Generation of distributed W-states over long distances

NASA Astrophysics Data System (ADS)

Li, Yi

2017-08-01

Ultra-secure quantum communication between distant locations requires distributed entangled states between nodes. Various methodologies have been proposed to tackle this technological challenge, of which the so-called DLCZ protocol is the most promising and widely adopted scheme. This paper aims to extend this well-known protocol to a multi-node setting where the entangled W-state is generated between nodes over long distances. The generation of multipartite W-states is the foundation of quantum networks, paving the way for quantum communication and distributed quantum computation.

Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.

PubMed

Kosoy, Roman; Nassir, Rami; Tian, Chao; White, Phoebe A; Butler, Lesley M; Silva, Gabriel; Kittles, Rick; Alarcon-Riquelme, Marta E; Gregersen, Peter K; Belmont, John W; De La Vega, Francisco M; Seldin, Michael F

2009-01-01

To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations. Copyright 2008 Wiley-Liss, Inc.

Vienna FORTRAN: A FORTRAN language extension for distributed memory multiprocessors

NASA Technical Reports Server (NTRS)

Chapman, Barbara; Mehrotra, Piyush; Zima, Hans

1991-01-01

Exploiting the performance potential of distributed memory machines requires a careful distribution of data across the processors. Vienna FORTRAN is a language extension of FORTRAN which provides the user with a wide range of facilities for such mapping of data structures. However, programs in Vienna FORTRAN are written using global data references. Thus, the user has the advantage of a shared memory programming paradigm while explicitly controlling the placement of data. The basic features of Vienna FORTRAN are presented along with a set of examples illustrating the use of these features.

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

PubMed

Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

2014-01-16

The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions. The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers.

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

PubMed Central

2014-01-01

Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions. Conclusions The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers. PMID:24433256

Neighborhood Perceptions Affect Dietary Behaviors and Diet Quality

ERIC Educational Resources Information Center

Keita, Akilah Dulin; Casazza, Krista; Thomas, Olivia; Fernandez, Jose R.

2011-01-01

Objective: The primary purpose of this study was to determine if perceived neighborhood disorder affected dietary quality within a multiethnic sample of children. Design: Children were recruited through the use of fliers, wide-distribution mailers, parent magazines, and school presentations from June 2005 to December 2008. Setting:…

Exploiting replication in distributed systems

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Joseph, T. A.

1989-01-01

Techniques are examined for replicating data and execution in directly distributed systems: systems in which multiple processes interact directly with one another while continuously respecting constraints on their joint behavior. Directly distributed systems are often required to solve difficult problems, ranging from management of replicated data to dynamic reconfiguration in response to failures. It is shown that these problems reduce to more primitive, order-based consistency problems, which can be solved using primitives such as the reliable broadcast protocols. Moreover, given a system that implements reliable broadcast primitives, a flexible set of high-level tools can be provided for building a wide variety of directly distributed application programs.

Effect of a fish stock's demographic structure on offspring survival and sensitivity to climate.

PubMed

Stige, Leif Christian; Yaragina, Natalia A; Langangen, Øystein; Bogstad, Bjarte; Stenseth, Nils Chr; Ottersen, Geir

2017-02-07

Commercial fishing generally removes large and old individuals from fish stocks, reducing mean age and age diversity among spawners. It is feared that these demographic changes lead to lower and more variable recruitment to the stocks. A key proposed pathway is that juvenation and reduced size distribution causes reduced ranges in spawning period, spawning location, and egg buoyancy; this is proposed to lead to reduced spatial distribution of fish eggs and larvae, more homogeneous ambient environmental conditions within each year-class, and reduced buffering against negative environmental influences. However, few, if any, studies have confirmed a causal link from spawning stock demographic structure through egg and larval distribution to year class strength at recruitment. We here show that high mean age and size in the spawning stock of Barents Sea cod (Gadus morhua) is positively associated with high abundance and wide spatiotemporal distribution of cod eggs. We find, however, no support for the hypothesis that a wide egg distribution leads to higher recruitment or a weaker recruitment-temperature correlation. These results are based on statistical analyses of a spatially resolved data set on cod eggs covering a period (1959-1993) with large changes in biomass and demographic structure of spawners. The analyses also account for significant effects of spawning stock biomass and a liver condition index on egg abundance and distribution. Our results suggest that the buffering effect of a geographically wide distribution of eggs and larvae on fish recruitment may be insignificant compared with other impacts.

An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification.

PubMed

Esfahani, Mohammad Shahrokh; Dougherty, Edward R

2015-01-01

Phenotype classification via genomic data is hampered by small sample sizes that negatively impact classifier design. Utilization of prior biological knowledge in conjunction with training data can improve both classifier design and error estimation via the construction of the optimal Bayesian classifier. In the genomic setting, gene/protein signaling pathways provide a key source of biological knowledge. Although these pathways are neither complete, nor regulatory, with no timing associated with them, they are capable of constraining the set of possible models representing the underlying interaction between molecules. The aim of this paper is to provide a framework and the mathematical tools to transform signaling pathways to prior probabilities governing uncertainty classes of feature-label distributions used in classifier design. Structural motifs extracted from the signaling pathways are mapped to a set of constraints on a prior probability on a Multinomial distribution. Being the conjugate prior for the Multinomial distribution, we propose optimization paradigms to estimate the parameters of a Dirichlet distribution in the Bayesian setting. The performance of the proposed methods is tested on two widely studied pathways: mammalian cell cycle and a p53 pathway model.

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

PubMed Central

De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

2016-01-01

Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

Diffusion of novel healthcare technologies to resource poor settings.

PubMed

Malkin, Robert; von Oldenburg Beer, Kim

2013-09-01

A new product has completed clinical trials in a distant, resource poor hospital using a few dozen prototypes. The data looks great. The novel medical device solves a widely felt problem. The next goal is to integrate the device into the country's healthcare system and spread the device to other countries. But how? In order to be widely used, the device must be manufactured and distributed. One option is to license the intellectual property (IP) to an interested third party, if one can be found. However, it is possible to manage the manufacturing and distribution without licensing. There are at least two common means for manufacturing a novel medical device targeted to resource poor settings: (a) formal (contract) manufacturing and (b) informal (local) manufacturing. There are three primary routes to diffusion of novel medical devices in the developing world: (1) local distributors (2) direct international sales and (3) international donations. Perhaps surprisingly, the least effective mechanism is direct importation through donation. The most successful mechanism, the method used by nearly all working medical devices in resource-poor settings, is the use of contract manufacturing and a local distributor. This article is written for the biomedical innovator and entrepreneur who wishes to make a novel healthcare technology or product available and accessible to healthcare providers and patients in the developing world. There are very few documented cases and little formal research in this area. To this end, this article describes and explores the manufacturing and distribution options in order to provide insights into when and how each can be applied to scale up a novel technology to make a difference in a resource poor setting.

Using process groups to implement failure detection in asynchronous environments

NASA Technical Reports Server (NTRS)

Ricciardi, Aleta M.; Birman, Kenneth P.

1991-01-01

Agreement on the membership of a group of processes in a distributed system is a basic problem that arises in a wide range of applications. Such groups occur when a set of processes cooperate to perform some task, share memory, monitor one another, subdivide a computation, and so forth. The group membership problems is discussed as it relates to failure detection in asynchronous, distributed systems. A rigorous, formal specification for group membership is presented under this interpretation. A solution is then presented for this problem.

Modeling Human Performance in Restless Bandits with Particle Filters

ERIC Educational Resources Information Center

Yi, Sheng Kung M.; Steyvers, Mark; Lee, Michael

2009-01-01

Bandit problems provide an interesting and widely-used setting for the study of sequential decision-making. In their most basic form, bandit problems require people to choose repeatedly between a small number of alternatives, each of which has an unknown rate of providing reward. We investigate restless bandit problems, where the distributions of…

Utility of Pamphlets in Promoting Knowledge and Positive Attitudes about Two Early Cancer Detection Procedures.

ERIC Educational Resources Information Center

Marty, Phillip J.; McDermott, Robert J.

Informational pamphlets about breast self-examination (BSE) and testicular self-examination (TSE) are widely distributed in health care settings, but the pamphlets' effectiveness in promoting knowledge and positive attitudes about these early cancer detection procedures is largely unknown. A study compared pamphlets with alternative methods of…

Minimum Wage Effects throughout the Wage Distribution

ERIC Educational Resources Information Center

Neumark, David; Schweitzer, Mark; Wascher, William

2004-01-01

This paper provides evidence on a wide set of margins along which labor markets can adjust in response to increases in the minimum wage, including wages, hours, employment, and ultimately labor income. Not surprisingly, the evidence indicates that low-wage workers are most strongly affected, while higher-wage workers are little affected. Workers…

Shallow ground-water quality beneath a major urban center: Denver, Colorado, USA

USGS Publications Warehouse

Bruce, B.W.; McMahon, P.B.

1996-01-01

A survey of the chemical quality of ground water in the unconsolidated alluvial aquifer beneath a major urban center (Denver, Colorado, USA) was performed in 1993 with the objective of characterizing the quality of shallow ground-water in the urban area and relating water quality to land use. Thirty randomly selected alluvial wells were each sampled once for a broad range of dissolved constituents. The urban land use at each well site was sub- classified into one of three land-use settings: residential, commercial, and industrial. Shallow ground-water quality was highly variable in the urban area and the variability could be related to these land-use setting classifications. Sulfate (SO4) was the predominant anion in most samples from the residential and commercial land-use settings, whereas bicarbonate (HCO3) was the predominant anion in samples from the industrial land-use setting, indicating a possible shift in redox conditions associated with land use. Only three of 30 samples had nitrate concentrations that exceeded the US national drinking-water standard of 10 mg l-1 as nitrogen, indicating that nitrate contamination of shallow ground water may not be a serious problem in this urban area. However, the highest median nitrate concentration (4.2 mg l-1) was in samples from the residential setting, where fertilizer application is assumed to be most intense. Twenty-seven of 30 samples had detectable pesticides and nine of 82 analyzed pesticide compounds were detected at low concentrations, indicating that pesticides are widely distributed in shallow ground water in this urban area. Although the highest median total pesticide concentration (0.17 ??g l-1) was in the commercial setting, the herbicides prometon and atrazine were found in each land-use setting. Similarly, 25 of 29 samples analyzed had detectable volatile organic compounds (VOCs) indicating these compounds are also widely distributed in this urban area. The total VOC concentrations in sampled wells ranged from nondetectable to 23 442 ??g l-1. Widespread detections and occasionally high concentrations point to VOCs as the major anthropogenic ground-water impact in this urban environment. Generally, the highest VOC concentrations occurred in samples from the industrial setting. The most frequently detected VOC was the gasoline additive methyl tertbutyl ether (MTBE, in 23 of 29 wells). Results from this study indicate that the quality of shallow ground water in major urban areas can be related to land-use settings. Moreover, some VOCs and pesticides may be widely distributed at low concentrations in shallow ground water throughout major urban areas. As a result, the differentiation between point and non-point sources for these compounds in urban areas may be difficult.

Characterization of Magnetospheric Spacecraft Charging Environments Using the LANL Magnetospheric Plasma Analyzer Data Set

NASA Technical Reports Server (NTRS)

Hardage, Donna (Technical Monitor); Davis, V. A.; Mandell, M. J.; Thomsen, M. F.

2003-01-01

An improved specification of the plasma environment has been developed for use in modeling spacecraft charging. It was developed by statistically analyzing a large part of the LANL Magnetospheric Plasma Analyzer (MPA) data set for ion and electron spectral signature correlation with spacecraft charging, including anisotropies. The objective is to identify a relatively simple characterization of the full particle distributions that yield an accurate predication of the observed charging under a wide variety of conditions.

How the deployment of attention determines what we see

PubMed Central

Treisman, Anne

2007-01-01

Attention is a tool to adapt what we see to our current needs. It can be focused narrowly on a single object or spread over several or distributed over the scene as a whole. In addition to increasing or decreasing the number of attended objects, these different deployments may have different effects on what we see. This chapter describes some research both on focused attention and its use in binding features, and on distributed attention and the kinds of information we gain and lose with the attention window opened wide. One kind of processing that we suggest occurs automatically with distributed attention results in a statistical description of sets of similar objects. Another gives the gist of the scene, which may be inferred from sets of features registered in parallel. Flexible use of these different modes of attention allows us to reconcile sharp capacity limits with a richer understanding of the visual scene. PMID:17387378

Execution time supports for adaptive scientific algorithms on distributed memory machines

NASA Technical Reports Server (NTRS)

Berryman, Harry; Saltz, Joel; Scroggs, Jeffrey

1990-01-01

Optimizations are considered that are required for efficient execution of code segments that consists of loops over distributed data structures. The PARTI (Parallel Automated Runtime Toolkit at ICASE) execution time primitives are designed to carry out these optimizations and can be used to implement a wide range of scientific algorithms on distributed memory machines. These primitives allow the user to control array mappings in a way that gives an appearance of shared memory. Computations can be based on a global index set. Primitives are used to carry out gather and scatter operations on distributed arrays. Communications patterns are derived at runtime, and the appropriate send and receive messages are automatically generated.

Execution time support for scientific programs on distributed memory machines

NASA Technical Reports Server (NTRS)

Berryman, Harry; Saltz, Joel; Scroggs, Jeffrey

1990-01-01

Optimizations are considered that are required for efficient execution of code segments that consists of loops over distributed data structures. The PARTI (Parallel Automated Runtime Toolkit at ICASE) execution time primitives are designed to carry out these optimizations and can be used to implement a wide range of scientific algorithms on distributed memory machines. These primitives allow the user to control array mappings in a way that gives an appearance of shared memory. Computations can be based on a global index set. Primitives are used to carry out gather and scatter operations on distributed arrays. Communications patterns are derived at runtime, and the appropriate send and receive messages are automatically generated.

Not to put too fine a point on it - does increasing precision of geographic referencing improve species distribution models for a wide-ranging migratory bat?

USGS Publications Warehouse

Hayes, Mark A.; Ozenberger, Katharine; Cryan, Paul M.; Wunder, Michael B.

2015-01-01

Bat specimens held in natural history museum collections can provide insights into the distribution of species. However, there are several important sources of spatial error associated with natural history specimens that may influence the analysis and mapping of bat species distributions. We analyzed the importance of geographic referencing and error correction in species distribution modeling (SDM) using occurrence records of hoary bats (Lasiurus cinereus). This species is known to migrate long distances and is a species of increasing concern due to fatalities documented at wind energy facilities in North America. We used 3,215 museum occurrence records collected from 1950–2000 for hoary bats in North America. We compared SDM performance using five approaches: generalized linear models, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy models. We evaluated results using three SDM performance metrics (AUC, sensitivity, and specificity) and two data sets: one comprised of the original occurrence data, and a second data set consisting of these same records after the locations were adjusted to correct for identifiable spatial errors. The increase in precision improved the mean estimated spatial error associated with hoary bat records from 5.11 km to 1.58 km, and this reduction in error resulted in a slight increase in all three SDM performance metrics. These results provide insights into the importance of geographic referencing and the value of correcting spatial errors in modeling the distribution of a wide-ranging bat species. We conclude that the considerable time and effort invested in carefully increasing the precision of the occurrence locations in this data set was not worth the marginal gains in improved SDM performance, and it seems likely that gains would be similar for other bat species that range across large areas of the continent, migrate, and are habitat generalists.

Effect of a fish stock's demographic structure on offspring survival and sensitivity to climate

PubMed Central

Stige, Leif Christian; Yaragina, Natalia A.; Langangen, Øystein; Bogstad, Bjarte; Stenseth, Nils Chr.; Ottersen, Geir

2017-01-01

Commercial fishing generally removes large and old individuals from fish stocks, reducing mean age and age diversity among spawners. It is feared that these demographic changes lead to lower and more variable recruitment to the stocks. A key proposed pathway is that juvenation and reduced size distribution causes reduced ranges in spawning period, spawning location, and egg buoyancy; this is proposed to lead to reduced spatial distribution of fish eggs and larvae, more homogeneous ambient environmental conditions within each year-class, and reduced buffering against negative environmental influences. However, few, if any, studies have confirmed a causal link from spawning stock demographic structure through egg and larval distribution to year class strength at recruitment. We here show that high mean age and size in the spawning stock of Barents Sea cod (Gadus morhua) is positively associated with high abundance and wide spatiotemporal distribution of cod eggs. We find, however, no support for the hypothesis that a wide egg distribution leads to higher recruitment or a weaker recruitment–temperature correlation. These results are based on statistical analyses of a spatially resolved data set on cod eggs covering a period (1959−1993) with large changes in biomass and demographic structure of spawners. The analyses also account for significant effects of spawning stock biomass and a liver condition index on egg abundance and distribution. Our results suggest that the buffering effect of a geographically wide distribution of eggs and larvae on fish recruitment may be insignificant compared with other impacts. PMID:28115694

A Distributed Fuzzy Associative Classifier for Big Data.

PubMed

Segatori, Armando; Bechini, Alessio; Ducange, Pietro; Marcelloni, Francesco

2017-09-19

Fuzzy associative classification has not been widely analyzed in the literature, although associative classifiers (ACs) have proved to be very effective in different real domain applications. The main reason is that learning fuzzy ACs is a very heavy task, especially when dealing with large datasets. To overcome this drawback, in this paper, we propose an efficient distributed fuzzy associative classification approach based on the MapReduce paradigm. The approach exploits a novel distributed discretizer based on fuzzy entropy for efficiently generating fuzzy partitions of the attributes. Then, a set of candidate fuzzy association rules is generated by employing a distributed fuzzy extension of the well-known FP-Growth algorithm. Finally, this set is pruned by using three purposely adapted types of pruning. We implemented our approach on the popular Hadoop framework. Hadoop allows distributing storage and processing of very large data sets on computer clusters built from commodity hardware. We have performed an extensive experimentation and a detailed analysis of the results using six very large datasets with up to 11,000,000 instances. We have also experimented different types of reasoning methods. Focusing on accuracy, model complexity, computation time, and scalability, we compare the results achieved by our approach with those obtained by two distributed nonfuzzy ACs recently proposed in the literature. We highlight that, although the accuracies result to be comparable, the complexity, evaluated in terms of number of rules, of the classifiers generated by the fuzzy distributed approach is lower than the one of the nonfuzzy classifiers.

Methane emissions from global wetlands: An assessment of the uncertainty associated with various wetland extent data sets

NASA Astrophysics Data System (ADS)

Zhang, Bowen; Tian, Hanqin; Lu, Chaoqun; Chen, Guangsheng; Pan, Shufen; Anderson, Christopher; Poulter, Benjamin

2017-09-01

A wide range of estimates on global wetland methane (CH4) fluxes has been reported during the recent two decades. This gives rise to urgent needs to clarify and identify the uncertainty sources, and conclude a reconciled estimate for global CH4 fluxes from wetlands. Most estimates by using bottom-up approach rely on wetland data sets, but these data sets show largely inconsistent in terms of both wetland extent and spatiotemporal distribution. A quantitative assessment of uncertainties associated with these discrepancies among wetland data sets has not been well investigated yet. By comparing the five widely used global wetland data sets (GISS, GLWD, Kaplan, GIEMS and SWAMPS-GLWD), it this study, we found large differences in the wetland extent, ranging from 5.3 to 10.2 million km2, as well as their spatial and temporal distributions among the five data sets. These discrepancies in wetland data sets resulted in large bias in model-estimated global wetland CH4 emissions as simulated by using the Dynamic Land Ecosystem Model (DLEM). The model simulations indicated that the mean global wetland CH4 emissions during 2000-2007 were 177.2 ± 49.7 Tg CH4 yr-1, based on the five different data sets. The tropical regions contributed the largest portion of estimated CH4 emissions from global wetlands, but also had the largest discrepancy. Among six continents, the largest uncertainty was found in South America. Thus, the improved estimates of wetland extent and CH4 emissions in the tropical regions and South America would be a critical step toward an accurate estimate of global CH4 emissions. This uncertainty analysis also reveals an important need for our scientific community to generate a global scale wetland data set with higher spatial resolution and shorter time interval, by integrating multiple sources of field and satellite data with modeling approaches, for cross-scale extrapolation.

NSW Executive Enhancements

DTIC Science & Technology

1981-06-01

independently on the same network. Given this reduction in scale, the projected impl widely distributed, fully replicated, synchronized dat design...Manager that "owns" other resources. This strategy requires minimum synchronization while providing advantages in reliability and robustness. 2 3...interactive tools on TENEX, transparent file motion and translation, and a primitive set of project management functions. This demonstration confirmed that

Design and Empirical Evaluation of Search Software for Legal Professionals on the WWW.

ERIC Educational Resources Information Center

Dempsey, Bert J.; Vreeland, Robert C.; Sumner, Robert G., Jr.; Yang, Kiduk

2000-01-01

Discussion of effective search aids for legal researchers on the World Wide Web focuses on the design and evaluation of two software systems developed to explore models for browsing and searching across a user-selected set of Web sites. Describes crawler-enhanced search engines, filters, distributed full-text searching, and natural language…

16 CFR 308.4 - Special rule for infrequent publications.

Code of Federal Regulations, 2010 CFR

2010-01-01

... advertises a pay-per-call service in a publication that meets the requirements set forth in § 308.4(c) may... conspicuous disclosure that a call to the advertised pay-per-call service may result in a substantial charge...) The publication referred to in § 308.4 (a) and (b) must be: (1) Widely distributed; (2) Printed...

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

PubMed

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

Estimation of distributional parameters for censored trace level water quality data: 1. Estimation techniques

USGS Publications Warehouse

Gilliom, Robert J.; Helsel, Dennis R.

1986-01-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensored observations, for determining the best performing parameter estimation method for any particular data set. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification.

Estimation of distributional parameters for censored trace-level water-quality data

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

Gilliom, R.J.; Helsel, D.R.

1984-01-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water-sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensored observations,more » for determining the best-performing parameter estimation method for any particular data set. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least-squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification. 6 figs., 6 tabs.« less

RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing.

PubMed

Chang, Lun-Ching; Das, Biswajit; Lih, Chih-Jian; Si, Han; Camalier, Corinne E; McGregor, Paul M; Polley, Eric

2016-01-01

With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we compared the observed coverage with the expected normal coverage. Thresholds for determining CNVs were selected to control the false-positive error rate. RefCNV prediction correlated significantly (r = 0.96-0.86) with CNV measured by digital polymerase chain reaction for MET (7q31), EGFR (7p12), or ERBB2 (17q12) in 13 tumor cell lines. The genome-wide CNV analysis showed a good overall correlation (Spearman's coefficient = 0.82) between RefCNV estimation and publicly available CNV data in Cancer Cell Line Encyclopedia. RefCNV also showed better performance than three other CNV estimation methods in genome-wide CNV analysis.

Detecting microsatellites within genomes: significant variation among algorithms.

PubMed

Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

2007-04-18

Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker). Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif. Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.

Detecting microsatellites within genomes: significant variation among algorithms

PubMed Central

Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

2007-01-01

Background Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker). Results Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif. Conclusion Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions. PMID:17442102

Characteristics of ovulation method acceptors: a cross-cultural assessment.

PubMed

Klaus, H; Labbok, M; Barker, D

1988-01-01

Five programs of instruction in the ovulation method (OM) in diverse geographic and cultural settings are described, and characteristics of approximately 200 consecutive OM acceptors in each program are examined. Major findings include: the religious background and family size of acceptors are variable, as is the level of previous contraceptive use. Acceptors are drawn from a wide range of socioeconomic and religious backgrounds; however, family planning intention was similarly distributed in all five countries. In sum, the ovulation method is accepted by persons from a variety of backgrounds within and between cultural setting.

Sexual size dimorphism predicts the frequency of sexual cannibalism within and among species of spiders.

PubMed

Wilder, Shawn M; Rypstra, Ann L

2008-09-01

Sexual cannibalism varies widely among spiders, but no general evolutionary hypothesis has emerged to explain its distribution across taxa. Sexual size dimorphism (SSD) also varies widely among spiders and could affect the vulnerability of males to cannibalistic attacks by females. We tested for a relationship between SSD and sexual cannibalism within and among species of spiders, using a broad taxonomic data set. For most species, cannibalism was more likely when males were much smaller than females. In addition, using phylogenetically controlled and uncontrolled analyses, there was a strong positive relationship between average SSD of a species and the frequency of sexual cannibalism. This is the first evidence that the degree of size difference between males and females is related to the phylogenetic distribution of sexual cannibalism among a broad range of spiders.

An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change

PubMed Central

Casajus, Nicolas; Périé, Catherine; Logan, Travis; Lambert, Marie-Claude; de Blois, Sylvie; Berteaux, Dominique

2016-01-01

An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one. PMID:27015274

An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change.

PubMed

Casajus, Nicolas; Périé, Catherine; Logan, Travis; Lambert, Marie-Claude; de Blois, Sylvie; Berteaux, Dominique

2016-01-01

An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one.

The added value of remote sensing products in constraining hydrological models

NASA Astrophysics Data System (ADS)

Nijzink, Remko C.; Almeida, Susana; Pechlivanidis, Ilias; Capell, René; Gustafsson, David; Arheimer, Berit; Freer, Jim; Han, Dawei; Wagener, Thorsten; Sleziak, Patrik; Parajka, Juraj; Savenije, Hubert; Hrachowitz, Markus

2017-04-01

The calibration of a hydrological model still depends on the availability of streamflow data, even though more additional sources of information (i.e. remote sensed data products) have become more widely available. In this research, the model parameters of four different conceptual hydrological models (HYPE, HYMOD, TUW, FLEX) were constrained with remotely sensed products. The models were applied over 27 catchments across Europe to cover a wide range of climates, vegetation and landscapes. The fluxes and states of the models were correlated with the relevant products (e.g. MOD10A snow with modelled snow states), after which new a-posteriori parameter distributions were determined based on a weighting procedure using conditional probabilities. Briefly, each parameter was weighted with the coefficient of determination of the relevant regression between modelled states/fluxes and products. In this way, final feasible parameter sets were derived without the use of discharge time series. Initial results show that improvements in model performance, with regard to streamflow simulations, are obtained when the models are constrained with a set of remotely sensed products simultaneously. In addition, we present a more extensive analysis to assess a model's ability to reproduce a set of hydrological signatures, such as rising limb density or peak distribution. Eventually, this research will enhance our understanding and recommendations in the use of remotely sensed products for constraining conceptual hydrological modelling and improving predictive capability, especially for data sparse regions.

Genome-Wide Association Study of the Genetic Determinants of Emphysema Distribution.

PubMed

Boueiz, Adel; Lutz, Sharon M; Cho, Michael H; Hersh, Craig P; Bowler, Russell P; Washko, George R; Halper-Stromberg, Eitan; Bakke, Per; Gulsvik, Amund; Laird, Nan M; Beaty, Terri H; Coxson, Harvey O; Crapo, James D; Silverman, Edwin K; Castaldi, Peter J; DeMeo, Dawn L

2017-03-15

Emphysema has considerable variability in the severity and distribution of parenchymal destruction throughout the lungs. Upper lobe-predominant emphysema has emerged as an important predictor of response to lung volume reduction surgery. Yet, aside from alpha-1 antitrypsin deficiency, the genetic determinants of emphysema distribution remain largely unknown. To identify the genetic influences of emphysema distribution in non-alpha-1 antitrypsin-deficient smokers. A total of 11,532 subjects with complete genotype and computed tomography densitometry data in the COPDGene (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease [COPD]; non-Hispanic white and African American), ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints), and GenKOLS (Genetics of Chronic Obstructive Lung Disease) studies were analyzed. Two computed tomography scan emphysema distribution measures (difference between upper-third and lower-third emphysema; ratio of upper-third to lower-third emphysema) were tested for genetic associations in all study subjects. Separate analyses in each study population were followed by a fixed effect metaanalysis. Single-nucleotide polymorphism-, gene-, and pathway-based approaches were used. In silico functional evaluation was also performed. We identified five loci associated with emphysema distribution at genome-wide significance. These loci included two previously reported associations with COPD susceptibility (4q31 near HHIP and 15q25 near CHRNA5) and three new associations near SOWAHB, TRAPPC9, and KIAA1462. Gene set analysis and in silico functional evaluation revealed pathways and cell types that may potentially contribute to the pathogenesis of emphysema distribution. This multicohort genome-wide association study identified new genomic loci associated with differential emphysematous destruction throughout the lungs. These findings may point to new biologic pathways on which to expand diagnostic and therapeutic approaches in chronic obstructive pulmonary disease. Clinical trial registered with www.clinicaltrials.gov (NCT 00608764).

Gendered use of experts in the media: Analysis of the gender gap in Finnish news journalism.

PubMed

Niemi, Mari K; Pitkänen, Ville

2017-04-01

Several studies conducted in Western democracies have indicated that men continue to be overrepresented and women underrepresented as experts in the media. This article explores the situation in Finland, a progressive and 'female-friendly' Nordic country with highly educated women who are widely present in the job market. The analysis is based on three sets of research data featuring a wide set of media data, a survey and interviews. This study reveals that public expertise continues to be male dominated in Finland: less than 30% of the experts interviewed in the news media are women. While the distribution of work and power in the labour market may explain some of the observed gender gap, journalistic practices and a masculine tradition of public expertise are likely to play a role as well.

Oak decline in central hardwood forests: frequency, spatial extent, and scale

Treesearch

Steven W Oak; Marty Spetich; Randall S. Morin

2015-01-01

Oak decline is a widely distributed disease that results from an interacting set of factors in the Central Hardwood Region. Episodes of decline have been reported since before the turn of the twentieth century and from every state in the region. It is a stress-mediated disease that results from the interactions of physiologically mature trees, abiotic and biotic...

A Review of the Stockton Training Series: Instructor Reports of Current Use and Future Application

ERIC Educational Resources Information Center

Krieger, Kenin M.; Whittingham, Martyn

2005-01-01

For the past decade, the Stockton training series has offered instructors a valuable training tool for use in a variety of clinical settings. Counselor educators were asked to reflect upon the series and its application for beginning leader training. Specifically, surveys were distributed to a wide range of instructors who train group leaders;…

STRIDE: Species Tree Root Inference from Gene Duplication Events.

