nonwiggler FELs.

Toward Exact Number: Young Children Use One-to-one Correspondence to Measure Set Identity but not Numerical Equality

PubMed Central

Izard, Véronique; Streri, Arlette; Spelke, Elizabeth S.

2014-01-01

Exact integer concepts are fundamental to a wide array of human activities, but their origins are obscure. Some have proposed that children are endowed with a system of natural number concepts, whereas others have argued that children construct these concepts by mastering verbal counting or other numeric symbols. This debate remains unresolved, because it is difficult to test children’s mastery of the logic of integer concepts without using symbols to enumerate large sets, and the symbols themselves could be a source of difficulty for children. Here, we introduce a new method, focusing on large quantities and avoiding the use of words or other symbols for numbers, to study children’s understanding of an essential property underlying integer concepts: the relation of exact numerical equality. Children aged 32-36 months, who possessed no symbols for exact numbers beyond 4, were given one-to-one correspondence cues to help them track a set of puppets, and their enumeration of the set was assessed by a non-verbal manual search task. Children used one-to-one correspondence relations to reconstruct exact quantities in sets of 5 or 6 objects, as long as the elements forming the sets remained the same individuals. In contrast, they failed to track exact quantities when one element was added, removed, or substituted for another. These results suggest an alternative to both nativist and symbol-based constructivist theories of the development of natural number concepts: Before learning symbols for exact numbers, children have a partial understanding of the properties of exact numbers. PMID:24680885

A MapReduce approach to diminish imbalance parameters for big deoxyribonucleic acid dataset.

PubMed

Kamal, Sarwar; Ripon, Shamim Hasnat; Dey, Nilanjan; Ashour, Amira S; Santhi, V

2016-07-01

In the age of information superhighway, big data play a significant role in information processing, extractions, retrieving and management. In computational biology, the continuous challenge is to manage the biological data. Data mining techniques are sometimes imperfect for new space and time requirements. Thus, it is critical to process massive amounts of data to retrieve knowledge. The existing software and automated tools to handle big data sets are not sufficient. As a result, an expandable mining technique that enfolds the large storage and processing capability of distributed or parallel processing platforms is essential. In this analysis, a contemporary distributed clustering methodology for imbalance data reduction using k-nearest neighbor (K-NN) classification approach has been introduced. The pivotal objective of this work is to illustrate real training data sets with reduced amount of elements or instances. These reduced amounts of data sets will ensure faster data classification and standard storage management with less sensitivity. However, general data reduction methods cannot manage very big data sets. To minimize these difficulties, a MapReduce-oriented framework is designed using various clusters of automated contents, comprising multiple algorithmic approaches. To test the proposed approach, a real DNA (deoxyribonucleic acid) dataset that consists of 90 million pairs has been used. The proposed model reduces the imbalance data sets from large-scale data sets without loss of its accuracy. The obtained results depict that MapReduce based K-NN classifier provided accurate results for big data of DNA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Method for Automatic Selection of Parameters in Normal Tissue Complication Probability Modeling.

PubMed

Christophides, Damianos; Appelt, Ane L; Gusnanto, Arief; Lilley, John; Sebag-Montefiore, David

2018-07-01

To present a fully automatic method to generate multiparameter normal tissue complication probability (NTCP) models and compare its results with those of a published model, using the same patient cohort. Data were analyzed from 345 rectal cancer patients treated with external radiation therapy to predict the risk of patients developing grade 1 or ≥2 cystitis. In total, 23 clinical factors were included in the analysis as candidate predictors of cystitis. Principal component analysis was used to decompose the bladder dose-volume histogram into 8 principal components, explaining more than 95% of the variance. The data set of clinical factors and principal components was divided into training (70%) and test (30%) data sets, with the training data set used by the algorithm to compute an NTCP model. The first step of the algorithm was to obtain a bootstrap sample, followed by multicollinearity reduction using the variance inflation factor and genetic algorithm optimization to determine an ordinal logistic regression model that minimizes the Bayesian information criterion. The process was repeated 100 times, and the model with the minimum Bayesian information criterion was recorded on each iteration. The most frequent model was selected as the final "automatically generated model" (AGM). The published model and AGM were fitted on the training data sets, and the risk of cystitis was calculated. The 2 models had no significant differences in predictive performance, both for the training and test data sets (P value > .05) and found similar clinical and dosimetric factors as predictors. Both models exhibited good explanatory performance on the training data set (P values > .44), which was reduced on the test data sets (P values < .05). The predictive value of the AGM is equivalent to that of the expert-derived published model. It demonstrates potential in saving time, tackling problems with a large number of parameters, and standardizing variable selection in NTCP modeling. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