PubMed

Emms, David M; Kelly, Steven

2017-12-01

The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Quantifying evenly distributed states in exclusion and nonexclusion processes

NASA Astrophysics Data System (ADS)

Binder, Benjamin J.; Landman, Kerry A.

2011-04-01

Spatial-point data sets, generated from a wide range of physical systems and mathematical models, can be analyzed by counting the number of objects in equally sized bins. We find that the bin counts are related to the Pólya distribution. New measures are developed which indicate whether or not a spatial data set, generated from an exclusion process, is at its most evenly distributed state, the complete spatial randomness (CSR) state. To this end, we define an index in terms of the variance between the bin counts. Limiting values of the index are determined when objects have access to the entire domain and when there are subregions of the domain that are inaccessible to objects. Using three case studies (Lagrangian fluid particles in chaotic laminar flows, cellular automata agents in discrete models, and biological cells within colonies), we calculate the indexes and verify that our theoretical CSR limit accurately predicts the state of the system. These measures should prove useful in many biological applications.

KeyWare: an open wireless distributed computing environment

NASA Astrophysics Data System (ADS)

Shpantzer, Isaac; Schoenfeld, Larry; Grindahl, Merv; Kelman, Vladimir

1995-12-01

Deployment of distributed applications in the wireless domain lack equivalent tools, methodologies, architectures, and network management that exist in LAN based applications. A wireless distributed computing environment (KeyWareTM) based on intelligent agents within a multiple client multiple server scheme was developed to resolve this problem. KeyWare renders concurrent application services to wireline and wireless client nodes encapsulated in multiple paradigms such as message delivery, database access, e-mail, and file transfer. These services and paradigms are optimized to cope with temporal and spatial radio coverage, high latency, limited throughput and transmission costs. A unified network management paradigm for both wireless and wireline facilitates seamless extensions of LAN- based management tools to include wireless nodes. A set of object oriented tools and methodologies enables direct asynchronous invocation of agent-based services supplemented by tool-sets matched to supported KeyWare paradigms. The open architecture embodiment of KeyWare enables a wide selection of client node computing platforms, operating systems, transport protocols, radio modems and infrastructures while maintaining application portability.

From "Where" to "What": Distributed Representations of Brand Associations in the Human Brain.

PubMed

Chen, Yu-Ping; Nelson, Leif D; Hsu, Ming

2015-08-01

Considerable attention has been given to the notion that there exists a set of human-like characteristics associated with brands, referred to as brand personality. Here we combine newly available machine learning techniques with functional neuroimaging data to characterize the set of processes that give rise to these associations. We show that brand personality traits can be captured by the weighted activity across a widely distributed set of brain regions previously implicated in reasoning, imagery, and affective processing. That is, as opposed to being constructed via reflective processes, brand personality traits appear to exist a priori inside the minds of consumers, such that we were able to predict what brand a person is thinking about based solely on the relationship between brand personality associations and brain activity. These findings represent an important advance in the application of neuroscientific methods to consumer research, moving from work focused on cataloguing brain regions associated with marketing stimuli to testing and refining mental constructs central to theories of consumer behavior.

From “Where” to “What”: Distributed Representations of Brand Associations in the Human Brain

PubMed Central

Chen, Yu-Ping; Nelson, Leif D.; Hsu, Ming

2015-01-01

Considerable attention has been given to the notion that there exists a set of human-like characteristics associated with brands, referred to as brand personality. Here we combine newly available machine learning techniques with functional neuroimaging data to characterize the set of processes that give rise to these associations. We show that brand personality traits can be captured by the weighted activity across a widely distributed set of brain regions previously implicated in reasoning, imagery, and affective processing. That is, as opposed to being constructed via reflective processes, brand personality traits appear to exist a priori inside the minds of consumers, such that we were able to predict what brand a person is thinking about based solely on the relationship between brand personality associations and brain activity. These findings represent an important advance in the application of neuroscientific methods to consumer research, moving from work focused on cataloguing brain regions associated with marketing stimuli to testing and refining mental constructs central to theories of consumer behavior. PMID:27065490

Fully Decentralized Semi-supervised Learning via Privacy-preserving Matrix Completion.

PubMed

Fierimonte, Roberto; Scardapane, Simone; Uncini, Aurelio; Panella, Massimo

2016-08-26

Distributed learning refers to the problem of inferring a function when the training data are distributed among different nodes. While significant work has been done in the contexts of supervised and unsupervised learning, the intermediate case of Semi-supervised learning in the distributed setting has received less attention. In this paper, we propose an algorithm for this class of problems, by extending the framework of manifold regularization. The main component of the proposed algorithm consists of a fully distributed computation of the adjacency matrix of the training patterns. To this end, we propose a novel algorithm for low-rank distributed matrix completion, based on the framework of diffusion adaptation. Overall, the distributed Semi-supervised algorithm is efficient and scalable, and it can preserve privacy by the inclusion of flexible privacy-preserving mechanisms for similarity computation. The experimental results and comparison on a wide range of standard Semi-supervised benchmarks validate our proposal.

Access, excess, and ethics--towards a sustainable distribution model for antibiotics.

PubMed

Heyman, Gabriel; Cars, Otto; Bejarano, Maria-Teresa; Peterson, Stefan

2014-05-01

The increasing antibiotic resistance is a global threat to health care as we know it. Yet there is no model of distribution ready for a new antibiotic that balances access against excessive or inappropriate use in rural settings in low- and middle-income countries (LMICs) where the burden of communicable diseases is high and access to quality health care is low. Departing from a hypothetical scenario of rising antibiotic resistance among pneumococci, 11 stakeholders in the health systems of various LMICs were interviewed one-on-one to give their view on how a new effective antibiotic should be distributed to balance access against the risk of inappropriate use. Transcripts were subjected to qualitative 'framework' analysis. The analysis resulted in four main themes: Barriers to rational access to antibiotics; balancing access and excess; learning from other communicable diseases; and a system-wide intervention. The tension between access to antibiotics and rational use stems from shortcomings found in the health systems of LMICs. Constructing a sustainable yet accessible model of antibiotic distribution for LMICs is a task of health system-wide proportions, which is why we strongly suggest using systems thinking in future research on this issue.

Access, excess, and ethics—towards a sustainable distribution model for antibiotics

PubMed Central

Heyman, Gabriel; Cars, Otto; Bejarano, Maria-Teresa

2014-01-01

The increasing antibiotic resistance is a global threat to health care as we know it. Yet there is no model of distribution ready for a new antibiotic that balances access against excessive or inappropriate use in rural settings in low- and middle-income countries (LMICs) where the burden of communicable diseases is high and access to quality health care is low. Departing from a hypothetical scenario of rising antibiotic resistance among pneumococci, 11 stakeholders in the health systems of various LMICs were interviewed one-on-one to give their view on how a new effective antibiotic should be distributed to balance access against the risk of inappropriate use. Transcripts were subjected to qualitative ‘framework’ analysis. The analysis resulted in four main themes: Barriers to rational access to antibiotics; balancing access and excess; learning from other communicable diseases; and a system-wide intervention. The tension between access to antibiotics and rational use stems from shortcomings found in the health systems of LMICs. Constructing a sustainable yet accessible model of antibiotic distribution for LMICs is a task of health system-wide proportions, which is why we strongly suggest using systems thinking in future research on this issue. PMID:24735111

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences

PubMed Central

2014-01-01

Background Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Results Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. Conclusion The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification. PMID:24418292

The concordance index C and the Mann-Whitney parameter Pr(X>Y) with randomly censored data.

PubMed

Koziol, James A; Jia, Zhenyu

2009-06-01

Harrell's c-index or concordance C has been widely used as a measure of separation of two survival distributions. In the absence of censored data, the c-index estimates the Mann-Whitney parameter Pr(X>Y), which has been repeatedly utilized in various statistical contexts. In the presence of randomly censored data, the c-index no longer estimates Pr(X>Y); rather, a parameter that involves the underlying censoring distributions. This is in contrast to Efron's maximum likelihood estimator of the Mann-Whitney parameter, which is recommended in the setting of random censorship.

Comet nuclear magnitudes and a new size distribution using archived NEAT data.

NASA Astrophysics Data System (ADS)

Bambery, R. J.; Hicks, M. D.; Pravdo, S. H.; Helin, E. F.; Lawrence, K. J.

2002-09-01

A reliable estimate of the size distribution of cometary nuclei provides important constraints on the formation and dynamical/physical evolution of these bodies as well as their relative proportions in the near-Earth population. The basic data of nuclear sizes has been difficult to obtain, due to the shroud of dust that envelopes the nucleus across a wide range of heliocentric distances. Only two comets, P/Halley and P/Borrelly, have had direct imaging of their nuclei from spacecraft encounters, though high spatial-resolution imaging by the Hubble Space Telescope has also yielded very reliable diameters [1]. Other observers have recently used ground-based photometry to obtain cumulative size-frequency distributions which are not in agreement [2,3]. One possible source of error is the need to include data from a wide range of telescopes and reduction techniques. We shall obtain a new estimate of the size-frequency distribution using a self-consistent data-set. The Near-Earth Asteroid Tracking (NEAT) Program at the Jet Propulsion laboratory remotely operates two 1.2-meter telescopes at widely geographically separated locations on a near-nightly basis. All NEAT data is archived and publically available through the SKYMORPH website (http:/skyview.gsfc.nasa.gov/skymorph/skymorph.html) Though optimized to discover near-Earth asteroids, we have obtained over 300 CCD images of approximately 40 short and long-period comets over the last 15 months. Though we model coma contamination for all images, we shall concentrate on the fraction of comets at heliocentric distances greater than 3 AU. Our data will be used to derive an independent comet size-frequency distribution .

Distributed Autonomous Control Action Based on Sensor and Mission Fusion

DTIC Science & Technology

2005-09-01

programmable control algorithm driven by the readings of two pressure switch sensors located on either side of the valve unit. Thus, a micro-controller...and Characterization The process of leak detection and characterization must be accomplished with a set of pressure switch sensors. This sensor...economically supplementing existing widely used pressure switch type sensors which are characterized by prohibitively long inertial lag responses

Autonomic Management in a Distributed Storage System

NASA Astrophysics Data System (ADS)

Tauber, Markus

2010-07-01

This thesis investigates the application of autonomic management to a distributed storage system. Effects on performance and resource consumption were measured in experiments, which were carried out in a local area test-bed. The experiments were conducted with components of one specific distributed storage system, but seek to be applicable to a wide range of such systems, in particular those exposed to varying conditions. The perceived characteristics of distributed storage systems depend on their configuration parameters and on various dynamic conditions. For a given set of conditions, one specific configuration may be better than another with respect to measures such as resource consumption and performance. Here, configuration parameter values were set dynamically and the results compared with a static configuration. It was hypothesised that under non-changing conditions this would allow the system to converge on a configuration that was more suitable than any that could be set a priori. Furthermore, the system could react to a change in conditions by adopting a more appropriate configuration. Autonomic management was applied to the peer-to-peer (P2P) and data retrieval components of ASA, a distributed storage system. The effects were measured experimentally for various workload and churn patterns. The management policies and mechanisms were implemented using a generic autonomic management framework developed during this work. The experimental evaluations of autonomic management show promising results, and suggest several future research topics. The findings of this thesis could be exploited in building other distributed storage systems that focus on harnessing storage on user workstations, since these are particularly likely to be exposed to varying, unpredictable conditions.

Interactive access and management for four-dimensional environmental data sets using McIDAS

NASA Technical Reports Server (NTRS)

Hibbard, William L.; Tripoli, Gregory J.

1995-01-01

This grant has fundamentally changed the way that meteorologists look at the output of their atmospheric models, through the development and wide distribution of the Vis5D system. The Vis5D system is also gaining acceptance among oceanographers and atmospheric chemists. Vis5D gives these scientists an interactive three-dimensional movie of their very large data sets that they can use to understand physical mechanisms and to trace problems to their sources. This grant has also helped to define the future direction of scientific visualization through the development of the VisAD system and its lattice data model. The VisAD system can be used to interactively steer and visualize scientific computations. A key element of this capability is the flexibility of the system's data model to adapt to a wide variety of scientific data, including the integration of several forms of scientific metadata.

The prevalence and geographic distribution of complex co-occurring disorders: a population study.

PubMed

Somers, J M; Moniruzzaman, A; Rezansoff, S N; Brink, J; Russolillo, A

2016-06-01

A subset of people with co-occurring substance use and mental disorders require coordinated support from health, social welfare and justice agencies to achieve diversion from homelessness, criminal recidivism and further health and social harms. Integrated models of care are typically concentrated in large urban centres. The present study aimed to empirically measure the prevalence and distribution of complex co-occurring disorders (CCD) in a large geographic region that includes urban as well as rural and remote settings. Linked data were examined in a population of roughly 3.7 million adults. Inclusion criteria for the CCD subpopulation were: physician diagnosed substance use and mental disorders; psychiatric hospitalisation; shelter assistance; and criminal convictions. Prevalence per 100 000 was calculated in 91 small areas representing urban, rural and remote settings. 2202 individuals met our inclusion criteria for CCD. Participants had high rates of hospitalisation (8.2 admissions), criminal convictions (8.6 sentences) and social assistance payments (over $36 000 CDN) in the past 5 years. There was wide variability in the geographic distribution of people with CCD, with high prevalence rates in rural and remote settings. People with CCD are not restricted to areas with large populations or to urban settings. The highest per capita rates of CCD were observed in relatively remote locations, where mental health and substance use services are typically in limited supply. Empirically supported interventions must be adapted to meet the needs of people living outside of urban settings with high rates of CCD.

ROSAT observations of clusters with wide-angle tailed radio sources

NASA Technical Reports Server (NTRS)

Burns, Jack O.

1993-01-01

The goal of these ROSAT PSPC pointed observations was to understand the nature of X-ray emission associated clusters that contain luminous wide-angle tailed (WAT) radio sources identified with the centrally dominant cluster galaxies. These 500 kpc diameter radio sources are strongly affected by confinement and interaction with the intracluster medium. So, a complete picture of the origin and evolution of these radio sources is not possible without detailed X-ray observations which sample the distribution and temperature of the surrounding hot gas. Two WAT clusters have been observed with the ROSAT PSPC to date. The first is Abell 2634 which contains the WAT 3C 465 and was approved for observations in AO-1. Unfortunately, these observations were broken into two widely separated pieces in time. The first data set containing about 9000 sec of integration arrived in mid-March, 1992. The second data set containing about 10,500 sec arrived just recently in early April (after a first tape was destroyed in the mail). The second cluster is 1919+479 which was approved for observations in AO-2. These ROSAT data arrived in October 1992.

The correlation of metrics in complex networks with applications in functional brain networks

NASA Astrophysics Data System (ADS)

Li, C.; Wang, H.; de Haan, W.; Stam, C. J.; Van Mieghem, P.

2011-11-01

An increasing number of network metrics have been applied in network analysis. If metric relations were known better, we could more effectively characterize networks by a small set of metrics to discover the association between network properties/metrics and network functioning. In this paper, we investigate the linear correlation coefficients between widely studied network metrics in three network models (Bárabasi-Albert graphs, Erdös-Rényi random graphs and Watts-Strogatz small-world graphs) as well as in functional brain networks of healthy subjects. The metric correlations, which we have observed and theoretically explained, motivate us to propose a small representative set of metrics by including only one metric from each subset of mutually strongly dependent metrics. The following contributions are considered important. (a) A network with a given degree distribution can indeed be characterized by a small representative set of metrics. (b) Unweighted networks, which are obtained from weighted functional brain networks with a fixed threshold, and Erdös-Rényi random graphs follow a similar degree distribution. Moreover, their metric correlations and the resultant representative metrics are similar as well. This verifies the influence of degree distribution on metric correlations. (c) Most metric correlations can be explained analytically. (d) Interestingly, the most studied metrics so far, the average shortest path length and the clustering coefficient, are strongly correlated and, thus, redundant. Whereas spectral metrics, though only studied recently in the context of complex networks, seem to be essential in network characterizations. This representative set of metrics tends to both sufficiently and effectively characterize networks with a given degree distribution. In the study of a specific network, however, we have to at least consider the representative set so that important network properties will not be neglected.

Trends in opioid analgesics sales to community pharmacies and hospitals in Italy (2000-2010).

PubMed

Caraceni, A T; Brunelli, C; Rocco, P; Minghetti, P

2013-08-01

Opioid consumption data in Italy have been widely studied. However, only aggregate data can be found in the published literature, and differences are expected by distribution setting (community pharmacies and hospitals). The aim of our paper is to analyse opioids sales trends in Italy in the decade 2000-2010, in an effort to explore such differences. Quarterly sales data of opioid medicinal products sold by wholesalers to both community pharmacies (retail) and to hospitals (non-retail) during the time period 2000-2010 were supplied by IMS Italy. Data were standardized using the Defined Daily Doses per day per 1000 inhabitants (DDDd/1000). Opioid sales have steadily increased during the time period considered going from 1.04 DDDd/1000 in 2000 to 4.9 in 2010 (+292%). Nonetheless relevant differences can be found both by distribution setting and drug type. In particular retail sales have increased by 286 % for WHO Step II opioids and by 575% for WHO Step III drugs, while non-retail sales have increased by 48% and 263%, respectively. In 2010, fentanyl and buprenorphine transdermal patches and oxycodone are more widely prescribed than morphine, in the retail setting, with fentanyl at large in the first position. In hospitals morphine and fentanyl almost equally share the 75% of the market. Data suggest that morphine is no more the opioid of first choice for severe pain in Italy, at least for outpatients. This is contradicting most international guidelines available in the 2000-2010 decade.

Turbulence hierarchy in a random fibre laser

PubMed Central

González, Iván R. Roa; Lima, Bismarck C.; Pincheira, Pablo I. R.; Brum, Arthur A.; Macêdo, Antônio M. S.; Vasconcelos, Giovani L.; de S. Menezes, Leonardo; Raposo, Ernesto P.; Gomes, Anderson S. L.; Kashyap, Raman

2017-01-01

Turbulence is a challenging feature common to a wide range of complex phenomena. Random fibre lasers are a special class of lasers in which the feedback arises from multiple scattering in a one-dimensional disordered cavity-less medium. Here we report on statistical signatures of turbulence in the distribution of intensity fluctuations in a continuous-wave-pumped erbium-based random fibre laser, with random Bragg grating scatterers. The distribution of intensity fluctuations in an extensive data set exhibits three qualitatively distinct behaviours: a Gaussian regime below threshold, a mixture of two distributions with exponentially decaying tails near the threshold and a mixture of distributions with stretched-exponential tails above threshold. All distributions are well described by a hierarchical stochastic model that incorporates Kolmogorov’s theory of turbulence, which includes energy cascade and the intermittence phenomenon. Our findings have implications for explaining the remarkably challenging turbulent behaviour in photonics, using a random fibre laser as the experimental platform. PMID:28561064

The effect of wind mixing on the vertical distribution of buoyant plastic debris

NASA Astrophysics Data System (ADS)

Kukulka, T.; Proskurowski, G.; Morét-Ferguson, S.; Meyer, D. W.; Law, K. L.

2012-04-01

Micro-plastic marine debris is widely distributed in vast regions of the subtropical gyres and has emerged as a major open ocean pollutant. The fate and transport of plastic marine debris is governed by poorly understood geophysical processes, such as ocean mixing within the surface boundary layer. Based on profile observations and a one-dimensional column model, we demonstrate that plastic debris is vertically distributed within the upper water column due to wind-driven mixing. These results suggest that total oceanic plastics concentrations are significantly underestimated by traditional surface measurements, requiring a reinterpretation of existing plastic marine debris data sets. A geophysical approach must be taken in order to properly quantify and manage this form of marine pollution.

Particle mobility size spectrometers: harmonization of technical standards and data structure to facilitate high quality long-term observations of atmospheric particle number size distributions

NASA Astrophysics Data System (ADS)

Wiedensohler, A.; Birmili, W.; Nowak, A.; Sonntag, A.; Weinhold, K.; Merkel, M.; Wehner, B.; Tuch, T.; Pfeifer, S.; Fiebig, M.; Fjäraa, A. M.; Asmi, E.; Sellegri, K.; Depuy, R.; Venzac, H.; Villani, P.; Laj, P.; Aalto, P.; Ogren, J. A.; Swietlicki, E.; Roldin, P.; Williams, P.; Quincey, P.; Hüglin, C.; Fierz-Schmidhauser, R.; Gysel, M.; Weingartner, E.; Riccobono, F.; Santos, S.; Grüning, C.; Faloon, K.; Beddows, D.; Harrison, R. M.; Monahan, C.; Jennings, S. G.; O'Dowd, C. D.; Marinoni, A.; Horn, H.-G.; Keck, L.; Jiang, J.; Scheckman, J.; McMurry, P. H.; Deng, Z.; Zhao, C. S.; Moerman, M.; Henzing, B.; de Leeuw, G.

2010-12-01

Particle mobility size spectrometers often referred to as DMPS (Differential Mobility Particle Sizers) or SMPS (Scanning Mobility Particle Sizers) have found a wide application in atmospheric aerosol research. However, comparability of measurements conducted world-wide is hampered by lack of generally accepted technical standards with respect to the instrumental set-up, measurement mode, data evaluation as well as quality control. This article results from several instrument intercomparison workshops conducted within the European infrastructure project EUSAAR (European Supersites for Atmospheric Aerosol Research). Under controlled laboratory conditions, the number size distribution from 20 to 200 nm determined by mobility size spectrometers of different design are within an uncertainty range of ±10% after correcting internal particle losses, while below and above this size range the discrepancies increased. Instruments with identical design agreed within ±3% in the peak number concentration when all settings were done carefully. Technical standards were developed for a minimum requirement of mobility size spectrometry for atmospheric aerosol measurements. Technical recommendations are given for atmospheric measurements including continuous monitoring of flow rates, temperature, pressure, and relative humidity for the sheath and sample air in the differential mobility analyser. In cooperation with EMEP (European Monitoring and Evaluation Program), a new uniform data structure was introduced for saving and disseminating the data within EMEP. This structure contains three levels: raw data, processed data, and final particle size distributions. Importantly, we recommend reporting raw measurements including all relevant instrument parameters as well as a complete documentation on all data transformation and correction steps. These technical and data structure standards aim to enhance the quality of long-term size distribution measurements, their comparability between different networks and sites, and their transparency and traceability back to raw data.

Distribution and nature of UV absorbers on Trition's surface

NASA Technical Reports Server (NTRS)

Stern, S. Alan

1995-01-01

Substantial evidence suggests that a UV (ultraviolet) Spectrally Absorbing Material (UV-SAM) exists on Triton's surface. This evidence is found in the positive slope in Triton's spectrum from the UV to the near-IR, and the increasing contrast in Triton's light curve in the blue and UV. Although it is now widely-thought that UV-SAM's exist on Triton, little is known about their distribution and spectral properties. The goal of this NDAP Project is to determine the spatial distribution and geological context of the UV-SAM material. We hope to determine if UV-SAM's on Triton are correlated with geologic wind streaks, craters, calderas, geomorphic/topographic units, regions containing (or lacking) volatile frosts, or some other process (e.g., magnetospheric interactions). Once the location and distribution of UV-SAM's has been determined, further constraints on their composition can be made by analyzing the spectrographic data set. To accomplish these goals, various data sets will be used, including Voyager 2 UV and visible images of Triton's surface, IUE and HST spectra of Triton, and a geologic map of the surface based on Voyager 2 and spectrophotometric data. The results of this research will be published in the planetary science literature.

Distribution and nature of UV absorbers on Triton's surface

NASA Technical Reports Server (NTRS)

Stern, S. Alan

1995-01-01

Substantial evidence suggests that a UV spectrally Absorbing Material (UV-SAM) exists on Triton's surface. This evidence is found in the positive slope in Triton's spectrum from the UV to the near-IR, and the increasing contrast in Triton's light curve in the blue and UV. Although it is now widely-thought that UV-SAMs exist on Triton, little is known about their distribution and spectral properties. The goal of this NDAP Project is to determine the spatial distribution and geological context of the UV-SaM material. We hope to determine if UV-SAMs on Triton are correlated with geologic wind streaks, craters, calderas, geomorphic/topographic units, regions containing (or lacking) volatile frosts, or some other process (e.g., magnetospheric interactions). Once the location and distribution of UV-SAMs has been determined, further constraints on their composition cable made by analyzing the spectrographic data set. To accomplish these goals, various data sets will be used, including Voyager 2 UV and visible images of Triton's surface, IUE and HST spectra of Triton, and a geologic map of the surface based on voyager 2 and spectrophotometric data. The results of this research will be published in the planetary science literature.

Distribution and nature of UV absorbers on Triton's surface

NASA Technical Reports Server (NTRS)

Stern, S. Alan

1994-01-01

Substantial evidence suggests that a UV Spectrally Absorbing Material (UV-SAM) exists on Triton's surface. This evidence is found in the positive slope in Triton's spectrum from the UV to the near-IR, and the increasing contrast in Triton's light curve in the blue and UV. Although it is now widely-thought that UV-SAM's exist on Triton, little is known about their distribution and spectral properties. The goal of this NDAP Project is to determine the spatial distribution and geological context of the UV-SAM material. We hope to determine if UV-SAM's on Triton are correlated with geologic wind streaks, craters, calderas, geomorphic/topographic units, regions containing (or lacking) volatile frosts, or some other process (e.g., magnetospheric interactions). Once the location and distribution of UV-SAM's has been determined, further constraints on their composition can be made by analyzing the spectrographic data set. To accomplish these goals, various data sets will be used, including Voyager 2 UV and visible images of Triton's surface, IUE and HST spectra of Triton, and a geologic map of the surface based on Voyager 2 and spectrophotometric data. The results of this research will be published in the planetary science literature.

A comparison of LMC and SDL complexity measures on binomial distributions

NASA Astrophysics Data System (ADS)

Piqueira, José Roberto C.

2016-02-01

The concept of complexity has been widely discussed in the last forty years, with a lot of thinking contributions coming from all areas of the human knowledge, including Philosophy, Linguistics, History, Biology, Physics, Chemistry and many others, with mathematicians trying to give a rigorous view of it. In this sense, thermodynamics meets information theory and, by using the entropy definition, López-Ruiz, Mancini and Calbet proposed a definition for complexity that is referred as LMC measure. Shiner, Davison and Landsberg, by slightly changing the LMC definition, proposed the SDL measure and the both, LMC and SDL, are satisfactory to measure complexity for a lot of problems. Here, SDL and LMC measures are applied to the case of a binomial probability distribution, trying to clarify how the length of the data set implies complexity and how the success probability of the repeated trials determines how complex the whole set is.

WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies.

PubMed

Pedretti, Alessandro; Mazzolari, Angelica; Vistoli, Giulio

2018-05-21

The manuscript describes WarpEngine, a novel platform implemented within the VEGA ZZ suite of software for performing distributed simulations both in local and wide area networks. Despite being tailored for structure-based virtual screening campaigns, WarpEngine possesses the required flexibility to carry out distributed calculations utilizing various pieces of software, which can be easily encapsulated within this platform without changing their source codes. WarpEngine takes advantages of all cheminformatics features implemented in the VEGA ZZ program as well as of its largely customizable scripting architecture thus allowing an efficient distribution of various time-demanding simulations. To offer an example of the WarpEngine potentials, the manuscript includes a set of virtual screening campaigns based on the ACE data set of the DUD-E collections using PLANTS as the docking application. Benchmarking analyses revealed a satisfactory linearity of the WarpEngine performances, the speed-up values being roughly equal to the number of utilized cores. Again, the computed scalability values emphasized that a vast majority (i.e., >90%) of the performed simulations benefit from the distributed platform presented here. WarpEngine can be freely downloaded along with the VEGA ZZ program at www.vegazz.net .

Technologies for Networked Enabled Operations

NASA Technical Reports Server (NTRS)

Glass, B.; Levine, J.

2005-01-01

Current point-to-point data links will not scale to support future integration of surveillance, security, and globally-distributed air traffic data, and already hinders efficiency and capacity. While the FAA and industry focus on a transition to initial system-wide information management (SWIM) capabilities, this paper describes a set of initial studies of NAS network-enabled operations technology gaps targeted for maturity in later SWIM spirals (201 5-2020 timeframe).

Environmentally Relevant Mixing Ratios in Cumulative Assessments: A Study of the Kinetics of Pyrethroids and Their Ester Cleavage Metabolites in Blood and Brain; and the Effect of a Pyrethroid Mixture on the Motor Activity of Rats

EPA Science Inventory

National surveys of United States households and child care centers have demonstrated that pyrethroids are widely distributed in indoor habited dwellings and this suggests that co-exposure to multiple pyrethroids occurs in nonoccupational settings. The purpose of this research wa...

A first look at chorioamnionitis management practice variation among US obstetricians.

PubMed

Greenberg, Mara B; Anderson, Britta L; Schulkin, Jay; Norton, Mary E; Aziz, Natali

2012-01-01

Objective. To examine practice patterns for diagnosis and treatment of chorioamnionitis among US obstetricians. Study Design. We distributed a mail-based survey to members of the American College of Obstetricians and Gynecologists, querying demographics, practice setting, and chorioamnionitis management strategies. We performed univariable and multivariable analyses. Results. Of 500 surveys distributed, 53.8% were returned, and 212 met study criteria and were analyzed. Most respondents work in group practice (66.0%), perform >100 deliveries per year (60.0%), have been in practice >10 years (77.3%), and work in a nonuniversity setting (85.1%). Temperature plus one additional criterion (61.3%) was the most common diagnostic strategy. Over 25 different primary antibiotic regimens were reported, including use of a single agent by 30.0% of respondents. A wide range of postpartum antibiotic duration was reported from no postpartum treatment (34.5% after vaginal delivery, 11.3% after cesarean delivery) to 48 hours of postpartum treatment (24.7% after vaginal delivery, 32.1% after cesarean delivery). No practitioner characteristic was independently associated with diagnostic or therapeutic strategies in multivariable analysis. Conclusion. There is a wide variation in contemporary clinical practices for the management of chorioamnionitis. This may represent a dearth of level I evidence. Future prospective clinical trials may provide more evidence-based practice recommendations for diagnosis and treatment of chorioamnionitis.

CFD Data Sets on the WWW for Education and Testing

NASA Technical Reports Server (NTRS)

Globus, Al; Lasinski, T. A. (Technical Monitor)

1995-01-01

The Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Ames Research Center has begun the development of a Computational Fluid Dynamics (CFD) data set archive on the World Wide Web (WWW) at URL http://www.nas.nasa.gov/NAS/DataSets/. Data sets are integrated with related information such as research papers, metadata, visualizations, etc. In this paper, four classes of users are identified and discussed: students, visualization developers, CFD practitioners, and management. Bandwidth and security issues are briefly reviewed and the status of the archive as of May 1995 is examined. Routine network distribution of data sets is likely to have profound implications for the conduct of science. The exact nature of these changes is subject to speculation, but the ability for anyone to examine the data, in addition to the investigator's analysis, may well play an important role in the future.

Transportability, distributability and rehosting experience with a kernel operating system interface set

NASA Technical Reports Server (NTRS)

Blumberg, F. C.; Reedy, A.; Yodis, E.

1986-01-01

For the past two years, PRC has been transporting and installing a software engineering environment framework, the Automated Product control Environment (APCE), at a number of PRC and government sites on a variety of different hardware. The APCE was designed using a layered architecture which is based on a standardized set of interfaces to host system services. This interface set called the APCE Interface Set (AIS), was designed to support many of the same goals as the Common Ada Programming Support Environment (APSE) Interface Set (CAIS). The APCE was developed to provide support for the full software lifecycle. Specific requirements of the APCE design included: automation of labor intensive administrative and logistical tasks: freedom for project team members to use existing tools: maximum transportability for APCE programs, interoperability of APCE database data, and distributability of both processes and data: and maximum performance on a wide variety of operating systems. A brief description is given of the APCE and AIS, a comparison of the AIS and CAIS both in terms of functionality and of philosophy and approach and a presentation of PRC's experience in rehosting AIS and transporting APCE programs and project data. Conclusions are drawn from this experience with respect to both the CAIS efforts and Space Station plans.

Distributed Adaptive Binary Quantization for Fast Nearest Neighbor Search.

PubMed

Xianglong Liu; Zhujin Li; Cheng Deng; Dacheng Tao

2017-11-01

Hashing has been proved an attractive technique for fast nearest neighbor search over big data. Compared with the projection based hashing methods, prototype-based ones own stronger power to generate discriminative binary codes for the data with complex intrinsic structure. However, existing prototype-based methods, such as spherical hashing and K-means hashing, still suffer from the ineffective coding that utilizes the complete binary codes in a hypercube. To address this problem, we propose an adaptive binary quantization (ABQ) method that learns a discriminative hash function with prototypes associated with small unique binary codes. Our alternating optimization adaptively discovers the prototype set and the code set of a varying size in an efficient way, which together robustly approximate the data relations. Our method can be naturally generalized to the product space for long hash codes, and enjoys the fast training linear to the number of the training data. We further devise a distributed framework for the large-scale learning, which can significantly speed up the training of ABQ in the distributed environment that has been widely deployed in many areas nowadays. The extensive experiments on four large-scale (up to 80 million) data sets demonstrate that our method significantly outperforms state-of-the-art hashing methods, with up to 58.84% performance gains relatively.

Genome-Wide Association Study of the Genetic Determinants of Emphysema Distribution

PubMed Central

Boueiz, Adel; Lutz, Sharon M.; Cho, Michael H.; Hersh, Craig P.; Bowler, Russell P.; Washko, George R.; Halper-Stromberg, Eitan; Bakke, Per; Gulsvik, Amund; Laird, Nan M.; Beaty, Terri H.; Coxson, Harvey O.; Crapo, James D.; Silverman, Edwin K.; Castaldi, Peter J.

2017-01-01

Rationale: Emphysema has considerable variability in the severity and distribution of parenchymal destruction throughout the lungs. Upper lobe–predominant emphysema has emerged as an important predictor of response to lung volume reduction surgery. Yet, aside from alpha-1 antitrypsin deficiency, the genetic determinants of emphysema distribution remain largely unknown. Objectives: To identify the genetic influences of emphysema distribution in non–alpha-1 antitrypsin–deficient smokers. Methods: A total of 11,532 subjects with complete genotype and computed tomography densitometry data in the COPDGene (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease [COPD]; non-Hispanic white and African American), ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints), and GenKOLS (Genetics of Chronic Obstructive Lung Disease) studies were analyzed. Two computed tomography scan emphysema distribution measures (difference between upper-third and lower-third emphysema; ratio of upper-third to lower-third emphysema) were tested for genetic associations in all study subjects. Separate analyses in each study population were followed by a fixed effect metaanalysis. Single-nucleotide polymorphism–, gene-, and pathway-based approaches were used. In silico functional evaluation was also performed. Measurements and Main Results: We identified five loci associated with emphysema distribution at genome-wide significance. These loci included two previously reported associations with COPD susceptibility (4q31 near HHIP and 15q25 near CHRNA5) and three new associations near SOWAHB, TRAPPC9, and KIAA1462. Gene set analysis and in silico functional evaluation revealed pathways and cell types that may potentially contribute to the pathogenesis of emphysema distribution. Conclusions: This multicohort genome-wide association study identified new genomic loci associated with differential emphysematous destruction throughout the lungs. These findings may point to new biologic pathways on which to expand diagnostic and therapeutic approaches in chronic obstructive pulmonary disease. Clinical trial registered with www.clinicaltrials.gov (NCT 00608764). PMID:27669027

Bayesian inference for disease prevalence using negative binomial group testing

PubMed Central

Pritchard, Nicholas A.; Tebbs, Joshua M.

2011-01-01

Group testing, also known as pooled testing, and inverse sampling are both widely used methods of data collection when the goal is to estimate a small proportion. Taking a Bayesian approach, we consider the new problem of estimating disease prevalence from group testing when inverse (negative binomial) sampling is used. Using different distributions to incorporate prior knowledge of disease incidence and different loss functions, we derive closed form expressions for posterior distributions and resulting point and credible interval estimators. We then evaluate our new estimators, on Bayesian and classical grounds, and apply our methods to a West Nile Virus data set. PMID:21259308

Mobility particle size spectrometers: harmonization of technical standards and data structure to facilitate high quality long-term observations of atmospheric particle number size distributions

NASA Astrophysics Data System (ADS)

Wiedensohler, A.; Birmili, W.; Nowak, A.; Sonntag, A.; Weinhold, K.; Merkel, M.; Wehner, B.; Tuch, T.; Pfeifer, S.; Fiebig, M.; Fjäraa, A. M.; Asmi, E.; Sellegri, K.; Depuy, R.; Venzac, H.; Villani, P.; Laj, P.; Aalto, P.; Ogren, J. A.; Swietlicki, E.; Williams, P.; Roldin, P.; Quincey, P.; Hüglin, C.; Fierz-Schmidhauser, R.; Gysel, M.; Weingartner, E.; Riccobono, F.; Santos, S.; Grüning, C.; Faloon, K.; Beddows, D.; Harrison, R.; Monahan, C.; Jennings, S. G.; O'Dowd, C. D.; Marinoni, A.; Horn, H.-G.; Keck, L.; Jiang, J.; Scheckman, J.; McMurry, P. H.; Deng, Z.; Zhao, C. S.; Moerman, M.; Henzing, B.; de Leeuw, G.; Löschau, G.; Bastian, S.

2012-03-01

Mobility particle size spectrometers often referred to as DMPS (Differential Mobility Particle Sizers) or SMPS (Scanning Mobility Particle Sizers) have found a wide range of applications in atmospheric aerosol research. However, comparability of measurements conducted world-wide is hampered by lack of generally accepted technical standards and guidelines with respect to the instrumental set-up, measurement mode, data evaluation as well as quality control. Technical standards were developed for a minimum requirement of mobility size spectrometry to perform long-term atmospheric aerosol measurements. Technical recommendations include continuous monitoring of flow rates, temperature, pressure, and relative humidity for the sheath and sample air in the differential mobility analyzer. We compared commercial and custom-made inversion routines to calculate the particle number size distributions from the measured electrical mobility distribution. All inversion routines are comparable within few per cent uncertainty for a given set of raw data. Furthermore, this work summarizes the results from several instrument intercomparison workshops conducted within the European infrastructure project EUSAAR (European Supersites for Atmospheric Aerosol Research) and ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) to determine present uncertainties especially of custom-built mobility particle size spectrometers. Under controlled laboratory conditions, the particle number size distributions from 20 to 200 nm determined by mobility particle size spectrometers of different design are within an uncertainty range of around ±10% after correcting internal particle losses, while below and above this size range the discrepancies increased. For particles larger than 200 nm, the uncertainty range increased to 30%, which could not be explained. The network reference mobility spectrometers with identical design agreed within ±4% in the peak particle number concentration when all settings were done carefully. The consistency of these reference instruments to the total particle number concentration was demonstrated to be less than 5%. Additionally, a new data structure for particle number size distributions was introduced to store and disseminate the data at EMEP (European Monitoring and Evaluation Program). This structure contains three levels: raw data, processed data, and final particle size distributions. Importantly, we recommend reporting raw measurements including all relevant instrument parameters as well as a complete documentation on all data transformation and correction steps. These technical and data structure standards aim to enhance the quality of long-term size distribution measurements, their comparability between different networks and sites, and their transparency and traceability back to raw data.

The structure of the clouds distributed operating system

NASA Technical Reports Server (NTRS)

Dasgupta, Partha; Leblanc, Richard J., Jr.

1989-01-01

A novel system architecture, based on the object model, is the central structuring concept used in the Clouds distributed operating system. This architecture makes Clouds attractive over a wide class of machines and environments. Clouds is a native operating system, designed and implemented at Georgia Tech. and runs on a set of generated purpose computers connected via a local area network. The system architecture of Clouds is composed of a system-wide global set of persistent (long-lived) virtual address spaces, called objects that contain persistent data and code. The object concept is implemented at the operating system level, thus presenting a single level storage view to the user. Lightweight treads carry computational activity through the code stored in the objects. The persistent objects and threads gives rise to a programming environment composed of shared permanent memory, dispensing with the need for hardware-derived concepts such as the file systems and message systems. Though the hardware may be distributed and may have disks and networks, the Clouds provides the applications with a logically centralized system, based on a shared, structured, single level store. The current design of Clouds uses a minimalist philosophy with respect to both the kernel and the operating system. That is, the kernel and the operating system support a bare minimum of functionality. Clouds also adheres to the concept of separation of policy and mechanism. Most low-level operating system services are implemented above the kernel and most high level services are implemented at the user level. From the measured performance of using the kernel mechanisms, we are able to demonstrate that efficient implementations are feasible for the object model on commercially available hardware. Clouds provides a rich environment for conducting research in distributed systems. Some of the topics addressed in this paper include distributed programming environments, consistency of persistent data and fault-tolerance.

Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach.

PubMed

Li, Dongmei; Le Pape, Marc A; Parikh, Nisha I; Chen, Will X; Dye, Timothy D

2013-01-01

Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. Multiple testing methods in microarray data analysis aim at controlling both Type I and Type II error rates; however, real microarray data do not always fit their distribution assumptions. Smyth's ubiquitous parametric method, for example, inadequately accommodates violations of normality assumptions, resulting in inflated Type I error rates. The Significance Analysis of Microarrays, another widely used microarray data analysis method, is based on a permutation test and is robust to non-normally distributed data; however, the Significance Analysis of Microarrays method fold change criteria are problematic, and can critically alter the conclusion of a study, as a result of compositional changes of the control data set in the analysis. We propose a novel approach, combining resampling with empirical Bayes methods: the Resampling-based empirical Bayes Methods. This approach not only reduces false discovery rates for non-normally distributed microarray data, but it is also impervious to fold change threshold since no control data set selection is needed. Through simulation studies, sensitivities, specificities, total rejections, and false discovery rates are compared across the Smyth's parametric method, the Significance Analysis of Microarrays, and the Resampling-based empirical Bayes Methods. Differences in false discovery rates controls between each approach are illustrated through a preterm delivery methylation study. The results show that the Resampling-based empirical Bayes Methods offer significantly higher specificity and lower false discovery rates compared to Smyth's parametric method when data are not normally distributed. The Resampling-based empirical Bayes Methods also offers higher statistical power than the Significance Analysis of Microarrays method when the proportion of significantly differentially expressed genes is large for both normally and non-normally distributed data. Finally, the Resampling-based empirical Bayes Methods are generalizable to next generation sequencing RNA-seq data analysis.

Data quality assessment for comparative effectiveness research in distributed data networks

PubMed Central

Brown, Jeffrey; Kahn, Michael; Toh, Sengwee

2015-01-01

Background Electronic health information routinely collected during healthcare delivery and reimbursement can help address the need for evidence about the real-world effectiveness, safety, and quality of medical care. Often, distributed networks that combine information from multiple sources are needed to generate this real-world evidence. Objective We provide a set of field-tested best practices and a set of recommendations for data quality checking for comparative effectiveness research (CER) in distributed data networks. Methods Explore the requirements for data quality checking and describe data quality approaches undertaken by several existing multi-site networks. Results There are no established standards regarding how to evaluate the quality of electronic health data for CER within distributed networks. Data checks of increasing complexity are often employed, ranging from consistency with syntactic rules to evaluation of semantics and consistency within and across sites. Temporal trends within and across sites are widely used, as are checks of each data refresh or update. Rates of specific events and exposures by age group, sex, and month are also common. Discussion Secondary use of electronic health data for CER holds promise but is complex, especially in distributed data networks that incorporate periodic data refreshes. The viability of a learning health system is dependent on a robust understanding of the quality, validity, and optimal secondary uses of routinely collected electronic health data within distributed health data networks. Robust data quality checking can strengthen confidence in findings based on distributed data network. PMID:23793049

Is the nestedness of metazoan parasite assemblages of marine fishes from the southeastern Pacific coast a pattern associated with the geographical distributional range of the host?

PubMed

González, M T; Oliva, M E

2009-04-01

Nested structure is a pattern originally described in island biogeography to characterize how a set of species is distributed among a set of islands. In parasite communities, nestedness has been intensively studied among individual fish from a locality. However, nested patterns among parasite assemblages from different host populations (localities) have scarcely been investigated. We recorded the occurrence of parasites in 9 fish species widely distributed along the southeastern Pacific coast to determine whether the ecto- and endoparasite assemblages of marine fishes show a nested structure associated with host distributional range. Nestedness was tested using Brualdi-Sanderson index of discrepancy (BR); and 5 null models incorporated in a 'Nestedness' programme (Ulrich, 2006). The ecto- and endoparasite richness do not show similar patterns of latitudinal gradients among fish hosts, with 33-66% of analysed ectoparasite assemblages, and 25-75% of endoparasite assemblages showing nested structures through the host distributional range. For ectoparasites, species richness gradients and nested structure (when present) might be associated with decreased host densities or could reflect negative environmental conditions in the distributional border of the host species, whereas for endoparasites might be caused by geographical breaks of prey or changes in prey availability (intermediate hosts). The sampled extension of the distributional range of the host species, as well as the lack of specificity of some parasites, could influence the detection of nestedness.

An Artificial Immune System-Inspired Multiobjective Evolutionary Algorithm with Application to the Detection of Distributed Computer Network Intrusions

DTIC Science & Technology

2007-03-01

Intelligence AIS Artificial Immune System ANN Artificial Neural Networks API Application Programming Interface BFS Breadth-First Search BIS Biological...problem domain is too large for only one algorithm’s application . It ranges from network - based sniffer systems, responsible for Enterprise-wide coverage...options to network administrators in choosing detectors to employ in future ID applications . Objectives Our hypothesis validity is based on a set

Software for rapid time dependent ChIP-sequencing analysis (TDCA).

PubMed

Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

2017-11-25

Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically relevant data analysis, and the uncovering of variations in the time-dependent behavior of chromatin. TDCA automates the analysis of TC ChIP-seq experiments, permitting researchers to easily obtain raw and modeled data for specific loci or groups of loci with similar behavior while also enhancing consistency of data analysis of TC data within the genomics field.

The ecological future of the North American bison: Conceiving long-term, large-scale conservation of a species

USGS Publications Warehouse

Sanderson, E.W.; Redford, Kent; Weber, Bill; Aune, K.; Baldes, Dick; Berger, J.; Carter, Dave; Curtin, C.; Derr, James N.; Dobrott, S.J.; Fearn, Eva; Fleener, Craig; Forrest, Steven C.; Gerlach, Craig; Gates, C. Cormack; Gross, J.E.; Gogan, P.; Grassel, Shaun M.; Hilty, Jodi A.; Jensen, Marv; Kunkel, Kyran; Lammers, Duane; List, R.; Minkowski, Karen; Olson, Tom; Pague, Chris; Robertson, Paul B.; Stephenson, Bob

2008-01-01

Many wide-ranging mammal species have experienced significant declines over the last 200 years; restoring these species will require long-term, large-scale recovery efforts. We highlight 5 attributes of a recent range-wide vision-setting exercise for ecological recovery of the North American bison (Bison bison) that are broadly applicable to other species and restoration targets. The result of the exercise, the “Vermejo Statement” on bison restoration, is explicitly (1) large scale, (2) long term, (3) inclusive, (4) fulfilling of different values, and (5) ambitious. It reads, in part, “Over the next century, the ecological recovery of the North American bison will occur when multiple large herds move freely across extensive landscapes within all major habitats of their historic range, interacting in ecologically significant ways with the fullest possible set of other native species, and inspiring, sustaining and connecting human cultures.” We refined the vision into a scorecard that illustrates how individual bison herds can contribute to the vision. We also developed a set of maps and analyzed the current and potential future distributions of bison on the basis of expert assessment. Although more than 500,000 bison exist in North America today, we estimated they occupy <1% of their historical range and in no place express the full range of ecological and social values of previous times. By formulating an inclusive, affirmative, and specific vision through consultation with a wide range of stakeholders, we hope to provide a foundation for conservation of bison, and other wide-ranging species, over the next 100 years.

Multi-objective problem of the modified distributed parallel machine and assembly scheduling problem (MDPMASP) with eligibility constraints

NASA Astrophysics Data System (ADS)

Amallynda, I.; Santosa, B.

2017-11-01

This paper proposes a new generalization of the distributed parallel machine and assembly scheduling problem (DPMASP) with eligibility constraints referred to as the modified distributed parallel machine and assembly scheduling problem (MDPMASP) with eligibility constraints. Within this generalization, we assume that there are a set non-identical factories or production lines, each one with a set unrelated parallel machine with different speeds in processing them disposed to a single assembly machine in series. A set of different products that are manufactured through an assembly program of a set of components (jobs) according to the requested demand. Each product requires several kinds of jobs with different sizes. Beside that we also consider to the multi-objective problem (MOP) of minimizing mean flow time and the number of tardy products simultaneously. This is known to be NP-Hard problem, is important to practice, as the former criterions to reflect the customer's demand and manufacturer's perspective. This is a realistic and complex problem with wide range of possible solutions, we propose four simple heuristics and two metaheuristics to solve it. Various parameters of the proposed metaheuristic algorithms are discussed and calibrated by means of Taguchi technique. All proposed algorithms are tested by Matlab software. Our computational experiments indicate that the proposed problem and fourth proposed algorithms are able to be implemented and can be used to solve moderately-sized instances, and giving efficient solutions, which are close to optimum in most cases.

A new method for analyzing IRAS data to determine the dust temperature distribution

NASA Technical Reports Server (NTRS)

Xie, Taoling; Goldsmith, Paul F.; Zhou, Weimin

1991-01-01

In attempting to analyze the four-band IRAS images of interstellar dust emission, it is found that an inversion theorem recently developed by Chen (1990) enables distribution of the dust to be determined as a function of temperature and thus the total dust column density, for each line of sight. The method and its application to a hypothetical IRAS data set created by assuming a power-law dust temperature distribution, which is characteristic of the actual IRAS data for the Monoceros R2 cloud, are reported. To use the method, the wavelength dependence of the dust emissivity is assumed and a simple function is fitted to the four intensity-wavelength data points. The method is shown to be very successful at retrieving the dust temperature distribution in this case and is expected to have wide applicability to astronomical problems of this type.

Visualization Techniques in Space and Atmospheric Sciences

NASA Technical Reports Server (NTRS)

Szuszczewicz, E. P. (Editor); Bredekamp, Joseph H. (Editor)

1995-01-01

Unprecedented volumes of data will be generated by research programs that investigate the Earth as a system and the origin of the universe, which will in turn require analysis and interpretation that will lead to meaningful scientific insight. Providing a widely distributed research community with the ability to access, manipulate, analyze, and visualize these complex, multidimensional data sets depends on a wide range of computer science and technology topics. Data storage and compression, data base management, computational methods and algorithms, artificial intelligence, telecommunications, and high-resolution display are just a few of the topics addressed. A unifying theme throughout the papers with regards to advanced data handling and visualization is the need for interactivity, speed, user-friendliness, and extensibility.

Methods, caveats and the future of large-scale microelectrode recordings in the non-human primate

PubMed Central

Dotson, Nicholas M.; Goodell, Baldwin; Salazar, Rodrigo F.; Hoffman, Steven J.; Gray, Charles M.

2015-01-01

Cognitive processes play out on massive brain-wide networks, which produce widely distributed patterns of activity. Capturing these activity patterns requires tools that are able to simultaneously measure activity from many distributed sites with high spatiotemporal resolution. Unfortunately, current techniques with adequate coverage do not provide the requisite spatiotemporal resolution. Large-scale microelectrode recording devices, with dozens to hundreds of microelectrodes capable of simultaneously recording from nearly as many cortical and subcortical areas, provide a potential way to minimize these tradeoffs. However, placing hundreds of microelectrodes into a behaving animal is a highly risky and technically challenging endeavor that has only been pursued by a few groups. Recording activity from multiple electrodes simultaneously also introduces several statistical and conceptual dilemmas, such as the multiple comparisons problem and the uncontrolled stimulus response problem. In this perspective article, we discuss some of the techniques that we, and others, have developed for collecting and analyzing large-scale data sets, and address the future of this emerging field. PMID:26578906

Measuring impact crater depth throughout the solar system

USGS Publications Warehouse

Robbins, Stuart J.; Watters, Wesley A.; Chappelow, John E.; Bray, Veronica J.; Daubar, Ingrid J.; Craddock, Robert A.; Beyer, Ross A.; Landis, Margaret E.; Ostrach, Lillian; Tornabene, Livio L.; Riggs, Jamie D.; Weaver, Brian P.

2018-01-01

One important, almost ubiquitous, tool for understanding the surfaces of solid bodies throughout the solar system is the study of impact craters. While measuring a distribution of crater diameters and locations is an important tool for a wide variety of studies, so too is measuring a crater's “depth.” Depth can inform numerous studies including the strength of a surface and modification rates in the local environment. There is, however, no standard data set, definition, or technique to perform this data‐gathering task, and the abundance of different definitions of “depth” and methods for estimating that quantity can lead to misunderstandings in and of the literature. In this review, we describe a wide variety of data sets and methods to analyze those data sets that have been, are currently, or could be used to derive different types of crater depth measurements. We also recommend certain nomenclature in doing so to help standardize practice in the field. We present a review section of all crater depths that have been published on different solar system bodies which shows how the field has evolved through time and how some common assumptions might not be wholly accurate. We conclude with several recommendations for researchers which could help different data sets to be more easily understood and compared.

COSPAR/PRBEM international working group activities report

NASA Astrophysics Data System (ADS)

Bourdarie, S.; Blake, B.; Cao, J. B.; Friedel, R.; Miyoshi, Y.; Panasyuk, M.; Underwood, C.

It is now clear to everybody that the current standard AE8 AP8 model for ionising particle specification in the radiation belts must be updated But such an objective is quite difficult to reach just as a reminder to develop AE8 AP8 model in the seventies was 10 persons full time for ten years It is clear that world-wide efforts must be combined because not any individual group has the human resource to perform these new models by themselves Under COSPAR umbrella an international group of expert well distributed around the world has been created to set up a common framework for everybody involved in this field Planned activities of the international group of experts are to - Define users needs - Provide guidelines for standard file format for ionising measurements - Set up guidelines to process in-situ data on a common basis - Decide in which form the new models will have to be - Centralise all progress done world-wide to advise the community - Try to organise world-wide activities as a project to ensure complementarities and more efficiencies between all efforts done Activities of this working group since its creation will be reported as well as future plans

Gaussian covariance graph models accounting for correlated marker effects in genome-wide prediction.

PubMed

Martínez, C A; Khare, K; Rahman, S; Elzo, M A

2017-10-01

Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G. In this study, methods adapting the theory of GCovGM to genome-wide prediction were developed (Bayes GCov, Bayes GCov-KR and Bayes GCov-H). In simulated data sets, improvements in correlation between phenotypes and predicted breeding values and accuracies of predicted breeding values were found. Our models account for correlation of marker effects and permit to accommodate general structures as opposed to models proposed in previous studies, which consider spatial correlation only. In addition, they allow incorporation of biological information in the prediction process through its use when constructing graph G, and their extension to the multi-allelic loci case is straightforward. © 2017 Blackwell Verlag GmbH.

Crossbedding of the Potomac Formation in Fairfax County, Virginia

USGS Publications Warehouse

Weir, Gordon Whitney

1976-01-01

Crossbedding in sandstone units is the most conspicuous sedimentary structure of the Potomac Formation in Fairfax County, Virginia. Most sets of crossbeds are a few feet thick and several feet wide and tens of feet long. Trough sets are dominant, but planar sets are also common. Dip directions of crossbeds show great variation, though westerly dips are sparse. The averages (resultant vectors) of crossbedding dip-directions measured at 33 localities do not show significant differences according to their geographic or stratigraphic distribution. The average dip-direction of the 292 crossbeds measured is N. 85? E. The data suggest that the depositional slope was easterly in Fairfax County throughout the time of deposition of the Potomac Formation. Major sand bodies, potential aquifers of the formation, are probably elongated along easterly trends.

Inequality spectra

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2017-03-01

Inequality indices are widely applied in economics and in the social sciences as quantitative measures of the socioeconomic inequality of human societies. The application of inequality indices extends to size-distributions at large, where these indices can be used as general gauges of statistical heterogeneity. Moreover, as inequality indices are plentiful, arrays of such indices facilitate high-detail quantification of statistical heterogeneity. In this paper we elevate from arrays of inequality indices to inequality spectra: continuums of inequality indices that are parameterized by a single control parameter. We present a general methodology of constructing Lorenz-based inequality spectra, apply the general methodology to establish four sets of inequality spectra, investigate the properties of these sets, and show how these sets generalize known inequality gauges such as: the Gini index, the extended Gini index, the Rényi index, and hill curves.

Estimation of distributional parameters for censored trace level water quality data. 1. Estimation Techniques

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

Gilliom, R.J.; Helsel, D.R.

1986-02-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensoredmore » observations, for determining the best performing parameter estimation method for any particular data det. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification.« less

On the optimality of a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner H.

1993-01-01

Rice developed a universal noiseless coding structure that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Variations of such noiseless coders have been used in many NASA applications. Custom VLSI coder and decoder modules capable of processing over 50 million samples per second have been fabricated and tested. In this study, the first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, for source symbol sets having a Laplacian distribution. Except for the default option, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery over a wide entropy range, and they confirm the optimality of the scheme. Comparison with other known techniques are performed on several widely used images and the results further validate the coder's optimality.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

NASA Astrophysics Data System (ADS)

Dykstra, D.; Bockelman, B.; Blomer, J.; Herner, K.; Levshina, T.; Slyz, M.

2015-12-01

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliary data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called "alien cache" to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

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

Dykstra, D.; Bockelman, B.; Blomer, J.

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliarymore » data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called 'alien cache' to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.« less

Stakeholder perceptions and operational barriers in the training and distribution of take-home naloxone within prisons in England.

PubMed

Sondhi, Arun; Ryan, George; Day, Ed

2016-02-03

The aim of the study was to assess potential barriers and challenges to the implementation of take-home naloxone (THN) across ten prisons in one region of England. Qualitative interviews deploying a grounded theory approach were utilised over a 12- to 18-month period that included an on-going structured dialogue with strategic and operational prison staff from the ten prisons and other key stakeholders (n = 17). Prisoner perceptions were addressed through four purposive focus groups belonging to different establishments (n = 26). Document analysis also included report minutes and access to management information and local performance reports. The data were thematically interpreted using visual mapping techniques. The distribution and implementation of THN in a prison setting was characterised by significant barriers and challenges. As a result, four main themes were identified: a wide range of negative and confused perceptions of THN amongst prison staff and prisoners; inherent difficulties with the identification and engagement of eligible prisoners; the need to focus on individual prison processes to enhance the effective distribution of THN; and the need for senior prison staff engagement. The distribution of THN within a custodial setting requires consideration of a number of important factors which are discussed.

Numerical and machine learning simulation of parametric distributions of groundwater residence time in streams and wells

NASA Astrophysics Data System (ADS)

Starn, J. J.; Belitz, K.; Carlson, C.

2017-12-01

Groundwater residence-time distributions (RTDs) are critical for assessing susceptibility of water resources to contamination. This novel approach for estimating regional RTDs was to first simulate groundwater flow using existing regional digital data sets in 13 intermediate size watersheds (each an average of 7,000 square kilometers) that are representative of a wide range of glacial systems. RTDs were simulated with particle tracking. We refer to these models as "general models" because they are based on regional, as opposed to site-specific, digital data. Parametric RTDs were created from particle RTDs by fitting 1- and 2-component Weibull, gamma, and inverse Gaussian distributions, thus reducing a large number of particle travel times to 3 to 7 parameters (shape, location, and scale for each component plus a mixing fraction) for each modeled area. The scale parameter of these distributions is related to the mean exponential age; the shape parameter controls departure from the ideal exponential distribution and is partly a function of interaction with bedrock and with drainage density. Given the flexible shape and mathematical similarity of these distributions, any of them are potentially a good fit to particle RTDs. The 1-component gamma distribution provided a good fit to basin-wide particle RTDs. RTDs at monitoring wells and streams often have more complicated shapes than basin-wide RTDs, caused in part by heterogeneity in the model, and generally require 2-component distributions. A machine learning model was trained on the RTD parameters using features derived from regionally available watershed characteristics such as recharge rate, material thickness, and stream density. RTDs appeared to vary systematically across the landscape in relation to watershed features. This relation was used to produce maps of useful metrics with respect to risk-based thresholds, such as the time to first exceedance, time to maximum concentration, time above the threshold (exposure time), and the time until last exceedance; thus, the parameters of groundwater residence time are measures of the intrinsic susceptibility of groundwater to contamination.