Increasing the Complexity of the Illumination May Reduce Gloss Constancy

PubMed Central

Wendt, Gunnar; Faul, Franz

2017-01-01

We examined in which way gradual changes in the geometric structure of the illumination affect the perceived glossiness of a surface. The test stimuli were computer-generated three-dimensional scenes with a single test object that was illuminated by three point light sources, whose relative positions in space were systematically varied. In the first experiment, the subjects were asked to adjust the microscale smoothness of a match object illuminated by a single light source such that it has the same perceived glossiness as the test stimulus. We found that small changes in the structure of the light field can induce dramatic changes in perceived glossiness and that this effect is modulated by the microscale smoothness of the test object. The results of a second experiment indicate that the degree of overlap of nearby highlights plays a major role in this effect: Whenever the degree of overlap in a group of highlights is so large that they perceptually merge into a single highlight, the glossiness of the surface is systematically underestimated. In addition, we examined the predictability of the smoothness settings by a linear model that is based on a set of four different global image statistics. PMID:29250308

Ensemble coding remains accurate under object and spatial visual working memory load.

PubMed

Epstein, Michael L; Emmanouil, Tatiana A

2017-10-01

A number of studies have provided evidence that the visual system statistically summarizes large amounts of information that would exceed the limitations of attention and working memory (ensemble coding). However the necessity of working memory resources for ensemble coding has not yet been tested directly. In the current study, we used a dual task design to test the effect of object and spatial visual working memory load on size averaging accuracy. In Experiment 1, we tested participants' accuracy in comparing the mean size of two sets under various levels of object visual working memory load. Although the accuracy of average size judgments depended on the difference in mean size between the two sets, we found no effect of working memory load. In Experiment 2, we tested the same average size judgment while participants were under spatial visual working memory load, again finding no effect of load on averaging accuracy. Overall our results reveal that ensemble coding can proceed unimpeded and highly accurately under both object and spatial visual working memory load, providing further evidence that ensemble coding reflects a basic perceptual process distinct from that of individual object processing.

Multiphasic Health Testing in the Clinic Setting

PubMed Central

LaDou, Joseph

1971-01-01

The economy of automated multiphasic health testing (amht) activities patterned after the high-volume Kaiser program can be realized in low-volume settings. amht units have been operated at daily volumes of 20 patients in three separate clinical environments. These programs have displayed economics entirely compatible with cost figures published by the established high-volume centers. This experience, plus the expanding capability of small, general purpose, digital computers (minicomputers) indicates that a group of six or more physicians generating 20 laboratory appraisals per day can economically justify a completely automated multiphasic health testing facility. This system would reside in the clinic or hospital where it is used and can be configured to do analyses such as electrocardiography and generate laboratory reports, and communicate with large computer systems in university medical centers. Experience indicates that the most effective means of implementing these benefits of automation is to make them directly available to the medical community with the physician playing the central role. Economic justification of a dedicated computer through low-volume health testing then allows, as a side benefit, automation of administrative as well as other diagnostic activities—for example, patient billing, computer-aided diagnosis, and computer-aided therapeutics. PMID:4935771

Combined target factor analysis and Bayesian soft-classification of interference-contaminated samples: forensic fire debris analysis.

PubMed

Williams, Mary R; Sigman, Michael E; Lewis, Jennifer; Pitan, Kelly McHugh

2012-10-10

A bayesian soft classification method combined with target factor analysis (TFA) is described and tested for the analysis of fire debris data. The method relies on analysis of the average mass spectrum across the chromatographic profile (i.e., the total ion spectrum, TIS) from multiple samples taken from a single fire scene. A library of TIS from reference ignitable liquids with assigned ASTM classification is used as the target factors in TFA. The class-conditional distributions of correlations between the target and predicted factors for each ASTM class are represented by kernel functions and analyzed by bayesian decision theory. The soft classification approach assists in assessing the probability that ignitable liquid residue from a specific ASTM E1618 class, is present in a set of samples from a single fire scene, even in the presence of unspecified background contributions from pyrolysis products. The method is demonstrated with sample data sets and then tested on laboratory-scale burn data and large-scale field test burns. The overall performance achieved in laboratory and field test of the method is approximately 80% correct classification of fire debris samples. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.