Complementarity and Area-Efficiency in the Prioritization of the Global Protected Area Network.

PubMed

Kullberg, Peter; Toivonen, Tuuli; Montesino Pouzols, Federico; Lehtomäki, Joona; Di Minin, Enrico; Moilanen, Atte

2015-01-01

Complementarity and cost-efficiency are widely used principles for protected area network design. Despite the wide use and robust theoretical underpinnings, their effects on the performance and patterns of priority areas are rarely studied in detail. Here we compare two approaches for identifying the management priority areas inside the global protected area network: 1) a scoring-based approach, used in recently published analysis and 2) a spatial prioritization method, which accounts for complementarity and area-efficiency. Using the same IUCN species distribution data the complementarity method found an equal-area set of priority areas with double the mean species ranges covered compared to the scoring-based approach. The complementarity set also had 72% more species with full ranges covered, and lacked any coverage only for half of the species compared to the scoring approach. Protected areas in our complementarity-based solution were on average smaller and geographically more scattered. The large difference between the two solutions highlights the need for critical thinking about the selected prioritization method. According to our analysis, accounting for complementarity and area-efficiency can lead to considerable improvements when setting management priorities for the global protected area network.

Particle size distribution of the stratospheric aerosol from SCIAMACHY limb measurements

NASA Astrophysics Data System (ADS)

Rozanov, Alexei; Malinina, Elizaveta; Bovensmann, Heinrich; Burrows, John

2017-04-01

A crucial role of the stratospheric aerosols for the radiative budget of the Earth's atmosphere and the consequences for the climate change are widely recognized. A reliable knowledge on physical and optical properties of the stratospheric aerosols as well as on their vertical and spatial distributing is a key issue to assure a proper initialization and running conditions for climate models. On a global scale this information can only be gained from space borne measurements. While a series of past, present and future instruments provide extensive date sets of such aerosol characteristics as extinction coefficient or backscattering ratio, information on a size distribution of the stratospheric aerosols is sparse. One of the important sources on vertically and spatially resolved information on the particle size distribution of stratospheric aerosols is provided by space borne measurements of the scattered solar light in limb viewing geometry performed in visible, near-infrared and short-wave infrared spectral ranges. SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) instrument operated on the European satellite Envisat from 2002 to 2102 was capable of providing spectral information needed to retrieve parameters of aerosol particle size distributions. In this presentation we discuss the retrieval method, present first validation results with SAGE II data and analyze first data sets of stratospheric aerosol particle size distribution parameters obtained from SCIAMACHY limb measurements. The research work was performed in the framework of ROMIC (Role of the middle atmosphere in climate) project.

Distributed augmented reality with 3-D lung dynamics--a planning tool concept.

PubMed

Hamza-Lup, Felix G; Santhanam, Anand P; Imielińska, Celina; Meeks, Sanford L; Rolland, Jannick P

2007-01-01

Augmented reality (AR) systems add visual information to the world by using advanced display techniques. The advances in miniaturization and reduced hardware costs make some of these systems feasible for applications in a wide set of fields. We present a potential component of the cyber infrastructure for the operating room of the future: a distributed AR-based software-hardware system that allows real-time visualization of three-dimensional (3-D) lung dynamics superimposed directly on the patient's body. Several emergency events (e.g., closed and tension pneumothorax) and surgical procedures related to lung (e.g., lung transplantation, lung volume reduction surgery, surgical treatment of lung infections, lung cancer surgery) could benefit from the proposed prototype.

Publishing biomedical journals on the World-Wide Web using an open architecture model.

PubMed Central

Shareck, E. P.; Greenes, R. A.

1996-01-01

BACKGROUND: In many respects, biomedical publications are ideally suited for distribution via the World-Wide Web, but economic concerns have prevented the rapid adoption of an on-line publishing model. PURPOSE: We report on our experiences with assisting biomedical journals in developing an online presence, issues that were encountered, and methods used to address these issues. Our approach is based on an open architecture that fosters adaptation and interconnection of biomedical resources. METHODS: We have worked with the New England Journal of Medicine (NEJM), as well as five other publishers. A set of tools and protocols was employed to develop a scalable and customizable solution for publishing journals on-line. RESULTS: In March, 1996, the New England Journal of Medicine published its first World-Wide Web issue. Explorations with other publishers have helped to generalize the model. CONCLUSIONS: Economic and technical issues play a major role in developing World-Wide Web publishing solutions. PMID:8947685

Optimized Global Digital Elevation Data Records (Invited)

NASA Astrophysics Data System (ADS)

Kobrick, M.; Farr, T.; Crippen, R. E.

2009-12-01

The Shuttle Radar Topography Mission (SRTM) used radar interferometry to map the Earth's topography between ±60° latitude - representing 80% of the land surface. The resulting digital elevation models bettered existing topographic data sets (including restricted military data) in accuracy, areal coverage and uniformity by several orders of magnitude, and the resulting data records have found broad application in most of the geosciences, military operations, even Google Earth. Despite their popularity the SRTM data have several limitations, including lack of coverage in polar regions and occasional small voids, or areas of no data in regions of high slope of low radar backscatter. Fortunately additional data sets have become available that, although lacking SRTM's data quality, are sufficient to mitigate many of these limitations. Primary among these is the Global Digital Elevation Model (GDEM) produced from ASTER stereo pairs. The MEaSUREs program is sponsoring an effort to merge these sets to produce and distribute an improved collection of data records that will optimize the topographic data, as well as make available additional non-topographic data products from the SRTM mission. There are four main areas of effort: (1) A systematic program to combine SRTM elevation data with those from other sensors, principally GDEM but also including SPOT stereo, the USGS’s National Elevation Data Set and others, to fill voids in the DEMs according to a prioritized plan, as well as extend the coverage beyond the current 60° latitude limit. (2) Combine the topographic data records with ICESat laser altimeter topography profiles to produce and distribute data records with enhanced ground control. (3) Document the existing SRTM radar image and ancillary data records, as well as generate image mosaics at multiple scales and distribute them via the world wide web. (4) Generate, document and distribute a standard and representative set of SRTM raw radar echo data, along with the appropriate ancillary tracking and pointing data necessary to process the echoes into DEMS using improved algorithms or

The Interplanetary Internet: a communications infrastructure for Mars exploration.

PubMed

Burleigh, Scott; Cerf, Vinton; Durst, Robert; Fall, Kevin; Hooke, Adrian; Scott, Keith; Weiss, Howard

2003-01-01

A strategy is being developed whereby the current set of internationally standardized space data communications protocols can be incrementally evolved so that a first version of an operational "Interplanetary Internet" is feasible by the end of the decade. This paper describes its architectural concepts, discusses the current set of standard space data communications capabilities that exist to support Mars exploration and reviews proposed new developments. We also speculate that these current capabilities can grow to support future scenarios where human intelligence is widely distributed across the Solar System and day-to-day communications dialog between planets is routine. c2003 American Institute of Aeronautics and Astronautics. Published by Elsevier Science Ltd. All rights reserved.

The Interplanetary Internet: a communications infrastructure for Mars exploration

NASA Technical Reports Server (NTRS)

Burleigh, Scott; Cerf, Vinton; Durst, Robert; Fall, Kevin; Hooke, Adrian; Scott, Keith; Weiss, Howard

2003-01-01

A strategy is being developed whereby the current set of internationally standardized space data communications protocols can be incrementally evolved so that a first version of an operational "Interplanetary Internet" is feasible by the end of the decade. This paper describes its architectural concepts, discusses the current set of standard space data communications capabilities that exist to support Mars exploration and reviews proposed new developments. We also speculate that these current capabilities can grow to support future scenarios where human intelligence is widely distributed across the Solar System and day-to-day communications dialog between planets is routine. c2003 American Institute of Aeronautics and Astronautics. Published by Elsevier Science Ltd. All rights reserved.

Experimental detection of steerability in Bell local states with two measurement settings

NASA Astrophysics Data System (ADS)

Orieux, Adeline; Kaplan, Marc; Venuti, Vivien; Pramanik, Tanumoy; Zaquine, Isabelle; Diamanti, Eleni

2018-04-01

Steering, a quantum property stronger than entanglement but weaker than non-locality in the quantum correlation hierarchy, is a key resource for one-sided device-independent quantum key distribution applications, in which only one of the communicating parties is trusted. A fine-grained steering inequality was introduced in (2014 Phys. Rev. A 90 050305), enabling for the first time the detection of steering in all steerable two-qubit Werner states using only two measurement settings. Here, we numerically and experimentally investigate this inequality for generalized Werner states and successfully detect steerability in a wide range of two-photon polarization-entangled Bell local states generated by a parametric down-conversion source.

Downlink power distributions for 2G and 3G mobile communication networks.

PubMed

Colombi, Davide; Thors, Björn; Persson, Tomas; Wirén, Niklas; Larsson, Lars-Eric; Jonsson, Mikael; Törnevik, Christer

2013-12-01

Knowledge of realistic power levels is key when conducting accurate EMF exposure assessments. In this study, downlink output power distributions for radio base stations in 2G and 3G mobile communication networks have been assessed. The distributions were obtained from network measurement data collected from the Operations Support System, which normally is used for network monitoring and management. Significant amounts of data were gathered simultaneously for large sets of radio base stations covering wide geographical areas and different environments. The method was validated with in situ measurements. For the 3G network, the 90th percentile of the averaged output power during high traffic hours was found to be 43 % of the maximum available power. The corresponding number for 2G, with two or more transceivers installed, was 65 % or below.

Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.)

PubMed Central

Aradhya, Mallikarjuna; Ibrahimov, Zakir; Toktoraliev, Biimyrza; Maghradze, David; Musayev, Mirza; Bobokashvili, Zviadi; Preece, John E.

2017-01-01

The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21–18 kyr BP) and LIG (130–116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut. PMID:29023476

Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.).

PubMed

Aradhya, Mallikarjuna; Velasco, Dianne; Ibrahimov, Zakir; Toktoraliev, Biimyrza; Maghradze, David; Musayev, Mirza; Bobokashvili, Zviadi; Preece, John E

2017-01-01

The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21-18 kyr BP) and LIG (130-116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.

Uncertainty in gridded CO 2 emissions estimates

DOE PAGES

Hogue, Susannah; Marland, Eric; Andres, Robert J.; ...

2016-05-19

We are interested in the spatial distribution of fossil-fuel-related emissions of CO 2 for both geochemical and geopolitical reasons, but it is important to understand the uncertainty that exists in spatially explicit emissions estimates. Working from one of the widely used gridded data sets of CO 2 emissions, we examine the elements of uncertainty, focusing on gridded data for the United States at the scale of 1° latitude by 1° longitude. Uncertainty is introduced in the magnitude of total United States emissions, the magnitude and location of large point sources, the magnitude and distribution of non-point sources, and from themore » use of proxy data to characterize emissions. For the United States, we develop estimates of the contribution of each component of uncertainty. At 1° resolution, in most grid cells, the largest contribution to uncertainty comes from how well the distribution of the proxy (in this case population density) represents the distribution of emissions. In other grid cells, the magnitude and location of large point sources make the major contribution to uncertainty. Uncertainty in population density can be important where a large gradient in population density occurs near a grid cell boundary. Uncertainty is strongly scale-dependent with uncertainty increasing as grid size decreases. In conclusion, uncertainty for our data set with 1° grid cells for the United States is typically on the order of ±150%, but this is perhaps not excessive in a data set where emissions per grid cell vary over 8 orders of magnitude.« less

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE PAGES

Yim, Won Cheol; Cushman, John C.

2017-07-22

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

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

Yim, Won Cheol; Cushman, John C.

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Analytical approaches to the determination of spin-dependent parton distribution functions at NNLO approximation

NASA Astrophysics Data System (ADS)

Salajegheh, Maral; Nejad, S. Mohammad Moosavi; Khanpour, Hamzeh; Tehrani, S. Atashbar

2018-05-01

In this paper, we present SMKA18 analysis, which is a first attempt to extract the set of next-to-next-leading-order (NNLO) spin-dependent parton distribution functions (spin-dependent PDFs) and their uncertainties determined through the Laplace transform technique and Jacobi polynomial approach. Using the Laplace transformations, we present an analytical solution for the spin-dependent Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution equations at NNLO approximation. The results are extracted using a wide range of proton g1p(x ,Q2) , neutron g1n(x ,Q2) , and deuteron g1d(x ,Q2) spin-dependent structure functions data set including the most recent high-precision measurements from COMPASS16 experiments at CERN, which are playing an increasingly important role in global spin-dependent fits. The careful estimations of uncertainties have been done using the standard Hessian error propagation. We will compare our results with the available spin-dependent inclusive deep inelastic scattering data set and other results for the spin-dependent PDFs in literature. The results obtained for the spin-dependent PDFs as well as spin-dependent structure functions are clearly explained both in the small and large values of x .

Monte Carlo simulation for uncertainty estimation on structural data in implicit 3-D geological modeling, a guide for disturbance distribution selection and parameterization

NASA Astrophysics Data System (ADS)

Pakyuz-Charrier, Evren; Lindsay, Mark; Ogarko, Vitaliy; Giraud, Jeremie; Jessell, Mark

2018-04-01

Three-dimensional (3-D) geological structural modeling aims to determine geological information in a 3-D space using structural data (foliations and interfaces) and topological rules as inputs. This is necessary in any project in which the properties of the subsurface matters; they express our understanding of geometries in depth. For that reason, 3-D geological models have a wide range of practical applications including but not restricted to civil engineering, the oil and gas industry, the mining industry, and water management. These models, however, are fraught with uncertainties originating from the inherent flaws of the modeling engines (working hypotheses, interpolator's parameterization) and the inherent lack of knowledge in areas where there are no observations combined with input uncertainty (observational, conceptual and technical errors). Because 3-D geological models are often used for impactful decision-making it is critical that all 3-D geological models provide accurate estimates of uncertainty. This paper's focus is set on the effect of structural input data measurement uncertainty propagation in implicit 3-D geological modeling. This aim is achieved using Monte Carlo simulation for uncertainty estimation (MCUE), a stochastic method which samples from predefined disturbance probability distributions that represent the uncertainty of the original input data set. MCUE is used to produce hundreds to thousands of altered unique data sets. The altered data sets are used as inputs to produce a range of plausible 3-D models. The plausible models are then combined into a single probabilistic model as a means to propagate uncertainty from the input data to the final model. In this paper, several improved methods for MCUE are proposed. The methods pertain to distribution selection for input uncertainty, sample analysis and statistical consistency of the sampled distribution. Pole vector sampling is proposed as a more rigorous alternative than dip vector sampling for planar features and the use of a Bayesian approach to disturbance distribution parameterization is suggested. The influence of incorrect disturbance distributions is discussed and propositions are made and evaluated on synthetic and realistic cases to address the sighted issues. The distribution of the errors of the observed data (i.e., scedasticity) is shown to affect the quality of prior distributions for MCUE. Results demonstrate that the proposed workflows improve the reliability of uncertainty estimation and diminish the occurrence of artifacts.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

PubMed Central

Smallbone, Kieran; Messiha, Hanan L.; Carroll, Kathleen M.; Winder, Catherine L.; Malys, Naglis; Dunn, Warwick B.; Murabito, Ettore; Swainston, Neil; Dada, Joseph O.; Khan, Farid; Pir, Pınar; Simeonidis, Evangelos; Spasić, Irena; Wishart, Jill; Weichart, Dieter; Hayes, Neil W.; Jameson, Daniel; Broomhead, David S.; Oliver, Stephen G.; Gaskell, Simon J.; McCarthy, John E.G.; Paton, Norman W.; Westerhoff, Hans V.; Kell, Douglas B.; Mendes, Pedro

2013-01-01

We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a “cycle of knowledge” strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought. PMID:23831062

Review of design and operational characteristics of the 0.3-meter transonic cryogenic tunnel

NASA Technical Reports Server (NTRS)

Ray, E. J.; Ladson, C. L.; Adcock, J. B.; Lawing, P. L.; Hall, R. M.

1979-01-01

The fundamentals of cryogenic testing are validated both analytically and experimentally employing the 0.3-m transonic cryogenic tunnel. The tunnel with its unique Reynolds number capability has been used for a wide variety of aerodynamic tests. Techniques regarding real-gas effects have been developed and cryogenic tunnel conditions are set and maintained accurately. It is shown that cryogenic cooling, by injecting nitrogen directly into the tunnel circuit, imposes no problems with temperature distribution or dynamic response characteristics.

A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set

PubMed Central

Santos, Hadassa C; Horimoto, Andréa V R; Tarazona-Santos, Eduardo; Rodrigues-Soares, Fernanda; Barreto, Mauricio L; Horta, Bernardo L; Lima-Costa, Maria F; Gouveia, Mateus H; Machado, Moara; Silva, Thiago M; Sanches, José M; Esteban, Nubia; Magalhaes, Wagner CS; Rodrigues, Maíra R; Kehdy, Fernanda S G; Pereira, Alexandre C

2016-01-01

The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals. PMID:26395555

Mapping face categorization in the human ventral occipitotemporal cortex with direct neural intracranial recordings.

PubMed

Rossion, Bruno; Jacques, Corentin; Jonas, Jacques

2018-02-26

The neural basis of face categorization has been widely investigated with functional magnetic resonance imaging (fMRI), identifying a set of face-selective local regions in the ventral occipitotemporal cortex (VOTC). However, indirect recording of neural activity with fMRI is associated with large fluctuations of signal across regions, often underestimating face-selective responses in the anterior VOTC. While direct recording of neural activity with subdural grids of electrodes (electrocorticography, ECoG) or depth electrodes (stereotactic electroencephalography, SEEG) offers a unique opportunity to fill this gap in knowledge, these studies rather reveal widely distributed face-selective responses. Moreover, intracranial recordings are complicated by interindividual variability in neuroanatomy, ambiguity in definition, and quantification of responses of interest, as well as limited access to sulci with ECoG. Here, we propose to combine SEEG in large samples of individuals with fast periodic visual stimulation to objectively define, quantify, and characterize face categorization across the whole VOTC. This approach reconciles the wide distribution of neural face categorization responses with their (right) hemispheric and regional specialization, and reveals several face-selective regions in anterior VOTC sulci. We outline the challenges of this research program to understand the neural basis of face categorization and high-level visual recognition in general. © 2018 New York Academy of Sciences.

Distribution and Characteristics of Seafloor Seepage Features in the Active Margin Offshore of SW Taiwan

NASA Astrophysics Data System (ADS)

Chen, T. T.; Hsu, H. H.; Liu, C. S.; Su, C. C.; Paull, C. K.; Chen, Y. H.; Caress, D. W.; Gwiazda, R.; Lundsten, E. M.

2017-12-01

In the active margin offshore of southwest (SW) Taiwan, west-vergent imbricated thrusts, folds and dipping strata are the main structural features. This is also the area where gas hydrates are widely distributed beneath the seafloor. Fluids from deep strata may migrate upwards along porous dipping layers or faults and then vent out to form seafloor seepage features in many of the gas hydrate prospects. A joint survey was conducted in May 2017 using MBARI mapping AUV and miniROV to investigate the seafloor seepage features. Numerous comet-shaped depressions (CSD) are mapped along flanks of several anticlinal ridges, and four carbonate mounds around CSD are observed from the ultra-high-resolution (1-m lateral resolution) bathymetry data collected by AUV. Samples of the carbonate mounds were collected by the mini-ROV, and their mineral compositions contain dolomite and ankerite. The AUV collected chirp sonar profiles and previously collected surface ship multichannel seismic reflection profiles across these seafloor features show that potential fluid migration pathways connect free gas trapped below the base of gas hydrate stability zone and the seafloor in the vicinity of these features. Our study suggests that the CSD could be an indicator of seafloor seepage and may be distribution widely in the active margin setting.

Plasma Diffusion in Self-Consistent Fluctuations

NASA Technical Reports Server (NTRS)

Smets, R.; Belmont, G.; Aunai, N.

2012-01-01

The problem of particle diffusion in position space, as a consequence ofeleclromagnetic fluctuations is addressed. Numerical results obtained with a self-consistent hybrid code are presented, and a method to calculate diffusion coefficient in the direction perpendicular to the mean magnetic field is proposed. The diffusion is estimated for two different types of fluctuations. The first type (resuiting from an agyrotropic in itiai setting)is stationary, wide band white noise, and associated to Gaussian probability distribution function for the magnetic fluctuations. The second type (result ing from a Kelvin-Helmholtz instability) is non-stationary, with a power-law spectrum, and a non-Gaussian probabi lity distribution function. The results of the study allow revisiting the question of loading particles of solar wind origin in the Earth magnetosphere.

US data policy for Earth observation from space

NASA Technical Reports Server (NTRS)

Shaffer, Lisa Robock

1992-01-01

Distribution of data from U.S. Earth observations satellites is subject to different data policies and regulations depending on whether the systems in question are operational or experimental. Specific laws, regulations, and policies are in place for the distribution of satellite data from the National Oceanic and Atmospheric Administration (NOAA) operational environmental satellites and from NASA experimental systems. There is a government wide policy for exchange of data for global change research. For the Earth Observing System (EOS) and its international partner programs, a set of data exchange principles is nearing completion. The debate over the future of the LANDSAT program in the U.S. will impact policy for the programs, but the outcome of the debate is not yet known.

Stochastic parameter estimation in nonlinear time-delayed vibratory systems with distributed delay

NASA Astrophysics Data System (ADS)

Torkamani, Shahab; Butcher, Eric A.

2013-07-01

The stochastic estimation of parameters and states in linear and nonlinear time-delayed vibratory systems with distributed delay is explored. The approach consists of first employing a continuous time approximation to approximate the delayed integro-differential system with a large set of ordinary differential equations having stochastic excitations. Then the problem of state and parameter estimation in the resulting stochastic ordinary differential system is represented as an optimal filtering problem using a state augmentation technique. By adapting the extended Kalman-Bucy filter to the augmented filtering problem, the unknown parameters of the time-delayed system are estimated from noise-corrupted, possibly incomplete measurements of the states. Similarly, the upper bound of the distributed delay can also be estimated by the proposed technique. As an illustrative example to a practical problem in vibrations, the parameter, delay upper bound, and state estimation from noise-corrupted measurements in a distributed force model widely used for modeling machine tool vibrations in the turning operation is investigated.

RAID Unbound: Storage Fault Tolerance in a Distributed Environment

NASA Technical Reports Server (NTRS)

Ritchie, Brian

1996-01-01

Mirroring, data replication, backup, and more recently, redundant arrays of independent disks (RAID) are all technologies used to protect and ensure access to critical company data. A new set of problems has arisen as data becomes more and more geographically distributed. Each of the technologies listed above provides important benefits; but each has failed to adapt fully to the realities of distributed computing. The key to data high availability and protection is to take the technologies' strengths and 'virtualize' them across a distributed network. RAID and mirroring offer high data availability, which data replication and backup provide strong data protection. If we take these concepts at a very granular level (defining user, record, block, file, or directory types) and them liberate them from the physical subsystems with which they have traditionally been associated, we have the opportunity to create a highly scalable network wide storage fault tolerance. The network becomes the virtual storage space in which the traditional concepts of data high availability and protection are implemented without their corresponding physical constraints.

Modular Knowledge Representation and Reasoning in the Semantic Web

NASA Astrophysics Data System (ADS)

Serafini, Luciano; Homola, Martin

Construction of modular ontologies by combining different modules is becoming a necessity in ontology engineering in order to cope with the increasing complexity of the ontologies and the domains they represent. The modular ontology approach takes inspiration from software engineering, where modularization is a widely acknowledged feature. Distributed reasoning is the other side of the coin of modular ontologies: given an ontology comprising of a set of modules, it is desired to perform reasoning by combination of multiple reasoning processes performed locally on each of the modules. In the last ten years, a number of approaches for combining logics has been developed in order to formalize modular ontologies. In this chapter, we survey and compare the main formalisms for modular ontologies and distributed reasoning in the Semantic Web. We select four formalisms build on formal logical grounds of Description Logics: Distributed Description Logics, ℰ-connections, Package-based Description Logics and Integrated Distributed Description Logics. We concentrate on expressivity and distinctive modeling features of each framework. We also discuss reasoning capabilities of each framework.

The Benford law behavior of the religious activity data

NASA Astrophysics Data System (ADS)

Mir, T. A.

2014-08-01

An important aspect of religious association is that adherents, as part of their religious duty, carry out various activities. One religious group known for keeping the elaborate records of day-to-day activities of its members is the Jehovah's Witnesses (JWs)-a worldwide Christian religious group. We analyse the historical records of the country-wide data associated with twelve different religious activities of JWs to see if there are any patterns in the distribution of the first digits as predicted by Benford's law. This law states that the first digits of numbers in data sets are not uniformly distributed but often, not always, follow a logarithmic distribution such that the numbers beginning with smaller digits appear more frequently than those with larger ones. We find that the data on religious activities like peak publishers, pioneer publishers, baptizations, public meetings, congregations, bible studies, time spent in door-to-door contacts, attendances at the memorial services, total literature and individual magazines distributed, new subscriptions and back-calls received excellently conforms to Benford's law.

Posterior consistency in conditional distribution estimation

PubMed Central

Pati, Debdeep; Dunson, David B.; Tokdar, Surya T.

2014-01-01

A wide variety of priors have been proposed for nonparametric Bayesian estimation of conditional distributions, and there is a clear need for theorems providing conditions on the prior for large support, as well as posterior consistency. Estimation of an uncountable collection of conditional distributions across different regions of the predictor space is a challenging problem, which differs in some important ways from density and mean regression estimation problems. Defining various topologies on the space of conditional distributions, we provide sufficient conditions for posterior consistency focusing on a broad class of priors formulated as predictor-dependent mixtures of Gaussian kernels. This theory is illustrated by showing that the conditions are satisfied for a class of generalized stick-breaking process mixtures in which the stick-breaking lengths are monotone, differentiable functions of a continuous stochastic process. We also provide a set of sufficient conditions for the case where stick-breaking lengths are predictor independent, such as those arising from a fixed Dirichlet process prior. PMID:25067858

Clustering redshift distributions for the Dark Energy Survey

NASA Astrophysics Data System (ADS)

Helsby, Jennifer

Accurate determination of photometric redshifts and their errors is critical for large scale structure and weak lensing studies for constraining cosmology from deep, wide imaging surveys. Current photometric redshift methods suffer from bias and scatter due to incomplete training sets. Exploiting the clustering between a sample of galaxies for which we have spectroscopic redshifts and a sample of galaxies for which the redshifts are unknown can allow us to reconstruct the true redshift distribution of the unknown sample. Here we use this method in both simulations and early data from the Dark Energy Survey (DES) to determine the true redshift distributions of galaxies in photometric redshift bins. We find that cross-correlating with the spectroscopic samples currently used for training provides a useful test of photometric redshifts and provides reliable estimates of the true redshift distribution in a photometric redshift bin. We discuss the use of the cross-correlation method in validating template- or learning-based approaches to redshift estimation and its future use in Stage IV surveys.

Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa).

PubMed

Nakamura, Yasuhide; Imai, Ichiro; Yamaguchi, Atsushi; Tuji, Akihiro; Not, Fabrice; Suzuki, Noritoshi

2015-07-01

Phaeodarians are a group of widely distributed marine cercozoans. These plankton organisms can exhibit a large biomass in the environment and are supposed to play an important role in marine ecosystems and in material cycles in the ocean. Accurate knowledge of phaeodarian classification is thus necessary to better understand marine biology, however, phylogenetic information on Phaeodaria is limited. The present study analyzed 18S rDNA sequences encompassing all existing phaeodarian orders, to clarify their phylogenetic relationships and improve their taxonomic classification. The monophyly of Phaeodaria was confirmed and strongly supported by phylogenetic analysis with a larger data set than in previous studies. The phaeodarian clade contained 11 subclades which generally did not correspond to the families and orders of the current classification system. Two families (Challengeriidae and Aulosphaeridae) and two orders (Phaeogromida and Phaeocalpida) are possibly polyphyletic or paraphyletic, and consequently the classification needs to be revised at both the family and order levels by integrative taxonomy approaches. Two morphological criteria, 1) the scleracoma type and 2) its surface structure, could be useful markers at the family level. Copyright © 2015 Elsevier GmbH. All rights reserved.

Mathematical modelling of Bit-Level Architecture using Reciprocal Quantum Logic

NASA Astrophysics Data System (ADS)

Narendran, S.; Selvakumar, J.

2018-04-01

Efficiency of high-performance computing is on high demand with both speed and energy efficiency. Reciprocal Quantum Logic (RQL) is one of the technology which will produce high speed and zero static power dissipation. RQL uses AC power supply as input rather than DC input. RQL has three set of basic gates. Series of reciprocal transmission lines are placed in between each gate to avoid loss of power and to achieve high speed. Analytical model of Bit-Level Architecture are done through RQL. Major drawback of reciprocal Quantum Logic is area, because of lack in proper power supply. To achieve proper power supply we need to use splitters which will occupy large area. Distributed arithmetic uses vector- vector multiplication one is constant and other is signed variable and each word performs as a binary number, they rearranged and mixed to form distributed system. Distributed arithmetic is widely used in convolution and high performance computational devices.

Cross-Language Distributions of High Frequency and Phonetically Similar Cognates

PubMed Central

Schepens, Job; Dijkstra, Ton; Grootjen, Franc; van Heuven, Walter J. B.

2013-01-01

The coinciding form and meaning similarity of cognates, e.g. ‘flamme’ (French), ‘Flamme’ (German), ‘vlam’ (Dutch), meaning ‘flame’ in English, facilitates learning of additional languages. The cross-language frequency and similarity distributions of cognates vary according to evolutionary change and language contact. We compare frequency and orthographic (O), phonetic (P), and semantic similarity of cognates, automatically identified in semi-complete lexicons of six widely spoken languages. Comparisons of P and O similarity reveal inconsistent mappings in language pairs with deep orthographies. The frequency distributions show that cognate frequency is reduced in less closely related language pairs as compared to more closely related languages (e.g., French-English vs. German-English). These frequency and similarity patterns may support a better understanding of cognate processing in natural and experimental settings. The automatically identified cognates are available in the supplementary materials, including the frequency and similarity measurements. PMID:23675449

WIC's promotion of infant formula in the United States

PubMed Central

Kent, George

2006-01-01

Background The United States' Special Supplemental Nutrition Program for Women, Infants and Children (WIC) distributes about half the infant formula used in the United States at no cost to the families. This is a matter of concern because it is known that feeding with infant formula results in worse health outcomes for infants than breastfeeding. Discussion The evidence that is available indicates that the WIC program has the effect of promoting the use of infant formula, thus placing infants at higher risk. Moreover, the program violates the widely accepted principles that have been set out in the International Code of Marketing of Breast-milk Substitutes and in the human right to adequate food. Summary There is no good reason for an agency of government to distribute large quantities of free infant formula. It is recommended that the large-scale distribution of free infant formula by the WIC program should be phased out. PMID:16722534

Mass measurement errors of Fourier-transform mass spectrometry (FTMS): distribution, recalibration, and application.

PubMed

Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

2009-02-01

The hybrid linear trap quadrupole Fourier-transform (LTQ-FT) ion cyclotron resonance mass spectrometer, an instrument with high accuracy and resolution, is widely used in the identification and quantification of peptides and proteins. However, time-dependent errors in the system may lead to deterioration of the accuracy of these instruments, negatively influencing the determination of the mass error tolerance (MET) in database searches. Here, a comprehensive discussion of LTQ/FT precursor ion mass error is provided. On the basis of an investigation of the mass error distribution, we propose an improved recalibration formula and introduce a new tool, FTDR (Fourier-transform data recalibration), that employs a graphic user interface (GUI) for automatic calibration. It was found that the calibration could adjust the mass error distribution to more closely approximate a normal distribution and reduce the standard deviation (SD). Consequently, we present a new strategy, LDSF (Large MET database search and small MET filtration), for database search MET specification and validation of database search results. As the name implies, a large-MET database search is conducted and the search results are then filtered using the statistical MET estimated from high-confidence results. By applying this strategy to a standard protein data set and a complex data set, we demonstrate the LDSF can significantly improve the sensitivity of the result validation procedure.

Nonparametric Bayesian inference for mean residual life functions in survival analysis.

PubMed

Poynor, Valerie; Kottas, Athanasios

2018-01-19

Modeling and inference for survival analysis problems typically revolves around different functions related to the survival distribution. Here, we focus on the mean residual life (MRL) function, which provides the expected remaining lifetime given that a subject has survived (i.e. is event-free) up to a particular time. This function is of direct interest in reliability, medical, and actuarial fields. In addition to its practical interpretation, the MRL function characterizes the survival distribution. We develop general Bayesian nonparametric inference for MRL functions built from a Dirichlet process mixture model for the associated survival distribution. The resulting model for the MRL function admits a representation as a mixture of the kernel MRL functions with time-dependent mixture weights. This model structure allows for a wide range of shapes for the MRL function. Particular emphasis is placed on the selection of the mixture kernel, taken to be a gamma distribution, to obtain desirable properties for the MRL function arising from the mixture model. The inference method is illustrated with a data set of two experimental groups and a data set involving right censoring. The supplementary material available at Biostatistics online provides further results on empirical performance of the model, using simulated data examples. © The Author 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The IEEE GRSS Standardized Remote Sensing Data Website: A Step Towards "Science 2.0" in Remote Sensing

NASA Astrophysics Data System (ADS)

Dell'Acqua, Fabio; Iannelli, Gianni Cristian; Kerekes, John; Lisini, Gianni; Moser, Gabriele; Ricardi, Niccolo; Pierce, Leland

2016-08-01

The issue of homogeneity in performance assessment of proposed algorithms for information extraction is generally perceived also in the Earth Observation (EO) domain. Different authors propose different datasets to test their developed algorithms and to the reader it is frequently difficult to assess which is better for his/her specific application, given the wide variability in test sets that makes pure comparison of e.g. accuracy values less meaningful than one would desire. With our work, we gave a modest contribution to ease the problem by making it possible to automatically distribute a limited set of possible "standard" open datasets, together with some ground truth info, and automatically assess processing results provided by the users.

Test Review for Preschool-Wide Evaluation Tool (PreSET) Manual: Assessing Universal Program-Wide Positive Behavior Support in Early Childhood

ERIC Educational Resources Information Center

Rodriguez, Billie Jo

2013-01-01

The Preschool-Wide Evaluation Tool (PreSET; Steed & Pomerleau, 2012) is published by Paul H. Brookes Publishing Company in Baltimore, MD. The PreSET purports to measure universal and program-wide features of early childhood programs' implementation fidelity of program-wide positive behavior intervention and support (PW-PBIS) and is,…

Canada's new medical school: The Northern Ontario School of Medicine: social accountability through distributed community engaged learning.

PubMed

Strasser, Roger P; Lanphear, Joel H; McCready, William G; Topps, Maureen H; Hunt, D Dan; Matte, Marie C

2009-10-01

Like many rural regions around the world, Northern Ontario has a chronic shortage of doctors. Recognizing that medical graduates who have grown up in a rural area are more likely to practice in the rural setting, the Government of Ontario, Canada, decided in 2001 to establish a new medical school in the region with a social accountability mandate to contribute to improving the health of the people and communities of Northern Ontario. The Northern Ontario School of Medicine (NOSM) is a joint initiative of Laurentian University and Lakehead University, which are located 700 miles apart. This paper outlines the development and implementation of NOSM, Canada's first new medical school in more than 30 years. NOSM is a rural distributed community-based medical school which actively seeks to recruit students into its MD program who come from Northern Ontario or from similar northern, rural, remote, Aboriginal, Francophone backgrounds. The holistic, cohesive curriculum for the MD program relies heavily on electronic communications to support distributed community engaged learning. In the classroom and in clinical settings, students explore cases from the perspective of physicians in Northern Ontario. Clinical education takes place in a wide range of community and health service settings, so that the students experience the diversity of communities and cultures in Northern Ontario. NOSM graduates will be skilled physicians ready and able to undertake postgraduate training anywhere, but with a special affinity for and comfort with pursuing postgraduate training and clinical practice in Northern Ontario.

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

PubMed

Huang, Yen-Tsung; Hsu, Thomas; Christiani, David C

2014-01-01

The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X (2) distributions that can be obtained using permutation with scaled X (2) approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (<2.8 × 10(-5)), including the PTEN pathway (7.8 × 10(-7)), the gene set up-regulated under heat shock (3.6 × 10(-6)), the gene sets involved in the immune profile for rejection of kidney transplantation (9.2 × 10(-6)) and for transcriptional control of leukocytes (2.2 × 10(-5)), and the ganglioside biosynthesis pathway (2.7 × 10(-5)). In conclusion, we present a new method for pathway analyses of copy number data, and causal mechanisms of the five pathways require further study.

A deep learning approach to estimate stress distribution: a fast and accurate surrogate of finite-element analysis.

PubMed

Liang, Liang; Liu, Minliang; Martin, Caitlin; Sun, Wei

2018-01-01

Structural finite-element analysis (FEA) has been widely used to study the biomechanics of human tissues and organs, as well as tissue-medical device interactions, and treatment strategies. However, patient-specific FEA models usually require complex procedures to set up and long computing times to obtain final simulation results, preventing prompt feedback to clinicians in time-sensitive clinical applications. In this study, by using machine learning techniques, we developed a deep learning (DL) model to directly estimate the stress distributions of the aorta. The DL model was designed and trained to take the input of FEA and directly output the aortic wall stress distributions, bypassing the FEA calculation process. The trained DL model is capable of predicting the stress distributions with average errors of 0.492% and 0.891% in the Von Mises stress distribution and peak Von Mises stress, respectively. This study marks, to our knowledge, the first study that demonstrates the feasibility and great potential of using the DL technique as a fast and accurate surrogate of FEA for stress analysis. © 2018 The Author(s).

Regression analysis using dependent Polya trees.

PubMed

Schörgendorfer, Angela; Branscum, Adam J

2013-11-30

Many commonly used models for linear regression analysis force overly simplistic shape and scale constraints on the residual structure of data. We propose a semiparametric Bayesian model for regression analysis that produces data-driven inference by using a new type of dependent Polya tree prior to model arbitrary residual distributions that are allowed to evolve across increasing levels of an ordinal covariate (e.g., time, in repeated measurement studies). By modeling residual distributions at consecutive covariate levels or time points using separate, but dependent Polya tree priors, distributional information is pooled while allowing for broad pliability to accommodate many types of changing residual distributions. We can use the proposed dependent residual structure in a wide range of regression settings, including fixed-effects and mixed-effects linear and nonlinear models for cross-sectional, prospective, and repeated measurement data. A simulation study illustrates the flexibility of our novel semiparametric regression model to accurately capture evolving residual distributions. In an application to immune development data on immunoglobulin G antibodies in children, our new model outperforms several contemporary semiparametric regression models based on a predictive model selection criterion. Copyright © 2013 John Wiley & Sons, Ltd.

IP-Based Video Modem Extender Requirements

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

Pierson, L G; Boorman, T M; Howe, R E

2003-12-16

Visualization is one of the keys to understanding large complex data sets such as those generated by the large computing resources purchased and developed by the Advanced Simulation and Computing program (aka ASCI). In order to be convenient to researchers, visualization data must be distributed to offices and large complex visualization theaters. Currently, local distribution of the visual data is accomplished by distance limited modems and RGB switches that simply do not scale to hundreds of users across the local, metropolitan, and WAN distances without incurring large costs in fiber plant installation and maintenance. Wide Area application over the DOEmore » Complex is infeasible using these limited distance RGB extenders. On the other hand, Internet Protocols (IP) over Ethernet is a scalable well-proven technology that can distribute large volumes of data over these distances. Visual data has been distributed at lower resolutions over IP in industrial applications. This document describes requirements of the ASCI program in visual signal distribution for the purpose of identifying industrial partners willing to develop products to meet ASCI's needs.« less

The Construction of 3-d Neutral Density for Arbitrary Data Sets

NASA Astrophysics Data System (ADS)

Riha, S.; McDougall, T. J.; Barker, P. M.

2014-12-01

The Neutral Density variable allows inference of water pathways from thermodynamic properties in the global ocean, and is therefore an essential component of global ocean circulation analysis. The widely used algorithm for the computation of Neutral Density yields accurate results for data sets which are close to the observed climatological ocean. Long-term numerical climate simulations, however, often generate a significant drift from present-day climate, which renders the existing algorithm inaccurate. To remedy this problem, new algorithms which operate on arbitrary data have been developed, which may potentially be used to compute Neutral Density during runtime of a numerical model.We review existing approaches for the construction of Neutral Density in arbitrary data sets, detail their algorithmic structure, and present an analysis of the computational cost for implementations on a single-CPU computer. We discuss possible strategies for the implementation in state-of-the-art numerical models, with a focus on distributed computing environments.

BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks.

PubMed

Richiardi, Jonas; Altmann, Andre; Milazzo, Anna-Clare; Chang, Catie; Chakravarty, M Mallar; Banaschewski, Tobias; Barker, Gareth J; Bokde, Arun L W; Bromberg, Uli; Büchel, Christian; Conrod, Patricia; Fauth-Bühler, Mira; Flor, Herta; Frouin, Vincent; Gallinat, Jürgen; Garavan, Hugh; Gowland, Penny; Heinz, Andreas; Lemaître, Hervé; Mann, Karl F; Martinot, Jean-Luc; Nees, Frauke; Paus, Tomáš; Pausova, Zdenka; Rietschel, Marcella; Robbins, Trevor W; Smolka, Michael N; Spanagel, Rainer; Ströhle, Andreas; Schumann, Gunter; Hawrylycz, Mike; Poline, Jean-Baptiste; Greicius, Michael D

2015-06-12

During rest, brain activity is synchronized between different regions widely distributed throughout the brain, forming functional networks. However, the molecular mechanisms supporting functional connectivity remain undefined. We show that functional brain networks defined with resting-state functional magnetic resonance imaging can be recapitulated by using measures of correlated gene expression in a post mortem brain tissue data set. The set of 136 genes we identify is significantly enriched for ion channels. Polymorphisms in this set of genes significantly affect resting-state functional connectivity in a large sample of healthy adolescents. Expression levels of these genes are also significantly associated with axonal connectivity in the mouse. The results provide convergent, multimodal evidence that resting-state functional networks correlate with the orchestrated activity of dozens of genes linked to ion channel activity and synaptic function. Copyright © 2015, American Association for the Advancement of Science.

Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs.

PubMed

Douguet, Dominique

2018-03-08

Presented here are several data sets that gather information collected from the labels of the FDA approved drugs: their molecular structures and those of the described active metabolites, their associated pharmacokinetics and pharmacodynamics data, and the history of their marketing authorization by the FDA. To date, 1852 chemical structures have been identified with a molecular weight less than 2000 of which 492 are or have active metabolites. To promote the sharing of data, the original web server was upgraded for browsing the database and downloading the data sets (http://chemoinfo.ipmc.cnrs.fr/edrug3d). It is believed that the multidimensional chemistry-oriented collections are an essential resource for a thorough analysis of the current drug chemical space. The data sets are envisioned as being used in a wide range of endeavors that include drug repurposing, drug design, privileged structures analyses, structure-activity relationship studies, and improving of absorption, distribution, metabolism, and elimination predictive models.

Multi-Instrument Manager Tool for Data Acquisition and Merging of Optical and Electrical Mobility Size Distributions

NASA Astrophysics Data System (ADS)

Tritscher, Torsten; Koched, Amine; Han, Hee-Siew; Filimundi, Eric; Johnson, Tim; Elzey, Sherrie; Avenido, Aaron; Kykal, Carsten; Bischof, Oliver F.

2015-05-01

Electrical mobility classification (EC) followed by Condensation Particle Counter (CPC) detection is the technique combined in Scanning Mobility Particle Sizers(SMPS) to retrieve nanoparticle size distributions in the range from 2.5 nm to 1 μm. The detectable size range of SMPS systems can be extended by the addition of an Optical Particle Sizer(OPS) that covers larger sizes from 300 nm to 10 μm. This optical sizing method reports an optical equivalent diameter, which is often different from the electrical mobility diameter measured by the standard SMPS technique. Multi-Instrument Manager (MIMTM) software developed by TSI incorporates algorithms that facilitate merging SMPS data sets with data based on optical equivalent diameter to compile single, wide-range size distributions. Here we present MIM 2.0, the next-generation of the data merging tool that offers many advanced features for data merging and post-processing. MIM 2.0 allows direct data acquisition with OPS and NanoScan SMPS instruments to retrieve real-time particle size distributions from 10 nm to 10 μm, which we show in a case study at a fireplace. The merged data can be adjusted using one of the merging options, which automatically determines an overall aerosol effective refractive index. As a result an indirect and average characterization of aerosol optical and shape properties is possible. The merging tool allows several pre-settings, data averaging and adjustments, as well as the export of data sets and fitted graphs. MIM 2.0 also features several post-processing options for SMPS data and differences can be visualized in a multi-peak sample over a narrow size range.

Information Power Grid: Distributed High-Performance Computing and Large-Scale Data Management for Science and Engineering

NASA Technical Reports Server (NTRS)

Johnston, William E.; Gannon, Dennis; Nitzberg, Bill

2000-01-01

We use the term "Grid" to refer to distributed, high performance computing and data handling infrastructure that incorporates geographically and organizationally dispersed, heterogeneous resources that are persistent and supported. This infrastructure includes: (1) Tools for constructing collaborative, application oriented Problem Solving Environments / Frameworks (the primary user interfaces for Grids); (2) Programming environments, tools, and services providing various approaches for building applications that use aggregated computing and storage resources, and federated data sources; (3) Comprehensive and consistent set of location independent tools and services for accessing and managing dynamic collections of widely distributed resources: heterogeneous computing systems, storage systems, real-time data sources and instruments, human collaborators, and communications systems; (4) Operational infrastructure including management tools for distributed systems and distributed resources, user services, accounting and auditing, strong and location independent user authentication and authorization, and overall system security services The vision for NASA's Information Power Grid - a computing and data Grid - is that it will provide significant new capabilities to scientists and engineers by facilitating routine construction of information based problem solving environments / frameworks. Such Grids will knit together widely distributed computing, data, instrument, and human resources into just-in-time systems that can address complex and large-scale computing and data analysis problems. Examples of these problems include: (1) Coupled, multidisciplinary simulations too large for single systems (e.g., multi-component NPSS turbomachine simulation); (2) Use of widely distributed, federated data archives (e.g., simultaneous access to metrological, topological, aircraft performance, and flight path scheduling databases supporting a National Air Space Simulation systems}; (3) Coupling large-scale computing and data systems to scientific and engineering instruments (e.g., realtime interaction with experiments through real-time data analysis and interpretation presented to the experimentalist in ways that allow direct interaction with the experiment (instead of just with instrument control); (5) Highly interactive, augmented reality and virtual reality remote collaborations (e.g., Ames / Boeing Remote Help Desk providing field maintenance use of coupled video and NDI to a remote, on-line airframe structures expert who uses this data to index into detailed design databases, and returns 3D internal aircraft geometry to the field); (5) Single computational problems too large for any single system (e.g. the rotocraft reference calculation). Grids also have the potential to provide pools of resources that could be called on in extraordinary / rapid response situations (such as disaster response) because they can provide common interfaces and access mechanisms, standardized management, and uniform user authentication and authorization, for large collections of distributed resources (whether or not they normally function in concert). IPG development and deployment is addressing requirements obtained by analyzing a number of different application areas, in particular from the NASA Aero-Space Technology Enterprise. This analysis has focussed primarily on two types of users: the scientist / design engineer whose primary interest is problem solving (e.g. determining wing aerodynamic characteristics in many different operating environments), and whose primary interface to IPG will be through various sorts of problem solving frameworks. The second type of user is the tool designer: the computational scientists who convert physics and mathematics into code that can simulate the physical world. These are the two primary users of IPG, and they have rather different requirements. The results of the analysis of the needs of these two types of users provides a broad set of requirements that gives rise to a general set of required capabilities. The IPG project is intended to address all of these requirements. In some cases the required computing technology exists, and in some cases it must be researched and developed. The project is using available technology to provide a prototype set of capabilities in a persistent distributed computing testbed. Beyond this, there are required capabilities that are not immediately available, and whose development spans the range from near-term engineering development (one to two years) to much longer term R&D (three to six years). Additional information is contained in the original.

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.

Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach.

PubMed

Abad-Grau, Mara M; Medina-Medina, Nuria; Montes-Soldado, Rosana; Matesanz, Fuencisla; Bafna, Vineet

2012-01-01

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker 2-Groups TDT (mTDT(2G)), a test which under the hypothesis of no linkage, asymptotically follows a χ2 distribution with 1 degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that mTDT(2G) test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, mTDT(2G) turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases.

Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

PubMed Central

Abad-Grau, Mara M.; Medina-Medina, Nuria; Montes-Soldado, Rosana; Matesanz, Fuencisla; Bafna, Vineet

2012-01-01

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker -Groups TDT ( ), a test which under the hypothesis of no linkage, asymptotically follows a distribution with degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases. PMID:22363405

The Role of Late-Acting Self-Incompatibility and Early-Acting Inbreeding Depression in Governing Female Fertility in Monkshood, Aconitum kusnezoffii

PubMed Central

Hao, Yi-Qi; Zhao, Xin-Feng; She, Deng-Ying; Xu, Bing; Zhang, Da-Yong; Liao, Wan-Jin

2012-01-01

Reduced seed yields following self-pollination have repeatedly been observed, but the underlying mechanisms remain elusive when self-pollen tubes can readily grow into ovaries, because pre-, post-zygotic late-acting self-incompatibility (LSI), or early-acting inbreeding depression (ID) can induce self-sterility. The main objective of this study was to differentiate these processes in Aconitum kusnezoffii, a plant lacking stigmatic or stylar inhibition of self-pollination. We performed a hand-pollination experiment in a natural population of A. kusnezoffii, compared seed set among five pollination treatments, and evaluated the distribution of seed size and seed set. Embryonic development suggested fertilization following self-pollination. A partial pre-zygotic LSI was suggested to account for the reduced seed set by two lines of evidence. The seed set of chase-pollination treatment significantly exceeded that of self-pollination treatment, and the proportion of unfertilized ovules was the highest following self-pollination. Meanwhile, early-acting ID, rather than post-zygotic LSI, was suggested by the findings that the size of aborted selfed seeds varied continuously and widely; and the selfed seed set both exhibited a continuous distribution and positively correlated with the crossed seed set. These results indicated that the embryos were aborted at different stages due to the expression of many deleterious alleles throughout the genome during seed maturation. No signature of post-zygotic LSI was found. Both partial pre-zygotic LSI and early-acting ID contribute to the reduction in selfed seed set in A. kusnezoffii, with pre-zygotic LSI rejecting part of the self-pollen and early-acting ID aborting part of the self-fertilized seeds. PMID:23056570

An Examination of Diameter Density Prediction with k-NN and Airborne Lidar

DOE PAGES

Strunk, Jacob L.; Gould, Peter J.; Packalen, Petteri; ...

2017-11-16

While lidar-based forest inventory methods have been widely demonstrated, performances of methods to predict tree diameters with airborne lidar (lidar) are not well understood. One cause for this is that the performance metrics typically used in studies for prediction of diameters can be difficult to interpret, and may not support comparative inferences between sampling designs and study areas. To help with this problem we propose two indices and use them to evaluate a variety of lidar and k nearest neighbor (k-NN) strategies for prediction of tree diameter distributions. The indices are based on the coefficient of determination ( R 2),more » and root mean square deviation (RMSD). Both of the indices are highly interpretable, and the RMSD-based index facilitates comparisons with alternative (non-lidar) inventory strategies, and with projects in other regions. K-NN diameter distribution prediction strategies were examined using auxiliary lidar for 190 training plots distribute across the 800 km 2 Savannah River Site in South Carolina, USA. In conclusion, we evaluate the performance of k-NN with respect to distance metrics, number of neighbors, predictor sets, and response sets. K-NN and lidar explained 80% of variability in diameters, and Mahalanobis distance with k = 3 neighbors performed best according to a number of criteria.« less

Reconstructing the historical distribution of the Amur Leopard (Panthera pardus orientalis) in Northeast China based on historical records

PubMed Central

Yang, Li; Huang, Mujiao; Zhang, Rui; Lv, Jiang; Ren, Yueheng; Jiang, Zhe; Zhang, Wei; Luan, Xiaofeng

2016-01-01

Abstract The range of the Amur leopard (Panthera pardus orientalis) has decreased dramatically over the last 100 years. This species is still under extreme risk of extinction and conservation efforts are rigorous. Understanding the long-term dynamics of the population decline would be helpful to offer insight into the mechanism behind the decline and endangerment and improve conservation perspectives and strategies. Historical data collection has been the challenge for reconstructing the historical distribution. In China, new gazetteers having systematic compilation and considerable local ecological data can be considered as an important complementary for reconstruction. Therefore, we have set up a data set (mainly based on the new gazetteers) in order to identify the historical range of the Amur Leopard from the 1950s to 2014. The result shows that the Amur leopard was historically widely distributed with large populations in Northeastern China, but it presented a sharp decline after the 1970s. The decline appeared from the plains to the mountains and northeast to southwest since the 1950s. Long-term historical data, mainly from new gazetteers, demonstrates that such resources are capable of tracking species change through time and offers an opportunity to reduce data shortage and enhance understanding in conservation. PMID:27408548

Prediction of resource volumes at untested locations using simple local prediction models

USGS Publications Warehouse

Attanasi, E.D.; Coburn, T.C.; Freeman, P.A.

2006-01-01

This paper shows how local spatial nonparametric prediction models can be applied to estimate volumes of recoverable gas resources at individual undrilled sites, at multiple sites on a regional scale, and to compute confidence bounds for regional volumes based on the distribution of those estimates. An approach that combines cross-validation, the jackknife, and bootstrap procedures is used to accomplish this task. Simulation experiments show that cross-validation can be applied beneficially to select an appropriate prediction model. The cross-validation procedure worked well for a wide range of different states of nature and levels of information. Jackknife procedures are used to compute individual prediction estimation errors at undrilled locations. The jackknife replicates also are used with a bootstrap resampling procedure to compute confidence bounds for the total volume. The method was applied to data (partitioned into a training set and target set) from the Devonian Antrim Shale continuous-type gas play in the Michigan Basin in Otsego County, Michigan. The analysis showed that the model estimate of total recoverable volumes at prediction sites is within 4 percent of the total observed volume. The model predictions also provide frequency distributions of the cell volumes at the production unit scale. Such distributions are the basis for subsequent economic analyses. ?? Springer Science+Business Media, LLC 2007.

Dielectric elastomer memory

NASA Astrophysics Data System (ADS)

O'Brien, Benjamin M.; McKay, Thomas G.; Xie, Sheng Q.; Calius, Emilio P.; Anderson, Iain A.

2011-04-01

Life shows us that the distribution of intelligence throughout flexible muscular networks is a highly successful solution to a wide range of challenges, for example: human hearts, octopi, or even starfish. Recreating this success in engineered systems requires soft actuator technologies with embedded sensing and intelligence. Dielectric Elastomer Actuator(s) (DEA) are promising due to their large stresses and strains, as well as quiet flexible multimodal operation. Recently dielectric elastomer devices were presented with built in sensor, driver, and logic capability enabled by a new concept called the Dielectric Elastomer Switch(es) (DES). DES use electrode piezoresistivity to control the charge on DEA and enable the distribution of intelligence throughout a DEA device. In this paper we advance the capabilities of DES further to form volatile memory elements. A set reset flip-flop with inverted reset line was developed based on DES and DEA. With a 3200V supply the flip-flop behaved appropriately and demonstrated the creation of dielectric elastomer memory capable of changing state in response to 1 second long set and reset pulses. This memory opens up applications such as oscillator, de-bounce, timing, and sequential logic circuits; all of which could be distributed throughout biomimetic actuator arrays. Future work will include miniaturisation to improve response speed, implementation into more complex circuits, and investigation of longer lasting and more sensitive switching materials.

Automatic image equalization and contrast enhancement using Gaussian mixture modeling.

PubMed

Celik, Turgay; Tjahjadi, Tardi

2012-01-01

In this paper, we propose an adaptive image equalization algorithm that automatically enhances the contrast in an input image. The algorithm uses the Gaussian mixture model to model the image gray-level distribution, and the intersection points of the Gaussian components in the model are used to partition the dynamic range of the image into input gray-level intervals. The contrast equalized image is generated by transforming the pixels' gray levels in each input interval to the appropriate output gray-level interval according to the dominant Gaussian component and the cumulative distribution function of the input interval. To take account of the hypothesis that homogeneous regions in the image represent homogeneous silences (or set of Gaussian components) in the image histogram, the Gaussian components with small variances are weighted with smaller values than the Gaussian components with larger variances, and the gray-level distribution is also used to weight the components in the mapping of the input interval to the output interval. Experimental results show that the proposed algorithm produces better or comparable enhanced images than several state-of-the-art algorithms. Unlike the other algorithms, the proposed algorithm is free of parameter setting for a given dynamic range of the enhanced image and can be applied to a wide range of image types.

Interacting epidemics on overlay networks

NASA Astrophysics Data System (ADS)

Funk, Sebastian; Jansen, Vincent A. A.

2010-03-01

The interaction between multiple pathogens spreading on networks connecting a given set of nodes presents an ongoing theoretical challenge. Here, we aim to understand such interactions by studying bond percolation of two different processes on overlay networks of arbitrary joint degree distribution. We find that an outbreak of a first pathogen providing immunity to another one spreading subsequently on a second network connecting the same set of nodes does so most effectively if the degrees on the two networks are positively correlated. In that case, the protection is stronger the more heterogeneous the degree distributions of the two networks are. If, on the other hand, the degrees are uncorrelated or negatively correlated, increasing heterogeneity reduces the potential of the first process to prevent the second one from reaching epidemic proportions. We generalize these results to cases where the edges of the two networks overlap to arbitrary amount, or where the immunity granted is only partial. If both processes grant immunity to each other, we find a wide range of possible situations of coexistence or mutual exclusion, depending on the joint degree distribution of the underlying networks and the amount of immunity granted mutually. These results generalize the concept of a coexistence threshold and illustrate the impact of large-scale network structure on the interaction between multiple spreading agents.

Reconstructing the historical distribution of the Amur Leopard (Panthera pardus orientalis) in Northeast China based on historical records.

PubMed

Yang, Li; Huang, Mujiao; Zhang, Rui; Lv, Jiang; Ren, Yueheng; Jiang, Zhe; Zhang, Wei; Luan, Xiaofeng

2016-01-01

The range of the Amur leopard (Panthera pardus orientalis) has decreased dramatically over the last 100 years. This species is still under extreme risk of extinction and conservation efforts are rigorous. Understanding the long-term dynamics of the population decline would be helpful to offer insight into the mechanism behind the decline and endangerment and improve conservation perspectives and strategies. Historical data collection has been the challenge for reconstructing the historical distribution. In China, new gazetteers having systematic compilation and considerable local ecological data can be considered as an important complementary for reconstruction. Therefore, we have set up a data set (mainly based on the new gazetteers) in order to identify the historical range of the Amur Leopard from the 1950s to 2014. The result shows that the Amur leopard was historically widely distributed with large populations in Northeastern China, but it presented a sharp decline after the 1970s. The decline appeared from the plains to the mountains and northeast to southwest since the 1950s. Long-term historical data, mainly from new gazetteers, demonstrates that such resources are capable of tracking species change through time and offers an opportunity to reduce data shortage and enhance understanding in conservation.

An Examination of Diameter Density Prediction with k-NN and Airborne Lidar

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

Strunk, Jacob L.; Gould, Peter J.; Packalen, Petteri

While lidar-based forest inventory methods have been widely demonstrated, performances of methods to predict tree diameters with airborne lidar (lidar) are not well understood. One cause for this is that the performance metrics typically used in studies for prediction of diameters can be difficult to interpret, and may not support comparative inferences between sampling designs and study areas. To help with this problem we propose two indices and use them to evaluate a variety of lidar and k nearest neighbor (k-NN) strategies for prediction of tree diameter distributions. The indices are based on the coefficient of determination ( R 2),more » and root mean square deviation (RMSD). Both of the indices are highly interpretable, and the RMSD-based index facilitates comparisons with alternative (non-lidar) inventory strategies, and with projects in other regions. K-NN diameter distribution prediction strategies were examined using auxiliary lidar for 190 training plots distribute across the 800 km 2 Savannah River Site in South Carolina, USA. In conclusion, we evaluate the performance of k-NN with respect to distance metrics, number of neighbors, predictor sets, and response sets. K-NN and lidar explained 80% of variability in diameters, and Mahalanobis distance with k = 3 neighbors performed best according to a number of criteria.« less

Distributed Monitoring of the R(sup 2) Statistic for Linear Regression

NASA Technical Reports Server (NTRS)

Bhaduri, Kanishka; Das, Kamalika; Giannella, Chris R.

2011-01-01

The problem of monitoring a multivariate linear regression model is relevant in studying the evolving relationship between a set of input variables (features) and one or more dependent target variables. This problem becomes challenging for large scale data in a distributed computing environment when only a subset of instances is available at individual nodes and the local data changes frequently. Data centralization and periodic model recomputation can add high overhead to tasks like anomaly detection in such dynamic settings. Therefore, the goal is to develop techniques for monitoring and updating the model over the union of all nodes data in a communication-efficient fashion. Correctness guarantees on such techniques are also often highly desirable, especially in safety-critical application scenarios. In this paper we develop DReMo a distributed algorithm with very low resource overhead, for monitoring the quality of a regression model in terms of its coefficient of determination (R2 statistic). When the nodes collectively determine that R2 has dropped below a fixed threshold, the linear regression model is recomputed via a network-wide convergecast and the updated model is broadcast back to all nodes. We show empirically, using both synthetic and real data, that our proposed method is highly communication-efficient and scalable, and also provide theoretical guarantees on correctness.

High mycorrhizal specificity in a widespread mycoheterotrophic plant, Eulophia zollingeri (Orchidaceae).

PubMed

Ogura-Tsujita, Yuki; Yukawa, Tomohisa

2008-01-01

Because mycoheterotrophic plants fully depend on their mycorrhizal partner for their carbon supply, the major limiting factor for the geographic distribution of these plants may be the presence of their mycorrhizal partner. Although this factor may seem to be a disadvantage for increasing geographic distribution, widespread mycoheterotrophic species nonetheless exist. The mechanism causing the wide distribution of some mycoheterotrophic species is, however, seldom discussed. We identified the mycorrhizal partner of a widespread mycoheterotrophic orchid, Eulophia zollingeri, using 12 individuals from seven populations in Japan, Myanmar, and Taiwan by DNA-based methods. All fungal ITS sequences from the roots closely related to those of Psathyrella candolleana (Coprinaceae) from GenBank accessions and herbarium specimens. These results indicate that E. zollingeri is exclusively associated with the P. candolleana species group. Further, the molecular data support the wide distribution and wide-ranging habitat of this fungal partner. Our data provide evidence that a mycoheterotrophic plant can achieve a wide distribution, even though it has a high mycorrhizal specificity, if its fungal partner is widely distributed.

Biostatistics Series Module 3: Comparing Groups: Numerical Variables.

PubMed

Hazra, Avijit; Gogtay, Nithya

2016-01-01

Numerical data that are normally distributed can be analyzed with parametric tests, that is, tests which are based on the parameters that define a normal distribution curve. If the distribution is uncertain, the data can be plotted as a normal probability plot and visually inspected, or tested for normality using one of a number of goodness of fit tests, such as the Kolmogorov-Smirnov test. The widely used Student's t-test has three variants. The one-sample t-test is used to assess if a sample mean (as an estimate of the population mean) differs significantly from a given population mean. The means of two independent samples may be compared for a statistically significant difference by the unpaired or independent samples t-test. If the data sets are related in some way, their means may be compared by the paired or dependent samples t-test. The t-test should not be used to compare the means of more than two groups. Although it is possible to compare groups in pairs, when there are more than two groups, this will increase the probability of a Type I error. The one-way analysis of variance (ANOVA) is employed to compare the means of three or more independent data sets that are normally distributed. Multiple measurements from the same set of subjects cannot be treated as separate, unrelated data sets. Comparison of means in such a situation requires repeated measures ANOVA. It is to be noted that while a multiple group comparison test such as ANOVA can point to a significant difference, it does not identify exactly between which two groups the difference lies. To do this, multiple group comparison needs to be followed up by an appropriate post hoc test. An example is the Tukey's honestly significant difference test following ANOVA. If the assumptions for parametric tests are not met, there are nonparametric alternatives for comparing data sets. These include Mann-Whitney U-test as the nonparametric counterpart of the unpaired Student's t-test, Wilcoxon signed-rank test as the counterpart of the paired Student's t-test, Kruskal-Wallis test as the nonparametric equivalent of ANOVA and the Friedman's test as the counterpart of repeated measures ANOVA.

Carrier capture efficiency in InGaN/GaN LEDs: Role of high temperature annealing

NASA Astrophysics Data System (ADS)

Vinattieri, A.; Batignani, F.; Bogani, F.; Meneghini, M.; Meneghesso, G.; Zanoni, E.; Zhu, D.; Humphreys, C. J.

2014-02-01

By means of time integrated (TI), time-resolved (TR) photoluminescence (PL) and PL excitation spectra, we investigate the role of an high temperature post-growth thermal annealing (TA) on a set of InGaN/GaN LED structures with different dislocation densities. We provide evidence of the nature of the radiative recombination from a wide distribution of non-interacting localised states and we show the beneficial effect of thermal annealing in reducing the contribution of non-radiative recombination in the well region.

A climate signal in exhumation patterns revealed by porphyry copper deposits

NASA Astrophysics Data System (ADS)

Yanites, Brian J.; Kesler, Stephen E.

2015-06-01

The processes that build and shape mountain landscapes expose important mineral resources. Mountain landscapes are widely thought to result from the interaction between tectonic uplift and exhumation by erosion. Both climate and tectonics affect rates of exhumation, but estimates of their relative importance vary. Porphyry copper deposits are emplaced at a depth of about 2 km in convergent tectonic settings; their exposure at the surface therefore can be used to track landscape exhumation. Here we analyse the distribution, ages and spatial density of exposed Cenozoic porphyry copper deposits using a global data set to quantify exhumation. We find that the deposits exhibit young ages and are sparsely distributed--both consistent with rapid exhumation--in regions with high precipitation, and deposits are older and more abundant in dry regions. This suggests that climate is driving erosion and mineral exposure in deposit-bearing mountain landscapes. Our findings show that the emplacement ages of porphyry copper deposits provide a means to estimate long-term exhumation rates in active orogens, and we conclude that climate-driven exhumation influences the age and abundance of exposed porphyry copper deposits around the world.

Online Cross-Validation-Based Ensemble Learning

PubMed Central

Benkeser, David; Ju, Cheng; Lendle, Sam; van der Laan, Mark

2017-01-01

Online estimators update a current estimate with a new incoming batch of data without having to revisit past data thereby providing streaming estimates that are scalable to big data. We develop flexible, ensemble-based online estimators of an infinite-dimensional target parameter, such as a regression function, in the setting where data are generated sequentially by a common conditional data distribution given summary measures of the past. This setting encompasses a wide range of time-series models and as special case, models for independent and identically distributed data. Our estimator considers a large library of candidate online estimators and uses online cross-validation to identify the algorithm with the best performance. We show that by basing estimates on the cross-validation-selected algorithm, we are asymptotically guaranteed to perform as well as the true, unknown best-performing algorithm. We provide extensions of this approach including online estimation of the optimal ensemble of candidate online estimators. We illustrate excellent performance of our methods using simulations and a real data example where we make streaming predictions of infectious disease incidence using data from a large database. PMID:28474419

Concurrent generation of multivariate mixed data with variables of dissimilar types.

PubMed

Amatya, Anup; Demirtas, Hakan

2016-01-01

Data sets originating from wide range of research studies are composed of multiple variables that are correlated and of dissimilar types, primarily of count, binary/ordinal and continuous attributes. The present paper builds on the previous works on multivariate data generation and develops a framework for generating multivariate mixed data with a pre-specified correlation matrix. The generated data consist of components that are marginally count, binary, ordinal and continuous, where the count and continuous variables follow the generalized Poisson and normal distributions, respectively. The use of the generalized Poisson distribution provides a flexible mechanism which allows under- and over-dispersed count variables generally encountered in practice. A step-by-step algorithm is provided and its performance is evaluated using simulated and real-data scenarios.

Competency criteria and the class inclusion task: modeling judgments and justifications.

PubMed

Thomas, H; Horton, J J

1997-11-01

Preschool age children's class inclusion task responses were modeled as mixtures of different probability distributions. The main idea: Different response strategies are equivalent to different probability distributions. A child displays cognitive strategy s if P (child uses strategy s, given the child's observed score X = x) = p(s) is the most probable strategy. The general approach is widely applicable to many settings. Both judgment and justification questions were asked. Judgment response strategies identified were subclass comparison, guessing, and inclusion logic. Children's justifications lagged their judgments in development. Although justification responses may be useful, C. J. Brainerd was largely correct: If a single response variable is to be selected, a judgments variable is likely the preferable one. But the process must be modeled to identify cognitive strategies, as B. Hodkin has demonstrated.

Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution.

PubMed

Lacombe-Harvey, Marie-Ève; Brzezinski, Ryszard; Beaulieu, Carole

2018-06-21

Actinobacteria, a large group of Gram-positive bacteria, secrete a wide range of extracellular enzymes involved in the degradation of organic compounds and biopolymers including the ubiquitous aminopolysaccharides chitin and chitosan. While chitinolytic enzymes are distributed in all kingdoms of life, actinobacteria are recognized as particularly good decomposers of chitinous material and several members of this taxon carry impressive sets of genes dedicated to chitin and chitosan degradation. Degradation of these polymers in actinobacteria is dependent on endo- and exo-acting hydrolases as well as lytic polysaccharide monooxygenases. Actinobacterial chitinases and chitosanases belong to nine major families of glycosyl hydrolases that share no sequence similarity. In this paper, the distribution of chitinolytic actinobacteria within different ecosystems is examined and their chitinolytic machinery is described and compared to those of other chitinolytic organisms.

Experimental verification of multipartite entanglement in quantum networks

PubMed Central

McCutcheon, W.; Pappa, A.; Bell, B. A.; McMillan, A.; Chailloux, A.; Lawson, T.; Mafu, M.; Markham, D.; Diamanti, E.; Kerenidis, I.; Rarity, J. G.; Tame, M. S.

2016-01-01

Multipartite entangled states are a fundamental resource for a wide range of quantum information processing tasks. In particular, in quantum networks, it is essential for the parties involved to be able to verify if entanglement is present before they carry out a given distributed task. Here we design and experimentally demonstrate a protocol that allows any party in a network to check if a source is distributing a genuinely multipartite entangled state, even in the presence of untrusted parties. The protocol remains secure against dishonest behaviour of the source and other parties, including the use of system imperfections to their advantage. We demonstrate the verification protocol in a three- and four-party setting using polarization-entangled photons, highlighting its potential for realistic photonic quantum communication and networking applications. PMID:27827361

Measurements of top-quark pair differential cross-sections in the lepton+jets channel in pp collisions at [Formula: see text] using the ATLAS detector.

PubMed

Aad, G; Abbott, B; Abdallah, J; Abdinov, O; Aben, R; Abolins, M; AbouZeid, O S; Abramowicz, H; Abreu, H; Abreu, R; Abulaiti, Y; Acharya, B S; Adamczyk, L; Adams, D L; Adelman, J; Adomeit, S; Adye, T; Affolder, A A; Agatonovic-Jovin, T; Agricola, J; Aguilar-Saavedra, J A; Ahlen, S P; Ahmadov, F; Aielli, G; Akerstedt, H; Åkesson, T P A; Akimov, A V; Alberghi, G L; Albert, J; Albrand, S; Alconada Verzini, M J; Aleksa, M; Aleksandrov, I N; Alexa, C; Alexander, G; Alexopoulos, T; Alhroob, M; Alimonti, G; Alio, L; Alison, J; Alkire, S P; Allbrooke, B M M; Allport, P P; Aloisio, A; Alonso, A; Alonso, F; Alpigiani, C; Altheimer, A; Alvarez Gonzalez, B; Álvarez Piqueras, D; Alviggi, M G; Amadio, B T; Amako, K; Amaral Coutinho, Y; Amelung, C; Amidei, D; Amor Dos Santos, S P; Amorim, A; Amoroso, S; Amram, N; Amundsen, G; Anastopoulos, C; Ancu, L S; Andari, N; Andeen, T; Anders, C F; Anders, G; Anders, J K; Anderson, K J; Andreazza, A; Andrei, V; Angelidakis, S; Angelozzi, I; Anger, P; Angerami, A; Anghinolfi, F; Anisenkov, A V; Anjos, N; Annovi, A; Antonelli, M; Antonov, A; Antos, J; Anulli, F; Aoki, M; Aperio Bella, L; Arabidze, G; Arai, Y; Araque, J P; Arce, A T H; Arduh, F A; Arguin, J-F; Argyropoulos, S; Arik, M; Armbruster, A J; Arnaez, O; Arnold, H; Arratia, M; Arslan, O; Artamonov, A; Artoni, G; Artz, S; Asai, S; Asbah, N; Ashkenazi, A; Åsman, B; Asquith, L; Assamagan, K; Astalos, R; Atkinson, M; Atlay, N B; Augsten, K; Aurousseau, M; Avolio, G; Axen, B; Ayoub, M K; Azuelos, G; Baak, M A; Baas, A E; Baca, M J; Bacci, C; Bachacou, H; Bachas, K; Backes, M; Backhaus, M; Bagiacchi, P; Bagnaia, P; Bai, Y; Bain, T; Baines, J T; Baker, O K; Baldin, E M; Balek, P; Balestri, T; Balli, F; Balunas, W K; Banas, E; Banerjee, Sw; Bannoura, A A E; Barak, L; Barberio, E L; Barberis, D; Barbero, M; Barillari, T; Barisonzi, M; Barklow, T; Barlow, N; Barnes, S L; Barnett, B M; Barnett, R M; Barnovska, Z; Baroncelli, A; Barone, G; Barr, A J; Barreiro, F; Barreiro Guimarães da Costa, J; Bartoldus, R; Barton, A E; Bartos, P; Basalaev, A; Bassalat, A; Basye, A; Bates, R L; Batista, S J; Batley, J R; Battaglia, M; Bauce, M; Bauer, F; Bawa, H S; Beacham, J B; Beattie, M D; Beau, T; Beauchemin, P H; Beccherle, R; Bechtle, P; Beck, H P; Becker, K; Becker, M; Beckingham, M; Becot, C; Beddall, A J; Beddall, A; Bednyakov, V A; Bee, C P; Beemster, L J; Beermann, T A; Begel, M; Behr, J K; Belanger-Champagne, C; Bell, W H; Bella, G; Bellagamba, L; Bellerive, A; Bellomo, M; Belotskiy, K; Beltramello, O; Benary, O; Benchekroun, D; Bender, M; Bendtz, K; Benekos, N; Benhammou, Y; Benhar Noccioli, E; Benitez Garcia, J A; Benjamin, D P; Bensinger, J R; Bentvelsen, S; Beresford, L; Beretta, M; Berge, D; Bergeaas Kuutmann, E; Berger, N; Berghaus, F; Beringer, J; Bernard, C; Bernard, N R; Bernius, C; Bernlochner, F U; Berry, T; Berta, P; Bertella, C; Bertoli, G; Bertolucci, F; Bertsche, C; Bertsche, D; Besana, M I; Besjes, G J; Bessidskaia Bylund, O; Bessner, M; Besson, N; Betancourt, C; Bethke, S; Bevan, A J; Bhimji, W; Bianchi, R M; Bianchini, L; Bianco, M; Biebel, O; Biedermann, D; Biesuz, N V; Biglietti, M; Bilbao De Mendizabal, J; Bilokon, H; Bindi, M; Binet, S; Bingul, A; Bini, C; Biondi, S; Bjergaard, D M; Black, C W; Black, J E; Black, K M; Blackburn, D; Blair, R E; Blanchard, J-B; Blanco, J E; Blazek, T; Bloch, I; Blocker, C; Blum, W; Blumenschein, U; Blunier, S; Bobbink, G J; Bobrovnikov, V S; Bocchetta, S S; Bocci, A; Bock, C; Boehler, M; Bogaerts, J A; Bogavac, D; Bogdanchikov, A G; Bohm, C; Boisvert, V; Bold, T; Boldea, V; Boldyrev, A S; Bomben, M; Bona, M; Boonekamp, M; Borisov, A; Borissov, G; Borroni, S; Bortfeldt, J; Bortolotto, V; Bos, K; Boscherini, D; Bosman, M; Boudreau, J; Bouffard, J; Bouhova-Thacker, E V; Boumediene, D; Bourdarios, C; Bousson, N; Boutle, S K; Boveia, A; Boyd, J; Boyko, I R; Bozic, I; Bracinik, J; Brandt, A; Brandt, G; Brandt, O; Bratzler, U; Brau, B; Brau, J E; Braun, H M; Breaden Madden, W D; Brendlinger, K; Brennan, A J; Brenner, L; Brenner, R; Bressler, S; Bristow, T M; Britton, D; Britzger, D; Brochu, F M; Brock, I; Brock, R; Bronner, J; Brooijmans, G; Brooks, T; Brooks, W K; Brosamer, J; Brost, E; Bruckman de Renstrom, P A; Bruncko, D; Bruneliere, R; Bruni, A; Bruni, G; Bruschi, M; Bruscino, N; Bryngemark, L; Buanes, T; Buat, Q; Buchholz, P; Buckley, A G; Budagov, I A; Buehrer, F; Bugge, L; Bugge, M K; Bulekov, O; Bullock, D; Burckhart, H; Burdin, S; Burgard, C D; Burghgrave, B; Burke, S; Burmeister, I; Busato, E; Büscher, D; Büscher, V; Bussey, P; Butler, J M; Butt, A I; Buttar, C M; Butterworth, J M; Butti, P; Buttinger, W; Buzatu, A; Buzykaev, A R; Urbán, S Cabrera; Caforio, D; Cairo, V M; Cakir, O; Calace, N; Calafiura, P; Calandri, A; Calderini, G; Calfayan, P; Caloba, L P; Calvet, D; Calvet, S; Camacho Toro, R; Camarda, S; Camarri, P; Cameron, D; Caminal Armadans, R; Campana, S; Campanelli, M; Campoverde, A; Canale, V; Canepa, A; Cano Bret, M; Cantero, J; Cantrill, R; Cao, T; Capeans Garrido, M D M; Caprini, I; Caprini, M; Capua, M; Caputo, R; Carbone, R M; Cardarelli, R; Cardillo, F; Carli, T; Carlino, G; Carminati, L; Caron, S; Carquin, E; Carrillo-Montoya, G D; Carter, J R; Carvalho, J; Casadei, D; Casado, M P; Casolino, M; Casper, D W; Castaneda-Miranda, E; Castelli, A; Gimenez, V Castillo; Castro, N F; Catastini, P; Catinaccio, A; Catmore, J R; Cattai, A; Caudron, J; Cavaliere, V; Cavalli, D; Cavalli-Sforza, M; Cavasinni, V; Ceradini, F; Alberich, L Cerda; Cerio, B C; Cerny, K; Cerqueira, A S; Cerri, A; Cerrito, L; Cerutti, F; Cerv, M; Cervelli, A; Cetin, S A; Chafaq, A; Chakraborty, D; Chalupkova, I; Chan, Y L; Chang, P; Chapman, J D; Charlton, D G; Chau, C C; Chavez Barajas, C A; Cheatham, S; Chegwidden, A; Chekanov, S; Chekulaev, S V; Chelkov, G A; Chelstowska, M A; Chen, C; Chen, H; Chen, K; Chen, L; Chen, S; Chen, S; Chen, X; Chen, Y; Cheng, H C; Cheng, Y; Cheplakov, A; Cheremushkina, E; Cherkaoui El Moursli, R; Chernyatin, V; Cheu, E; Chevalier, L; Chiarella, V; Chiarelli, G; Chiodini, G; Chisholm, A S; 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2016-01-01

Measurements of normalized differential cross-sections of top-quark pair production are presented as a function of the top-quark, [Formula: see text] system and event-level kinematic observables in proton-proton collisions at a centre-of-mass energy of [Formula: see text]. The observables have been chosen to emphasize the [Formula: see text] production process and to be sensitive to effects of initial- and final-state radiation, to the different parton distribution functions, and to non-resonant processes and higher-order corrections. The dataset corresponds to an integrated luminosity of 20.3 fb[Formula: see text], recorded in 2012 with the ATLAS detector at the CERN Large Hadron Collider. Events are selected in the lepton+jets channel, requiring exactly one charged lepton and at least four jets with at least two of the jets tagged as originating from a  b -quark. The measured spectra are corrected for detector effects and are compared to several Monte Carlo simulations. The results are in fair agreement with the predictions over a wide kinematic range. Nevertheless, most generators predict a harder top-quark transverse momentum distribution at high values than what is observed in the data. Predictions beyond NLO accuracy improve the agreement with data at high top-quark transverse momenta. Using the current settings and parton distribution functions, the rapidity distributions are not well modelled by any generator under consideration. However, the level of agreement is improved when more recent sets of parton distribution functions are used.

Leads Detection Using Mixture Statistical Distribution Based CRF Algorithm from Sentinel-1 Dual Polarization SAR Imagery

NASA Astrophysics Data System (ADS)

Zhang, Yu; Li, Fei; Zhang, Shengkai; Zhu, Tingting

2017-04-01

Synthetic Aperture Radar (SAR) is significantly important for polar remote sensing since it can provide continuous observations in all days and all weather. SAR can be used for extracting the surface roughness information characterized by the variance of dielectric properties and different polarization channels, which make it possible to observe different ice types and surface structure for deformation analysis. In November, 2016, Chinese National Antarctic Research Expedition (CHINARE) 33rd cruise has set sails in sea ice zone in Antarctic. Accurate leads spatial distribution in sea ice zone for routine planning of ship navigation is essential. In this study, the semantic relationship between leads and sea ice categories has been described by the Conditional Random Fields (CRF) model, and leads characteristics have been modeled by statistical distributions in SAR imagery. In the proposed algorithm, a mixture statistical distribution based CRF is developed by considering the contexture information and the statistical characteristics of sea ice for improving leads detection in Sentinel-1A dual polarization SAR imagery. The unary potential and pairwise potential in CRF model is constructed by integrating the posteriori probability estimated from statistical distributions. For mixture statistical distribution parameter estimation, Method of Logarithmic Cumulants (MoLC) is exploited for single statistical distribution parameters estimation. The iteration based Expectation Maximal (EM) algorithm is investigated to calculate the parameters in mixture statistical distribution based CRF model. In the posteriori probability inference, graph-cut energy minimization method is adopted in the initial leads detection. The post-processing procedures including aspect ratio constrain and spatial smoothing approaches are utilized to improve the visual result. The proposed method is validated on Sentinel-1A SAR C-band Extra Wide Swath (EW) Ground Range Detected (GRD) imagery with a pixel spacing of 40 meters near Prydz Bay area, East Antarctica. Main work is listed as follows: 1) A mixture statistical distribution based CRF algorithm has been developed for leads detection from Sentinel-1A dual polarization images. 2) The assessment of the proposed mixture statistical distribution based CRF method and single distribution based CRF algorithm has been presented. 3) The preferable parameters sets including statistical distributions, the aspect ratio threshold and spatial smoothing window size have been provided. In the future, the proposed algorithm will be developed for the operational Sentinel series data sets processing due to its less time consuming cost and high accuracy in leads detection.

SEARCH Workshop on Large-Scale Atmosphere/Cryosphere Observations

NASA Technical Reports Server (NTRS)

2002-01-01

The purpose of the workshop held in Seattle during 27-29 November 2001 was to review existing land, sea ice, and atmospheric observations and the prospect for an Arctic System Reanalysis, through white papers, invited speakers, and panels. A major task for SEARCH was to determine how existing observation systems can be best used and enhanced to understand and anticipate the course of the ongoing changes in the Arctic. The primary workshop conclusion is that there is no cohesion among various Arctic disciplines and data types to form a complete observation set of Arctic change; a second workshop conclusion is that present data sets are vastly underutilized in understanding Arctic change; a third conclusion is that a distributed observing system must accommodate a wide range of spatial patterns of variability.

New features in the design code Tlie

NASA Astrophysics Data System (ADS)

van Zeijts, Johannes

1993-12-01

We present features recently installed in the arbitrary-order accelerator design code Tlie. The code uses the MAD input language, and implements programmable extensions modeled after the C language that make it a powerful tool in a wide range of applications: from basic beamline design to high precision-high order design and even control room applications. The basic quantities important in accelerator design are easily accessible from inside the control language. Entities like parameters in elements (strength, current), transfer maps (either in Taylor series or in Lie algebraic form), lines, and beams (either as sets of particles or as distributions) are among the type of variables available. These variables can be set, used as arguments in subroutines, or just typed out. The code is easily extensible with new datatypes.

Comparison of Chest Wall and Lymphatic Radiotherapy Techniques in Patients with Left Breast Carcinoma.

PubMed

Gültekin, Melis; Karabuğa, Mehmet; Yıldız, Ferah; Özyiğit, Gökhan; Cengiz, Mustafa; Zorlu, Faruk; Akyol, Fadıl; Gürkaynak, Murat

2014-04-01

The aim of this study was to find the most appropriate technique for postmastectomy chest wall (CW) and lymphatic irradiation. Partially wide tangent, 30/70 photon/electron mix, 20/80 photon/electron mix and CW and internal mammary en face electron field, were studied on computerized tomography (CT) scans of 10 left breast carcinoma patients and dosimetric calculations have been studied. Dose volume histograms (DVH) obtained from treatment planning system (TPS) were used for minimal, maximal and mean doses received by the clinical target volumes and critical structures. Partially wide tangent field resulted in the most homogeneous dose distribution for the CW and a significantly lower lung and heart doses compared with all other techniques. However, right breast dose was significantly higher for partially wide tangent technique than that each of the other techniques. Approximately 0.6-7.9% differences were found between thermoluminescent dosimeter (TLD) and treatment planning system (TPS). The daily surface doses calculating using Gafchromic® external beam therapy (EBT) dosimetry films were 161.8±2.7 cGy for the naked, 241.0±1.5 cGy when 0.5 cm bolus was used and 255.3±2.7 cGy when 1 cm bolus was used. As a result of this study, partially wide tangent field was found to be the most appropriate technique in terms of the dose distribution, treatment planning and set-up procedure. The main disadvantage of this technique was the higher dose to the contralateral breast comparing the other techniques.

Preventing Community-wide Transmission of Cryptosporidium: A Proactive Public Health Response to a Swimming Pool–Associated Outbreak — Auglaize County, Ohio, USA

PubMed Central

Cope, J.R.; Prosser, A.; Nowicki, S.; Roberts, M.W.; Scheer, D.; Anderson, C.; Longsworth, A.; Parsons, C.; Goldschmidt, D.; Johnston, S.; Bishop, H.; Xiao, L.; Hill, V.; Beach, M.; Hlavsa, M.C.

2015-01-01

Summary The incidence of recreational water–associated outbreaks in the United States has significantly increased, driven, at least in part, by outbreaks both caused by Cryptosporidium and associated with treated recreational water venues. Because of the parasite's extreme chlorine tolerance, transmission can occur even in well-maintained treated recreational water venues, (e.g., pools) and a focal cryptosporidiosis outbreak can evolve into a community-wide outbreak associated with multiple recreational water venues and settings (e.g., child care facilities). In August 2004 in Auglaize County, Ohio, multiple cryptosporidiosis cases were identified and anecdotally linked to Pool A. Within 5 days of the first case being reported, Pool A was hyperchlorinated to achieve 99.9% Cryptosporidium inactivition. A case-control study was launched to epidemiologically ascertain the outbreak source 11 days later. A total of 150 confirmed and probable cases were identified; the temporal distribution of illness onset was peaked, indicating a point-source exposure. Cryptosporidiosis was significantly associated with swimming in Pool A (matched odds ratio 121.7, 95% confidence interval 27.4–∞) but not with another venue or setting. The findings of this investigation suggest that proactive implementation of control measures, when increased Cryptosporidium transmission is detected but before an outbreak source is epidemiologically ascertained, might prevent a focal cryptosporidiosis outbreak from evolving into a community-wide outbreak. PMID:25907106

Estimating air chemical emissions from research activities using stack measurement data.

PubMed

Ballinger, Marcel Y; Duchsherer, Cheryl J; Woodruff, Rodger K; Larson, Timothy V

2013-03-01

Current methods of estimating air emissions from research and development (R&D) activities use a wide range of release fractions or emission factors with bases ranging from empirical to semi-empirical. Although considered conservative, the uncertainties and confidence levels of the existing methods have not been reported. Chemical emissions were estimated from sampling data taken from four research facilities over 10 years. The approach was to use a Monte Carlo technique to create distributions of annual emission estimates for target compounds detected in source test samples. Distributions were created for each year and building sampled for compounds with sufficient detection frequency to qualify for the analysis. The results using the Monte Carlo technique without applying a filter to remove negative emission values showed almost all distributions spanning zero, and 40% of the distributions having a negative mean. This indicates that emissions are so low as to be indistinguishable from building background. Application of a filter to allow only positive values in the distribution provided a more realistic value for emissions and increased the distribution mean by an average of 16%. Release fractions were calculated by dividing the emission estimates by a building chemical inventory quantity. Two variations were used for this quantity: chemical usage, and chemical usage plus one-half standing inventory. Filters were applied so that only release fraction values from zero to one were included in the resulting distributions. Release fractions had a wide range among chemicals and among data sets for different buildings and/or years for a given chemical. Regressions of release fractions to molecular weight and vapor pressure showed weak correlations. Similarly, regressions of mean emissions to chemical usage, chemical inventory, molecular weight, and vapor pressure also gave weak correlations. These results highlight the difficulties in estimating emissions from R&D facilities using chemical inventory data. Air emissions from research operations are difficult to estimate because of the changing nature of research processes and the small quantity and wide variety of chemicals used. Analysis of stack measurements taken over multiple facilities and a 10-year period using a Monte Carlo technique provided a method to quantify the low emissions and to estimate release fractions based on chemical inventories. The variation in release fractions did not correlate well with factors investigated, confirming the complexities in estimating R&D emissions.

Sediment unmixing using detrital geochronology

USGS Publications Warehouse

Sharman, Glenn R.; Johnstone, Samuel

2017-01-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the influence of environmental forcings (e.g., tectonism, climate) on the earth’s surface. Here we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First we summarize ‘top-down’ mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions (‘parents’) that characterize a derived sample or set of samples (‘daughters’). Second we propose the use of ‘bottom-up’ methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable mixtures over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

Sediment unmixing using detrital geochronology

NASA Astrophysics Data System (ADS)

Sharman, Glenn R.; Johnstone, Samuel A.

2017-11-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the effect of environmental forcing (e.g., tectonism, climate) on the Earth's surface. Here, we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First, we summarize 'top-down' mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions ('parents') that characterize a derived sample or set of samples ('daughters'). Second, we propose the use of 'bottom-up' methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable that is well mixed over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has the potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

Perceptions of a campus-wide condom distribution programme: An exploratory study

PubMed Central

Francis, Diane B; Noar, Seth M; Widman, Laura; Willoughby, Jessica Fitts; Sanchez, Diana M; Garrett, Kyla P

2016-01-01

Objective Condom distribution programmes are an important means of preventing sexually transmitted infections (STIs); yet little research has examined their perceived and actual impact on college campuses. Design Quantitative, cross-sectional study. Setting Large public university in the Southeastern USA. Method Approximately 2 months after a campus-wide condom distribution programme began, we utilised intercept surveys with 355 students (68% women; 43% racial/ethnic minorities) to examine their perceptions of the availability, accessibility and acceptability of condoms, and their perceptions and use of the newly installed condom dispensers. Results Students perceived condoms to be available and accessible on campus after implementation of the condom dispensers. Students had heard about the dispensers from other people (36%), through social media (18%) and the campus newspaper (15%). Most students (71%) had seen the dispensers. Almost one in four students (23%) had taken a condom from the dispensers; among those who were sexually active during the 2months that the dispensers were available, 33% had used them. More than one-third of students (37%) – and 53% of sexually active students – indicated intentions to use the dispensers in the next 6months. Multiple regression analysis controlling for age, gender and race revealed that prior condom use, attitudes about the dispensers and comfort with the dispensers were significant predictors of sexually active students’ intentions to use the dispensers (p<.001). Conclusion Overall, results indicate that over a short time period, this condom distribution programme was successful in reaching students and providing free condoms. Implications for implementing condom distribution programmes on college campuses as well as future directions for research are discussed. PMID:27917002

Equipment management user's handbook for property custodians

NASA Technical Reports Server (NTRS)

1993-01-01

The NASA Equipment Management User's Handbook for Property Custodians is issued as an instructional guide for personnel designated as property custodians and technical personnel involved in the acquisition, management, and use of NASA-owned equipment. This handbook provides general information and basic operational procedures for processing equipment transactions through the agency-wide NASA Equipment Management System (NEMS). Each NASA installation must prepare supplementary instructions for local requirements beyond the scope of NASA-wide policies and procedures contained herein, or as specified for local implementation in NHB 4200.1, 'NASA Equipment Management Manual.' NHB 4200.1 sets forth policy, uniform performance standards, and procedural guidance to NASA personnel for the acquisition, management, and use of NASA-owned equipment. This handbook is a controlled document, issued in loose-leaf form and revised by page changes. Additional copies for internal use may be obtained through normal distribution.

Complex Fluids and Hydraulic Fracturing.

PubMed

Barbati, Alexander C; Desroches, Jean; Robisson, Agathe; McKinley, Gareth H

2016-06-07

Nearly 70 years old, hydraulic fracturing is a core technique for stimulating hydrocarbon production in a majority of oil and gas reservoirs. Complex fluids are implemented in nearly every step of the fracturing process, most significantly to generate and sustain fractures and transport and distribute proppant particles during and following fluid injection. An extremely wide range of complex fluids are used: naturally occurring polysaccharide and synthetic polymer solutions, aqueous physical and chemical gels, organic gels, micellar surfactant solutions, emulsions, and foams. These fluids are loaded over a wide range of concentrations with particles of varying sizes and aspect ratios and are subjected to extreme mechanical and environmental conditions. We describe the settings of hydraulic fracturing (framed by geology), fracturing mechanics and physics, and the critical role that non-Newtonian fluid dynamics and complex fluids play in the hydraulic fracturing process.

Estimating error rates for firearm evidence identifications in forensic science

PubMed Central

Song, John; Vorburger, Theodore V.; Chu, Wei; Yen, James; Soons, Johannes A.; Ott, Daniel B.; Zhang, Nien Fan

2018-01-01

Estimating error rates for firearm evidence identification is a fundamental challenge in forensic science. This paper describes the recently developed congruent matching cells (CMC) method for image comparisons, its application to firearm evidence identification, and its usage and initial tests for error rate estimation. The CMC method divides compared topography images into correlation cells. Four identification parameters are defined for quantifying both the topography similarity of the correlated cell pairs and the pattern congruency of the registered cell locations. A declared match requires a significant number of CMCs, i.e., cell pairs that meet all similarity and congruency requirements. Initial testing on breech face impressions of a set of 40 cartridge cases fired with consecutively manufactured pistol slides showed wide separation between the distributions of CMC numbers observed for known matching and known non-matching image pairs. Another test on 95 cartridge cases from a different set of slides manufactured by the same process also yielded widely separated distributions. The test results were used to develop two statistical models for the probability mass function of CMC correlation scores. The models were applied to develop a framework for estimating cumulative false positive and false negative error rates and individual error rates of declared matches and non-matches for this population of breech face impressions. The prospect for applying the models to large populations and realistic case work is also discussed. The CMC method can provide a statistical foundation for estimating error rates in firearm evidence identifications, thus emulating methods used for forensic identification of DNA evidence. PMID:29331680

Cone of Darkness: Finding Blank-sky Positions for Multi-object Wide-field Observations

NASA Astrophysics Data System (ADS)

Lorente, N. P. F.

2014-05-01

We present the Cone of Darkness, an application to automatically configure blank-sky positions for a series of stacked, wide-field observations, such as those carried out by the SAMI instrument on the Anglo-Australian Telescope (AAT). The Sydney-AAO Multi-object Integral field spectrograph (SAMI) uses a plug-plate to mount its 13×61 core imaging fibre bundles (hexabundles) in the optical plane at the telescope's prime focus. To make the most efficient use of each plug-plate, several observing fields are typically stacked to produce a single plate. When choosing blank-sky positions for the observations it is most effective to select these such that one set of 26 holes gives valid sky positions for all fields on the plate. However, when carried out manually this selection process is tedious and includes a significant risk of error. The Cone of Darkness software aims to provide uniform blank-sky position coverage over the field of observation, within the limits set by the distribution of target positions and the chosen input catalogs. This will then facilitate the production of the best representative median sky spectrum for use in sky subtraction. The application, written in C++, is configurable, making it usable for a range of instruments. Given the plate characteristics and the positions of target holes, the software segments the unallocated space on the plate and determines the position which best fits the uniform distribution requirement. This position is checked, for each field, against the selected catalog using a TAP ADQL search. The process is then repeated until the desired number of sky positions is attained.

Estimating error rates for firearm evidence identifications in forensic science.

PubMed

Song, John; Vorburger, Theodore V; Chu, Wei; Yen, James; Soons, Johannes A; Ott, Daniel B; Zhang, Nien Fan

2018-03-01

Estimating error rates for firearm evidence identification is a fundamental challenge in forensic science. This paper describes the recently developed congruent matching cells (CMC) method for image comparisons, its application to firearm evidence identification, and its usage and initial tests for error rate estimation. The CMC method divides compared topography images into correlation cells. Four identification parameters are defined for quantifying both the topography similarity of the correlated cell pairs and the pattern congruency of the registered cell locations. A declared match requires a significant number of CMCs, i.e., cell pairs that meet all similarity and congruency requirements. Initial testing on breech face impressions of a set of 40 cartridge cases fired with consecutively manufactured pistol slides showed wide separation between the distributions of CMC numbers observed for known matching and known non-matching image pairs. Another test on 95 cartridge cases from a different set of slides manufactured by the same process also yielded widely separated distributions. The test results were used to develop two statistical models for the probability mass function of CMC correlation scores. The models were applied to develop a framework for estimating cumulative false positive and false negative error rates and individual error rates of declared matches and non-matches for this population of breech face impressions. The prospect for applying the models to large populations and realistic case work is also discussed. The CMC method can provide a statistical foundation for estimating error rates in firearm evidence identifications, thus emulating methods used for forensic identification of DNA evidence. Published by Elsevier B.V.

Learning and recognition of on-premise signs from weakly labeled street view images.

PubMed

Tsai, Tsung-Hung; Cheng, Wen-Huang; You, Chuang-Wen; Hu, Min-Chun; Tsui, Arvin Wen; Chi, Heng-Yu

2014-03-01

Camera-enabled mobile devices are commonly used as interaction platforms for linking the user's virtual and physical worlds in numerous research and commercial applications, such as serving an augmented reality interface for mobile information retrieval. The various application scenarios give rise to a key technique of daily life visual object recognition. On-premise signs (OPSs), a popular form of commercial advertising, are widely used in our living life. The OPSs often exhibit great visual diversity (e.g., appearing in arbitrary size), accompanied with complex environmental conditions (e.g., foreground and background clutter). Observing that such real-world characteristics are lacking in most of the existing image data sets, in this paper, we first proposed an OPS data set, namely OPS-62, in which totally 4649 OPS images of 62 different businesses are collected from Google's Street View. Further, for addressing the problem of real-world OPS learning and recognition, we developed a probabilistic framework based on the distributional clustering, in which we proposed to exploit the distributional information of each visual feature (the distribution of its associated OPS labels) as a reliable selection criterion for building discriminative OPS models. Experiments on the OPS-62 data set demonstrated the outperformance of our approach over the state-of-the-art probabilistic latent semantic analysis models for more accurate recognitions and less false alarms, with a significant 151.28% relative improvement in the average recognition rate. Meanwhile, our approach is simple, linear, and can be executed in a parallel fashion, making it practical and scalable for large-scale multimedia applications.

Restricted access Improved hydrogeophysical characterization and monitoring through parallel modeling and inversion of time-domain resistivity andinduced-polarization data

USGS Publications Warehouse

Johnson, Timothy C.; Versteeg, Roelof J.; Ward, Andy; Day-Lewis, Frederick D.; Revil, André

2010-01-01

Electrical geophysical methods have found wide use in the growing discipline of hydrogeophysics for characterizing the electrical properties of the subsurface and for monitoring subsurface processes in terms of the spatiotemporal changes in subsurface conductivity, chargeability, and source currents they govern. Presently, multichannel and multielectrode data collections systems can collect large data sets in relatively short periods of time. Practitioners, however, often are unable to fully utilize these large data sets and the information they contain because of standard desktop-computer processing limitations. These limitations can be addressed by utilizing the storage and processing capabilities of parallel computing environments. We have developed a parallel distributed-memory forward and inverse modeling algorithm for analyzing resistivity and time-domain induced polar-ization (IP) data. The primary components of the parallel computations include distributed computation of the pole solutions in forward mode, distributed storage and computation of the Jacobian matrix in inverse mode, and parallel execution of the inverse equation solver. We have tested the corresponding parallel code in three efforts: (1) resistivity characterization of the Hanford 300 Area Integrated Field Research Challenge site in Hanford, Washington, U.S.A., (2) resistivity characterization of a volcanic island in the southern Tyrrhenian Sea in Italy, and (3) resistivity and IP monitoring of biostimulation at a Superfund site in Brandywine, Maryland, U.S.A. Inverse analysis of each of these data sets would be limited or impossible in a standard serial computing environment, which underscores the need for parallel high-performance computing to fully utilize the potential of electrical geophysical methods in hydrogeophysical applications.

Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub.

PubMed

Suarez-Gonzalez, Adriana; Good, Sara V

2014-03-01

A vast quantity of empirical evidence suggests that insufficient quantity or quality of pollen may lead to a reduction in fruit set, in particular for self-incompatible species. This study uses an integrative approach that combines field research with marker gene analysis to understand the factors affecting reproductive success in a widely distributed self-incompatible species, Prunus virginiana (Rosaceae). Twelve patches of P. virginiana distributed within three populations that differed in degree of disturbance were examined. Two of the sites were small (7-35 km(2)) remnants of forest in an intensively used agricultural landscape, while the third was continuous (350 km(2)) and less disturbed. Field studies (natural and hand cross-pollinations) were combined with marker gene analyses (microsatellites and S-locus) in order to explore potential factors affecting pollen delivery and consequently reproductive success at landscape (between populations) and fine scales (within populations). Reductions in reproductive output were found in the two fragments compared with the continuous population, and suggest that pollen is an important factor limiting fruit production. Genetic analyses carried out in one of the fragments and in the continuous site suggest that even though S-allele diversity is high in both populations, the fragment exhibits an increase in biparental inbreeding and correlated paternity. The increase in biparental inbreeding in the fragment is potentially attributable to variation in the density of individuals and/or the spatial distribution of genotypes among populations, both of which could alter mating dynamics. By using a novel integrative approach, this study shows that even though P. virginiana is a widespread species, fragmented populations can experience significant reductions in fruit set and pollen limitation in the field. Deatiled examination of one fragmented population suggests that these linitations may be explained by an increase in biparental inbreeding, correlated paternity and fine-scale genetic structure. The consistency of the field and fine-scale genetic analyses, and the consistency of the results within patches and across years, suggest that these are important processes driving pollen limitation in the fragment.

Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub

PubMed Central

Suarez-Gonzalez, Adriana; Good, Sara V.

2014-01-01

Background and Aims A vast quantity of empirical evidence suggests that insufficient quantity or quality of pollen may lead to a reduction in fruit set, in particular for self-incompatible species. This study uses an integrative approach that combines field research with marker gene analysis to understand the factors affecting reproductive success in a widely distributed self-incompatible species, Prunus virginiana (Rosaceae). Methods Twelve patches of P. virginiana distributed within three populations that differed in degree of disturbance were examined. Two of the sites were small (7–35 km2) remnants of forest in an intensively used agricultural landscape, while the third was continuous (350 km2) and less disturbed. Field studies (natural and hand cross-pollinations) were combined with marker gene analyses (microsatellites and S-locus) in order to explore potential factors affecting pollen delivery and consequently reproductive success at landscape (between populations) and fine scales (within populations). Key Results Reductions in reproductive output were found in the two fragments compared with the continuous population, and suggest that pollen is an important factor limiting fruit production. Genetic analyses carried out in one of the fragments and in the continuous site suggest that even though S-allele diversity is high in both populations, the fragment exhibits an increase in biparental inbreeding and correlated paternity. The increase in biparental inbreeding in the fragment is potentially attributable to variation in the density of individuals and/or the spatial distribution of genotypes among populations, both of which could alter mating dynamics. Conclusions By using a novel integrative approach, this study shows that even though P. virginiana is a widespread species, fragmented populations can experience significant reductions in fruit set and pollen limitation in the field. Deatiled examination of one fragmented population suggests that these linitations may be explained by an increase in biparental inbreeding, correlated paternity and fine-scale genetic structure. The consistency of the field and fine-scale genetic analyses, and the consistency of the results within patches and across years, suggest that these are important processes driving pollen limitation in the fragment. PMID:24327534

Abundance and distribution of immature mosquitoes in urban rivers proximate to their larval habitats.

PubMed

Ma, Minghai; Huang, Minsheng; Leng, Peien

2016-11-01

Whether ecological restoration of polluted urban rivers would provide suitable breeding habitats for some mosquitoes was not clear yet. It was therefore important to determine how altered river conditions influence mosquito ecology. Monthly data on water quality and larval density were obtained to determine the effects of river systems on the distribution and abundance of immature mosquitoes in two coastal cities in Eastern China. In total, 5 species within two genera of mosquitoes were collected and identified in habitat with vegetation from three positive rivers. Culex pipiens pallens was the most abundant and widely distributed species. A new species (Culex fuscanus) was reported in certain districts. Physico-chemical parameters of river water were important, but not the only, set of influences on immature mosquito breeding. Aquatic vegetation could increase the likelihood of mosquito breeding while artificial aeration might prevent the approach of mosquitoes. Slow-moving water might be a new potential marginal habitat type for some Culex and Aedes albopictus. Variation of river system with ecological restoration might influence the abundance and distribution of immature mosquitoes. Copyright © 2016. Published by Elsevier B.V.

Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories

NASA Technical Reports Server (NTRS)

Elsila, Jamie E.; Aponte, Jose C.; Blackmond, Donna G.; Burton, Aaron S.; Dworkin, Jason P.; Glavin, Daniel P.

2016-01-01

The analysis of amino acids in meteorites dates back over 50 years; however, it is only in recent years that research has expanded beyond investigations of a narrow set of meteorite groups (exemplied by the Murchison meteorite) into meteorites of other types and classes. These new studies have shown a wide diversity in the abundance and distribution of amino acids across carbonaceous chondrite groups, highlighting the role of parent body processes and composition in the creation, preservation, or alteration of amino acids. Although most chiral amino acids are racemic in meteorites, the enantiomeric distribution of some amino acids, particularly of the nonprotein amino acid isovaline, has also been shown to vary both within certain meteorites and across carbonaceous meteorite groups. Large -enantiomeric excesses of some extraterrestrial protein amino acids (up to 60) have also been observed in rare cases and point to nonbiological enantiomeric enrichment processes prior to the emergence of life. In this Outlook, we review these recent meteoritic analyses, focusing on variations in abundance, structural distributions, and enantiomeric distributions of amino acids and discussing possible explanations for these observations and the potential for future work.

A diffuse radar scattering model from Martian surface rocks

NASA Technical Reports Server (NTRS)

Calvin, W. M.; Jakosky, B. M.; Christensen, P. R.

1987-01-01

Remote sensing of Mars has been done with a variety of instrumentation at various wavelengths. Many of these data sets can be reconciled with a surface model of bonded fines (or duricrust) which varies widely across the surface and a surface rock distribution which varies less so. A surface rock distribution map from -60 to +60 deg latitude has been generated by Christensen. Our objective is to model the diffuse component of radar reflection based on this surface distribution of rocks. The diffuse, rather than specular, scattering is modeled because the diffuse component arises due to scattering from rocks with sizes on the order of the wavelength of the radar beam. Scattering for radio waves of 12.5 cm is then indicative of the meter scale and smaller structure of the surface. The specular term is indicative of large scale surface undulations and should not be causally related to other surface physical properties. A simplified model of diffuse scattering is described along with two rock distribution models. The results of applying the models to a planet of uniform fractional rock coverage with values ranging from 5 to 20% are discussed.

Impacts of climate change on marine top predators: Advances and future challenges

NASA Astrophysics Data System (ADS)

Hobday, Alistair J.; Arrizabalaga, Haritz; Evans, Karen; Nicol, Simon; Young, Jock W.; Weng, Kevin C.

2015-03-01

Oceanic top predators are the subject of studies by researchers under the international Climate Impacts on Oceanic Top Predators (CLIOTOP) program. A wide range of data sets have shown that environmental conditions, such as temperature and marine productivity, affect the distribution and biological processes of these species, and thus the activities of the humans that depend on them. In this special issue, 25 papers arising from the 2nd CLIOTOP symposium, held in Noumea, New Caledonia in February 2013 report the importance of realistic physical descriptions of oceanic processes for climate change projections, demonstrate a wide range of predator responses to historical climate variability, describe new analytical approaches for understanding the physiology, behaviour and trophodynamics, and project future distributions for a range of species. Several contributions discuss the implications for conservation and fisheries and show that resolving ecosystem management challenges and conflicts in the face of climate change is possible, but will require attention by decision-makers to issues that are broader than their traditional mandate. In the coming years, an increased focus on the development of management options to reduce the impacts of climate change on top predators and their dependent industries is needed.

Hydrogeologic and geospatial data for the assesment of focused recharge to the Carbonate-Rock Aquifer in Genesee County, New York

USGS Publications Warehouse

Reddy, James E.; Kappel, William M.

2010-01-01

Existing hydrogeologic and geospatial data useful for the assessment of focused recharge to the carbonate-rock aquifer in the central part of Genesee County, NY, were compiled from numerous local, State, and Federal agency sources. Data sources utilized in this pilot study include available geospatial datasets from Federal and State agencies, interviews with local highway departments and the Genesee County Soil and Water Conservation District, and an initial assessment of karst features through the analysis of ortho-photographs, with minimal field verification. The compiled information is presented in a series of county-wide and quadrangle maps. The county-wide maps present generalized hydrogeologic conditions including distribution of geologic units, major faults, and karst features, and bedrock-surface and water-table configurations. Ten sets of quadrangle maps of the area that overlies the carbonate-rock aquifer present more detailed and additional information including distribution of bedrock outcrops, thin and (or) permeable soils, and karst features such as sinkholes and swallets. Water-resource managers can utilize the information summarized in this report as a guide to their assessment of focused recharge to, and the potential for surface contaminants to reach the carbonate-rock aquifer.

Usefulness of multiplex PCR methods and respiratory viruses’ distribution in children below 15 years old according to age, seasons and clinical units in France: A 3 years retrospective study

PubMed Central

Collin, Gilles; Ichou, Houria; Charpentier, Charlotte; Bendhafer, Samia; Dumitrescu, Madalina; Allal, Lahcene; Cojocaru, Bogdan; Desfrère, Luc; Descamps, Diane; Mandelbrot, Laurent; Houhou-Fidouh, Nadhira

2017-01-01

Background To date, only influenza and RSV testing are recommended for respiratory viruses’ detection in paediatric units. In this study, we described, according to seasons, ages and clinical units, the results obtained in children (<15 years old) by multiplex-PCR (mPCR) tests allowing a quick and wide range detection of all respiratory viruses. These results were also compared with RSV specific detection. Methods All nasopharyngeal mPCR and RSV tests requested by clinicians in our French teaching hospitals group between 2011 and 2014 were retrospectively included. All repeated samples for the same children in the same month were discarded. Results Of the 381 mPCR tests (344 children) performed, 51.4% were positive. Positivity and viral co-infection rates were higher in the 6–36 months old strata (81% and 25%, p<0.0001 and p = 0.04, respectively). Viral distribution showed strong variations across ages. During specific influenza epidemic periods, only 1/39 (2.5%) mPCR tests were positive for influenza and 19/39 (48.7%) for other viruses. During specific RSV epidemic periods, only 8/46 (17.4%) mPCR tests were positive for RSV and 14/46 (30.4%) for other viruses. 477/1529 (31.2%) of RSV immunochromatography-tests were positive. Among the negatives immunochromatography-test also explored by mPCR, 28/62 (31%) were positive for other respiratory viruses. Conclusion This study provides a wide description of respiratory viruses’ distribution among children in hospital settings using mPCR over 3 years. It emphasizes the number of undiagnosed respiratory viruses according to the current diagnosis practice in France and gives a better picture of respiratory viruses identified in hospital settings by mPCR all over the year in France. PMID:28235002

The effects of sampling bias and model complexity on the predictive performance of MaxEnt species distribution models.

PubMed

Syfert, Mindy M; Smith, Matthew J; Coomes, David A

2013-01-01

Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern presence data from New Zealand, we assessed whether (a) choosing to correct for geographical sampling bias and (b) using complex environmental response curves have strong effects on goodness of fit. SDMs were trained on tree fern data, obtained from an online biodiversity data portal, with two sources that differed in size and geographical sampling bias: a small, widely-distributed set of herbarium specimens and a large, spatially clustered set of ecological survey records. We attempted to correct for geographical sampling bias by incorporating sampling bias grids in the SDMs, created from all georeferenced vascular plants in the datasets, and explored model complexity issues by fitting a wide variety of environmental response curves (known as "feature types" in MaxEnt). In each case, goodness of fit was assessed by comparing predicted range maps with tree fern presences and absences using an independent national dataset to validate the SDMs. We found that correcting for geographical sampling bias led to major improvements in goodness of fit, but did not entirely resolve the problem: predictions made with clustered ecological data were inferior to those made with the herbarium dataset, even after sampling bias correction. We also found that the choice of feature type had negligible effects on predictive performance, indicating that simple feature types may be sufficient once sampling bias is accounted for. Our study emphasizes the importance of reducing geographical sampling bias, where possible, in datasets used to train SDMs, and the effectiveness and essentialness of sampling bias correction within MaxEnt.

FastSKAT: Sequence kernel association tests for very large sets of markers.

PubMed

Lumley, Thomas; Brody, Jennifer; Peloso, Gina; Morrison, Alanna; Rice, Kenneth

2018-06-22

The sequence kernel association test (SKAT) is widely used to test for associations between a phenotype and a set of genetic variants that are usually rare. Evaluating tail probabilities or quantiles of the null distribution for SKAT requires computing the eigenvalues of a matrix related to the genotype covariance between markers. Extracting the full set of eigenvalues of this matrix (an n×n matrix, for n subjects) has computational complexity proportional to n 3 . As SKAT is often used when n>104, this step becomes a major bottleneck in its use in practice. We therefore propose fastSKAT, a new computationally inexpensive but accurate approximations to the tail probabilities, in which the k largest eigenvalues of a weighted genotype covariance matrix or the largest singular values of a weighted genotype matrix are extracted, and a single term based on the Satterthwaite approximation is used for the remaining eigenvalues. While the method is not particularly sensitive to the choice of k, we also describe how to choose its value, and show how fastSKAT can automatically alert users to the rare cases where the choice may affect results. As well as providing faster implementation of SKAT, the new method also enables entirely new applications of SKAT that were not possible before; we give examples grouping variants by topologically associating domains, and comparing chromosome-wide association by class of histone marker. © 2018 WILEY PERIODICALS, INC.

Habitat suitability and ecological niche profile of major malaria vectors in Cameroon

PubMed Central

2009-01-01

Background Suitability of environmental conditions determines a species distribution in space and time. Understanding and modelling the ecological niche of mosquito disease vectors can, therefore, be a powerful predictor of the risk of exposure to the pathogens they transmit. In Africa, five anophelines are responsible for over 95% of total malaria transmission. However, detailed knowledge of the geographic distribution and ecological requirements of these species is to date still inadequate. Methods Indoor-resting mosquitoes were sampled from 386 villages covering the full range of ecological settings available in Cameroon, Central Africa. Using a predictive species distribution modeling approach based only on presence records, habitat suitability maps were constructed for the five major malaria vectors Anopheles gambiae, Anopheles funestus, Anopheles arabiensis, Anopheles nili and Anopheles moucheti. The influence of 17 climatic, topographic, and land use variables on mosquito geographic distribution was assessed by multivariate regression and ordination techniques. Results Twenty-four anopheline species were collected, of which 17 are known to transmit malaria in Africa. Ecological Niche Factor Analysis, Habitat Suitability modeling and Canonical Correspondence Analysis revealed marked differences among the five major malaria vector species, both in terms of ecological requirements and niche breadth. Eco-geographical variables (EGVs) related to human activity had the highest impact on habitat suitability for the five major malaria vectors, with areas of low population density being of marginal or unsuitable habitat quality. Sunlight exposure, rainfall, evapo-transpiration, relative humidity, and wind speed were among the most discriminative EGVs separating "forest" from "savanna" species. Conclusions The distribution of major malaria vectors in Cameroon is strongly affected by the impact of humans on the environment, with variables related to proximity to human settings being among the best predictors of habitat suitability. The ecologically more tolerant species An. gambiae and An. funestus were recorded in a wide range of eco-climatic settings. The other three major vectors, An. arabiensis, An. moucheti, and An. nili, were more specialized. Ecological niche and species distribution modelling should help improve malaria vector control interventions by targeting places and times where the impact on vector populations and disease transmission can be optimized. PMID:20028559

Habitat suitability and ecological niche profile of major malaria vectors in Cameroon.

PubMed

Ayala, Diego; Costantini, Carlo; Ose, Kenji; Kamdem, Guy C; Antonio-Nkondjio, Christophe; Agbor, Jean-Pierre; Awono-Ambene, Parfait; Fontenille, Didier; Simard, Frédéric

2009-12-23

Suitability of environmental conditions determines a species distribution in space and time. Understanding and modelling the ecological niche of mosquito disease vectors can, therefore, be a powerful predictor of the risk of exposure to the pathogens they transmit. In Africa, five anophelines are responsible for over 95% of total malaria transmission. However, detailed knowledge of the geographic distribution and ecological requirements of these species is to date still inadequate. Indoor-resting mosquitoes were sampled from 386 villages covering the full range of ecological settings available in Cameroon, Central Africa. Using a predictive species distribution modeling approach based only on presence records, habitat suitability maps were constructed for the five major malaria vectors Anopheles gambiae, Anopheles funestus, Anopheles arabiensis, Anopheles nili and Anopheles moucheti. The influence of 17 climatic, topographic, and land use variables on mosquito geographic distribution was assessed by multivariate regression and ordination techniques. Twenty-four anopheline species were collected, of which 17 are known to transmit malaria in Africa. Ecological Niche Factor Analysis, Habitat Suitability modeling and Canonical Correspondence Analysis revealed marked differences among the five major malaria vector species, both in terms of ecological requirements and niche breadth. Eco-geographical variables (EGVs) related to human activity had the highest impact on habitat suitability for the five major malaria vectors, with areas of low population density being of marginal or unsuitable habitat quality. Sunlight exposure, rainfall, evapo-transpiration, relative humidity, and wind speed were among the most discriminative EGVs separating "forest" from "savanna" species. The distribution of major malaria vectors in Cameroon is strongly affected by the impact of humans on the environment, with variables related to proximity to human settings being among the best predictors of habitat suitability. The ecologically more tolerant species An. gambiae and An. funestus were recorded in a wide range of eco-climatic settings. The other three major vectors, An. arabiensis, An. moucheti, and An. nili, were more specialized. Ecological niche and species distribution modelling should help improve malaria vector control interventions by targeting places and times where the impact on vector populations and disease transmission can be optimized.

On the deterministic and stochastic use of hydrologic models

USGS Publications Warehouse

Farmer, William H.; Vogel, Richard M.

2016-01-01

Environmental simulation models, such as precipitation-runoff watershed models, are increasingly used in a deterministic manner for environmental and water resources design, planning, and management. In operational hydrology, simulated responses are now routinely used to plan, design, and manage a very wide class of water resource systems. However, all such models are calibrated to existing data sets and retain some residual error. This residual, typically unknown in practice, is often ignored, implicitly trusting simulated responses as if they are deterministic quantities. In general, ignoring the residuals will result in simulated responses with distributional properties that do not mimic those of the observed responses. This discrepancy has major implications for the operational use of environmental simulation models as is shown here. Both a simple linear model and a distributed-parameter precipitation-runoff model are used to document the expected bias in the distributional properties of simulated responses when the residuals are ignored. The systematic reintroduction of residuals into simulated responses in a manner that produces stochastic output is shown to improve the distributional properties of the simulated responses. Every effort should be made to understand the distributional behavior of simulation residuals and to use environmental simulation models in a stochastic manner.

A Monte-Carlo Analysis of Organic Aerosol Volatility with Aerosol Microphysics

NASA Astrophysics Data System (ADS)

Gao, C. Y.; Tsigaridis, K.; Bauer, S. E.

2016-12-01

A newly developed box model scheme, MATRIX-VBS, includes the volatility-basis set (VBS) framework in an aerosol microphysical scheme MATRIX (Multiconfiguration Aerosol TRacker of mIXing state), which resolves aerosol mass and number concentrations and aerosol mixing state. The new scheme advanced the representation of organic aerosols in Earth system models by improving the traditional and simplistic treatment of organic aerosols as non-volatile and with a fixed size distribution. Further development includes adding the condensation of organics on coarse mode aerosols - dust and sea salt, thus making all organics in the system semi-volatile. To test and simplify the model, a Monte-Carlo analysis is performed to pin point which processes affect organics the most under which chemical and meteorological conditions. Since the model's parameterizations have the ability to capture a very wide range of conditions, from very clean to very polluted and for a wide range of meteorological conditions, all possible scenarios on Earth across the whole parameter space, including temperature, location, emissions and oxidant levels, are examined. The Monte-Carlo simulations provide quantitative information on the sensitivity of the newly developed model and help us understand how organics are affecting the size distribution, mixing state and volatility distribution at varying levels of meteorological conditions and pollution levels. In addition, these simulations give information on which parameters play a critical role in the aerosol distribution and evolution in the atmosphere and which do not, that will facilitate the simplification of the box model, an important step in its implementation in the global model.

Global EOS: exploring the 300-ms-latency region

NASA Astrophysics Data System (ADS)

Mascetti, L.; Jericho, D.; Hsu, C.-Y.

2017-10-01

EOS, the CERN open-source distributed disk storage system, provides the highperformance storage solution for HEP analysis and the back-end for various work-flows. Recently EOS became the back-end of CERNBox, the cloud synchronisation service for CERN users. EOS can be used to take advantage of wide-area distributed installations: for the last few years CERN EOS uses a common deployment across two computer centres (Geneva-Meyrin and Budapest-Wigner) about 1,000 km apart (∼20-ms latency) with about 200 PB of disk (JBOD). In late 2015, the CERN-IT Storage group and AARNET (Australia) set-up a challenging R&D project: a single EOS instance between CERN and AARNET with more than 300ms latency (16,500 km apart). This paper will report about the success in deploy and run a distributed storage system between Europe (Geneva, Budapest), Australia (Melbourne) and later in Asia (ASGC Taipei), allowing different type of data placement and data access across these four sites.

Gyrokinetic water-bag modeling of a plasma column: Magnetic moment distribution and finite Larmor radius effects

NASA Astrophysics Data System (ADS)

Klein, R.; Gravier, E.; Morel, P.; Besse, N.; Bertrand, P.

2009-08-01

Describing turbulent transport in fusion plasmas is a major concern in magnetic confinement fusion. It is now widely known that kinetic and fluid descriptions can lead to significantly different properties. Although more accurate, the kinetic calculation of turbulent transport is much more demanding of computer resources than fluid simulations. An alternative approach is based on a water-bag representation of the distribution function that is not an approximation but rather a special class of initial conditions, allowing one to reduce the full kinetic Vlasov equation into a set of hydrodynamics equations while keeping its kinetic character [P. Morel, E. Gravier, N. Besse et al., Phys. Plasmas 14, 112109 (2007)]. In this paper, the water-bag concept is used in a gyrokinetic context to study finite Larmor radius effects with the possibility of using the full Larmor radius distribution instead of an averaged Larmor radius. The resulting model is used to study the ion temperature gradient (ITG) instability.

The molecular spectrum and distribution of haemoglobinopathies in Cyprus: a 20-year retrospective study

PubMed Central

Kountouris, Petros; Kousiappa, Ioanna; Papasavva, Thessalia; Christopoulos, George; Pavlou, Eleni; Petrou, Miranda; Feleki, Xenia; Karitzie, Eleni; Phylactides, Marios; Fanis, Pavlos; Lederer, Carsten W.; Kyrri, Andreani R.; Kalogerou, Eleni; Makariou, Christiana; Ioannou, Christiana; Kythreotis, Loukas; Hadjilambi, Georgia; Andreou, Nicoletta; Pangalou, Evangelia; Savvidou, Irene; Angastiniotis, Michael; Hadjigavriel, Michael; Sitarou, Maria; Kolnagou, Annita; Kleanthous, Marina; Christou, Soteroula

2016-01-01

Haemoglobinopathies are the most common monogenic diseases, posing a major public health challenge worldwide. Cyprus has one the highest prevalences of thalassaemia in the world and has been the first country to introduce a successful population-wide prevention programme, based on premarital screening. In this study, we report the most significant and comprehensive update on the status of haemoglobinopathies in Cyprus for at least two decades. First, we identified and analysed all known 592 β-thalassaemia patients and 595 Hb H disease patients in Cyprus. Moreover, we report the molecular spectrum of α-, β- and δ-globin gene mutations in the population and their geographic distribution, using a set of 13824 carriers genotyped from 1995 to 2015, and estimate relative allele frequencies in carriers of β- and δ-globin gene mutations. Notably, several mutations are reported for the first time in the Cypriot population, whereas important differences are observed in the distribution of mutations across different districts of the island. PMID:27199182

The Diesel Combustion Collaboratory: Combustion Researchers Collaborating over the Internet

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

C. M. Pancerella; L. A. Rahn; C. Yang

2000-02-01

The Diesel Combustion Collaborator (DCC) is a pilot project to develop and deploy collaborative technologies to combustion researchers distributed throughout the DOE national laboratories, academia, and industry. The result is a problem-solving environment for combustion research. Researchers collaborate over the Internet using DCC tools, which include: a distributed execution management system for running combustion models on widely distributed computers, including supercomputers; web-accessible data archiving capabilities for sharing graphical experimental or modeling data; electronic notebooks and shared workspaces for facilitating collaboration; visualization of combustion data; and video-conferencing and data-conferencing among researchers at remote sites. Security is a key aspect of themore » collaborative tools. In many cases, the authors have integrated these tools to allow data, including large combustion data sets, to flow seamlessly, for example, from modeling tools to data archives. In this paper the authors describe the work of a larger collaborative effort to design, implement and deploy the DCC.« less

An educational distributed Cosmic Ray detector network based on ArduSiPM

NASA Astrophysics Data System (ADS)

Bocci, V.; Chiodi, G.; Fresch, P.; Iacoangeli, F.; Recchia, L.

2017-10-01

The advent of high performance microcontrollers equipped with analog and digital peripherals, makes the design of a complete particle detector and a relative acquisition system on a single microcontroller chip possible. The existence of a world wide data infrastructure such as the internet, allows for the conception of a distributed network of cheap detectors able to elaborate and send data as well as to respond to setting commands. The internet infrastructure enables the distribution of the absolute time, with precision of a few milliseconds, to all devices independently of their physical location, when the sky view is accessible it possible to use a GPS module to reach synchronization of tens of nanoseconds. These devices can be far apart from each other and their relative distance can range from a few meters to thousands of kilometers. This allows for the design of a crowdsourcing experiment of citizen science, based on the use of many small scintillation-based particle detectors to monitor the high energetic cosmic ray and the radiation environment.

Jet Topics: Disentangling Quarks and Gluons at Colliders

NASA Astrophysics Data System (ADS)

Metodiev, Eric M.; Thaler, Jesse

2018-06-01

We introduce jet topics: a framework to identify underlying classes of jets from collider data. Because of a close mathematical relationship between distributions of observables in jets and emergent themes in sets of documents, we can apply recent techniques in "topic modeling" to extract jet topics from the data with minimal or no input from simulation or theory. As a proof of concept with parton shower samples, we apply jet topics to determine separate quark and gluon jet distributions for constituent multiplicity. We also determine separate quark and gluon rapidity spectra from a mixed Z -plus-jet sample. While jet topics are defined directly from hadron-level multidifferential cross sections, one can also predict jet topics from first-principles theoretical calculations, with potential implications for how to define quark and gluon jets beyond leading-logarithmic accuracy. These investigations suggest that jet topics will be useful for extracting underlying jet distributions and fractions in a wide range of contexts at the Large Hadron Collider.

Simultaneous small- and wide-angle scattering at high X-ray energies.

PubMed

Daniels, J E; Pontoni, D; Hoo, Rui Ping; Honkimäki, V

2010-07-01

Combined small- and wide-angle X-ray scattering (SAXS/WAXS) is a powerful technique for the study of materials at length scales ranging from atomic/molecular sizes (a few angstroms) to the mesoscopic regime ( approximately 1 nm to approximately 1 microm). A set-up to apply this technique at high X-ray energies (E > 50 keV) has been developed. Hard X-rays permit the execution of at least three classes of investigations that are significantly more difficult to perform at standard X-ray energies (8-20 keV): (i) in situ strain analysis revealing anisotropic strain behaviour both at the atomic (WAXS) as well as at the mesoscopic (SAXS) length scales, (ii) acquisition of WAXS patterns to very large q (>20 A(-1)) thus allowing atomic pair distribution function analysis (SAXS/PDF) of micro- and nano-structured materials, and (iii) utilization of complex sample environments involving thick X-ray windows and/or samples that can be penetrated only by high-energy X-rays. Using the reported set-up a time resolution of approximately two seconds was demonstrated. It is planned to further improve this time resolution in the near future.

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML)

PubMed Central

Lechevalier, D.; Ak, R.; Ferguson, M.; Law, K. H.; Lee, Y.-T. T.; Rachuri, S.

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain. PMID:29202125

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML).

PubMed

Park, J; Lechevalier, D; Ak, R; Ferguson, M; Law, K H; Lee, Y-T T; Rachuri, S

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain.

SPOTting model parameters using a ready-made Python package

NASA Astrophysics Data System (ADS)

Houska, Tobias; Kraft, Philipp; Breuer, Lutz

2015-04-01

The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for optimization methods. Here we see simple algorithms like the MCMC struggling to find the global optimum of the function, while algorithms like SCE-UA and DE-MCZ show their strengths. Thirdly, we apply an uncertainty analysis of a one-dimensional physically based hydrological model build with the Catchment Modelling Framework (CMF). The model is driven by meteorological and groundwater data from a Free Air Carbon Enrichment (FACE) experiment in Linden (Hesse, Germany). Simulation results are evaluated with measured soil moisture data. We search for optimal parameter sets of the van Genuchten-Mualem function and find different equally optimal solutions with some of the algorithms. The case studies reveal that the implemented SPOT methods work sufficiently well. They further show the benefit of having one tool at hand that includes a number of parameter search methods, likelihood functions and a priori parameter distributions within one platform independent package.

Digital rights management for digital cinema

NASA Astrophysics Data System (ADS)

Kirovski, Darko; Peinado, Marcus; Petitcolas, Fabien A. P.

2001-12-01

There is a wide consensus among the feature film production studios that the Internet era brings a new paradigm for film distribution to cinemas worldwide. The benefits of digital cinema to both producers and cinemas are numerous: significantly lower distribution and maintenance costs, immediate access to film libraries, higher presentation quality, and strong potential for developing new business models. Despite these advantages, the studios are still reluctant to jump into the digital age. The main showstopper for digital cinema is the danger of widespread piracy. Piracy already costs Hollywood an estimated two billion dollars annually and digital cinema without proper copyright enforcement could increase this number. In this paper, we present a copyright management system that aims at providing the set of necessary security tools: standard cryptographic primitives and copyright protection mechanisms that enable a reliable and secure feature film delivery system.

Additional Security Considerations for Grid Management

NASA Technical Reports Server (NTRS)

Eidson, Thomas M.

2003-01-01

The use of Grid computing environments is growing in popularity. A Grid computing environment is primarily a wide area network that encompasses multiple local area networks, where some of the local area networks are managed by different organizations. A Grid computing environment also includes common interfaces for distributed computing software so that the heterogeneous set of machines that make up the Grid can be used more easily. The other key feature of a Grid is that the distributed computing software includes appropriate security technology. The focus of most Grid software is on the security involved with application execution, file transfers, and other remote computing procedures. However, there are other important security issues related to the management of a Grid and the users who use that Grid. This note discusses these additional security issues and makes several suggestions as how they can be managed.

An atlas of ultraviolet spectra of star-forming galaxies

NASA Technical Reports Server (NTRS)

Kinney, A. L.; Bohlin, R. C.; Calzetti, D.; Panagia, N.; Wyse, Rosemary F. G.

1993-01-01

A systematic study is presented of the UV spectra of star-forming galaxies of different morphological type and activity class using a sample drawn from a uniformly reduced IUE data set. The spectra for a wide variety of galaxies, including normal spiral, LINER, starburst, blue compact, blue compact dwarf, and Seyfert 2 galaxies, are presented in the form of spectral energy distributions to demonstrate the overall characteristics according to morphology and activity class and in the form of absolute flux distributions to better show the absorption and emission features of individual objects. The data support the picture based on UV spectra of the Orbiting Astronomical Observatory and of the Astronautical Netherlands Satellite that spiral galaxies of later Hubble class have more flux at the shortest UV wavelengths than do spiral galaxies of earlier Hubble class.

A Methodology to Seperate and Analyze a Seismic Wide Angle Profile

NASA Astrophysics Data System (ADS)

Weinzierl, Wolfgang; Kopp, Heidrun

2010-05-01

General solutions of inverse problems can often be obtained through the introduction of probability distributions to sample the model space. We present a simple approach of defining an a priori space in a tomographic study and retrieve the velocity-depth posterior distribution by a Monte Carlo method. Utilizing a fitting routine designed for very low statistics to setup and analyze the obtained tomography results, it is possible to statistically separate the velocity-depth model space derived from the inversion of seismic refraction data. An example of a profile acquired in the Lesser Antilles subduction zone reveals the effectiveness of this approach. The resolution analysis of the structural heterogeneity includes a divergence analysis which proves to be capable of dissecting long wide-angle profiles for deep crust and upper mantle studies. The complete information of any parameterised physical system is contained in the a posteriori distribution. Methods for analyzing and displaying key properties of the a posteriori distributions of highly nonlinear inverse problems are therefore essential in the scope of any interpretation. From this study we infer several conclusions concerning the interpretation of the tomographic approach. By calculating a global as well as singular misfits of velocities we are able to map different geological units along a profile. Comparing velocity distributions with the result of a tomographic inversion along the profile we can mimic the subsurface structures in their extent and composition. The possibility of gaining a priori information for seismic refraction analysis by a simple solution to an inverse problem and subsequent resolution of structural heterogeneities through a divergence analysis is a new and simple way of defining a priori space and estimating the a posteriori mean and covariance in singular and general form. The major advantage of a Monte Carlo based approach in our case study is the obtained knowledge of velocity depth distributions. Certainly the decision of where to extract velocity information on the profile for setting up a Monte Carlo ensemble is limiting the a priori space. However, the general conclusion of analyzing the velocity field according to distinct reference distributions gives us the possibility to define the covariance according to any geological unit if we have a priori information on the velocity depth distributions. Using the wide angle data recorded across the Lesser Antilles arc, we are able to resolve a shallow feature like the backstop by a robust and simple divergence analysis. We demonstrate the effectiveness of the new methodology to extract some key features and properties from the inversion results by including information concerning the confidence level of results.

Frequency-Locked Detector Threshold Setting Criteria Based on Mean-Time-To-Lose-Lock (MTLL) for GPS Receivers

PubMed Central

Zhao, Na; Qin, Honglei; Sun, Kewen; Ji, Yuanfa

2017-01-01

Frequency-locked detector (FLD) has been widely utilized in tracking loops of Global Positioning System (GPS) receivers to indicate their locking status. The relation between FLD and lock status has been seldom discussed. The traditional PLL experience is not suitable for FLL. In this paper, the threshold setting criteria for frequency-locked detector in the GPS receiver has been proposed by analyzing statistical characteristic of FLD output. The approximate probability distribution of frequency-locked detector is theoretically derived by using a statistical approach, which reveals the relationship between probabilities of frequency-locked detector and the carrier-to-noise ratio (C/N0) of the received GPS signal. The relationship among mean-time-to-lose-lock (MTLL), detection threshold and lock probability related to C/N0 can be further discovered by utilizing this probability. Therefore, a theoretical basis for threshold setting criteria in frequency locked loops for GPS receivers is provided based on mean-time-to-lose-lock analysis. PMID:29207546

Frequency-Locked Detector Threshold Setting Criteria Based on Mean-Time-To-Lose-Lock (MTLL) for GPS Receivers.

PubMed

Jin, Tian; Yuan, Heliang; Zhao, Na; Qin, Honglei; Sun, Kewen; Ji, Yuanfa

2017-12-04

Frequency-locked detector (FLD) has been widely utilized in tracking loops of Global Positioning System (GPS) receivers to indicate their locking status. The relation between FLD and lock status has been seldom discussed. The traditional PLL experience is not suitable for FLL. In this paper, the threshold setting criteria for frequency-locked detector in the GPS receiver has been proposed by analyzing statistical characteristic of FLD output. The approximate probability distribution of frequency-locked detector is theoretically derived by using a statistical approach, which reveals the relationship between probabilities of frequency-locked detector and the carrier-to-noise ratio ( C / N ₀) of the received GPS signal. The relationship among mean-time-to-lose-lock (MTLL), detection threshold and lock probability related to C / N ₀ can be further discovered by utilizing this probability. Therefore, a theoretical basis for threshold setting criteria in frequency locked loops for GPS receivers is provided based on mean-time-to-lose-lock analysis.

A Doubly Stochastic Change Point Detection Algorithm for Noisy Biological Signals.

PubMed

Gold, Nathan; Frasch, Martin G; Herry, Christophe L; Richardson, Bryan S; Wang, Xiaogang

2017-01-01

Experimentally and clinically collected time series data are often contaminated with significant confounding noise, creating short, noisy time series. This noise, due to natural variability and measurement error, poses a challenge to conventional change point detection methods. We propose a novel and robust statistical method for change point detection for noisy biological time sequences. Our method is a significant improvement over traditional change point detection methods, which only examine a potential anomaly at a single time point. In contrast, our method considers all suspected anomaly points and considers the joint probability distribution of the number of change points and the elapsed time between two consecutive anomalies. We validate our method with three simulated time series, a widely accepted benchmark data set, two geological time series, a data set of ECG recordings, and a physiological data set of heart rate variability measurements of fetal sheep model of human labor, comparing it to three existing methods. Our method demonstrates significantly improved performance over the existing point-wise detection methods.

Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes.

PubMed

Bamba, Masaru; Nakata, Sayuri; Aoki, Seishiro; Takayama, Koji; Núñez-Farfán, Juan; Ito, Motomi; Miya, Masaki; Kajita, Tadashi

2016-12-01

To understand the geographic distributions of rhizobia that associated with widely distributed wild legumes, 66 nodules obtained from 41 individuals including three sea-dispersed legumes (Vigna marina, Vigna luteola, and Canavalia rosea) distributed across the tropical and subtropical coastal regions of the world were studied. Partial sequences of 16S rRNA and nodC genes extracted from the nodules showed that only Bradyrhizobium and Sinorhizobium were associated with the pantropical legumes, and some of the symbiont strains were widely distributed over the Pacific. Horizontal gene transfer of nodulation genes were observed within the Bradyrhizobium and Sinorhizobium lineages. BLAST searches in GenBank also identified records of these strains from various legumes across the world, including crop species. However, one of the rhizobial strains was not found in GenBank, which implies the strain may have adapted to the littoral environment. Our results suggested that some rhizobia, which associate with the widespread sea-dispersed legume, distribute across a broad geographic range. By establishing symbiotic relationships with widely distributed rhizobia, the pantropical legumes may also be able to extend their range much further than other legume species.

Measurements of top-quark pair differential cross-sections in the lepton+jets channel in pp collisions at $$\\sqrt{s}=8\\,~{\\mathrm {TeV}}$$ using the ATLAS detector

DOE PAGES

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

2016-10-03

Measurements of normalized differential cross-sections of top-quark pair production are presented as a function of the top-quark, tmore » $$\\bar{t}$$ system and event-level kinematic observables in proton–proton collisions at a centre-of-mass energy of √s=8TeV. The observables have been chosen to emphasize the t$$\\bar{t}$$ production process and to be sensitive to effects of initial- and final-state radiation, to the different parton distribution functions, and to non-resonant processes and higher-order corrections. The dataset corresponds to an integrated luminosity of 20.3 fb - 1 , recorded in 2012 with the ATLAS detector at the CERN Large Hadron Collider. Events are selected in the lepton+jets channel, requiring exactly one charged lepton and at least four jets with at least two of the jets tagged as originating from a b-quark. The measured spectra are corrected for detector effects and are compared to several Monte Carlo simulations. The results are in fair agreement with the predictions over a wide kinematic range. Nevertheless, most generators predict a harder top-quark transverse momentum distribution at high values than what is observed in the data. Predictions beyond NLO accuracy improve the agreement with data at high top-quark transverse momenta. Using the current settings and parton distribution functions, the rapidity distributions are not well modelled by any generator under consideration. However, the level of agreement is improved when more recent sets of parton distribution functions are used.« less

Novel face-detection method under various environments

NASA Astrophysics Data System (ADS)

Jing, Min-Quan; Chen, Ling-Hwei

2009-06-01

We propose a method to detect a face with different poses under various environments. On the basis of skin color information, skin regions are first extracted from an input image. Next, the shoulder part is cut out by using shape information and the head part is then identified as a face candidate. For a face candidate, a set of geometric features is applied to determine if it is a profile face. If not, then a set of eyelike rectangles extracted from the face candidate and the lighting distribution are used to determine if the face candidate is a nonprofile face. Experimental results show that the proposed method is robust under a wide range of lighting conditions, different poses, and races. The detection rate for the HHI face database is 93.68%. For the Champion face database, the detection rate is 95.15%.

The valuation of the EQ-5D in Portugal.

PubMed

Ferreira, Lara N; Ferreira, Pedro L; Pereira, Luis N; Oppe, Mark

2014-03-01

The EQ-5D is a preference-based measure widely used in cost-utility analysis (CUA). Several countries have conducted surveys to derive value sets, but this was not the case for Portugal. The purpose of this study was to estimate a value set for the EQ-5D for Portugal using the time trade-off (TTO). A representative sample of the Portuguese general population (n = 450) stratified by age and gender valued 24 health states. Face-to-face interviews were conducted by trained interviewers. Each respondent ranked and valued seven health states using the TTO. Several models were estimated at both the individual and aggregated levels to predict health state valuations. Alternative functional forms were considered to account for the skewed distribution of these valuations. The models were analyzed in terms of their coefficients, overall fit and the ability for predicting the TTO values. Random effects models were estimated using generalized least squares and were robust across model specification. The results are generally consistent with other value sets. This research provides the Portuguese EQ-5D value set based on the preferences of the Portuguese general population as measured by the TTO. This value set is recommended for use in CUA conducted in Portugal.

Distribution of Aedes mosquitoes in the Kilimanjaro Region of northern Tanzania.

PubMed

Hertz, Julian T; Lyaruu, Lucille J; Ooi, Eng Eong; Mosha, Franklin W; Crump, John A

2016-05-01

Little is known about the presence and distribution of Aedes mosquitoes in northern Tanzania despite the occurence of viruses transmitted by these mosquitoes such as Chikungunya virus (CHIKV) and Dengue virus (DENV) in the region. Adult and larval mosquitoes were collected from rural and urban settings across a wide range of altitudes in the Kilimanjaro Region using the Mosquito Magnet CO2 Trap for collection of adults and old tires for breeding of larvae. Polymerase chain reaction assays were performed on captured adult mosquitoes to detect the presence of CHIKV and DENV. A total of 2609 Aedes aegypti adult mosquitoes were collected; no other Aedes species larvae were found. Mosquito yields were significantly higher in urban settings than rural settings (26.5 vs. 1.9 mosquitoes per day, p = 0.037). A total of 6570 Ae. aegypti larvae were collected from old tires; no other Aedes species larvae were found. Of the 2609 adult mosquitoes collected, none tested positive for CHIKV or DENV. As far as we are aware, this paper reports for the first time the presence of Ae. aegypti in the Kilimanjaro Region of northern Tanzania. Although CHIKV and DENV were not isolated from any of the collected mosquitoes in this study, the apparent absence of other Aedes species in the area suggests that Ae. aegypti is the primary local vector of these infections.

Family Life and Developmental Idealism in Yazd, Iran

PubMed Central

Abbasi-Shavazi, Mohammad Jalal; Askari-Nodoushan, Abbas

2012-01-01

BACKGROUND This paper is motivated by the theory that developmental idealism has been disseminated globally and has become an international force for family and demographic change. Developmental idealism is a set of cultural beliefs and values about development and how development relates to family and demographic behavior. It holds that modern societies are causal forces producing modern families, that modern families help to produce modern societies, and that modern family change is to be expected. OBJECTIVE We examine the extent to which developmental idealism has been disseminated in Iran. We also investigate predictors of the dissemination of developmental idealism. METHODS We use survey data collected in 2007 from a sample of women in Yazd, a city in Iran. We examine the distribution of developmental idealism in the sample and the multivariate predictors of developmental idealism. RESULTS We find considerable support for the expectation that many elements of developmental idealism have been widely disseminated. Statistically significant majorities associate development with particular family attributes, believe that development causes change in families, believe that fertility reductions and age-at-marriage increases help foster development, and perceive family trends in Iran headed toward modernity. As predicted, parental education, respondent education, and income affect adherence to developmental idealism. CONCLUSIONS Developmental idealism has been widely disseminated in Yazd, Iran and is related to social and demographic factors in predicted ways. COMMENTS Although our data come from only one city, we expect that developmental idealism has been widely distributed in Iran, with important implications for family and demographic behavior. PMID:22942772

Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

PubMed

Froese, Jens G; Smith, Carl S; Durr, Peter A; McAlpine, Clive A; van Klinken, Rieks D

2017-01-01

Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia

PubMed Central

2017-01-01

Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs’ resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations. PMID:28472113

Pulsing of a focused mantle plume: Evidence from the distribution of foundation chain hotspot volcanism

NASA Astrophysics Data System (ADS)

O'Connor, John M.; Stoffers, Peter; Wijbrans, Jan R.

2002-05-01

Using the rare case of a hotspot chain crossing a fossil microplate, we reveal fundamental mantle plume characteristics by comparing hotspot volcanism in a sequence of contrasting tectonic settings. Key new 40Ar/39Ar ages show that the Foundation mantle plume pulses hot masses from depth with an apparent periodicity of one Myr. Synchronous magmatism over large distances indicates that masses associated with individual pulses are focused initially into similarly sized zones under the Pacific plate. Since the plume, spreading on impact with the lithosphere, influences a very wide area, apparently unconnected hotspot volcanism can be produced simultaneously across wide swaths, often crosscutting seamount chains. Our model might explain in part much of the midplate volcanism scattered across the Pacific seafloor indicating the episodic addition of significantly greater masses of plume material into the upper mantle than suggested by the narrowness of major seamount chains.

Affordable Digital Planetariums with WorldWide Telescope

NASA Astrophysics Data System (ADS)

Rosenfield, P.; Connolly, A.; Fay, J.; Sayres, C.; Tofflemire, B.

2011-09-01

Digital planetariums can provide a broader range of educational experiences than the more classical planetariums that use star-balls. This is because of their ability to project images, content from current research, and the 3-D distribution of the stars and galaxies. While there are hundreds of planetariums in the country, the reason that few of these are fully digital is the cost. In collaboration with Microsoft Research (MSR), we have developed a way to digitize existing planetariums for approximately $40,000 using freely available software. We describe here how off the shelf equipment, together with a WorldWide Telescope client, can provide a rich and truly interactive experience. This will enable students and the public to pan though multi-wavelength full-sky scientific data sets, explore 3-D visualizations of our Solar System (including trajectories of millions of minor planets), near-by stars, and the SDSS galaxy catalog.

Probabilistic motor sequence learning in a virtual reality serial reaction time task.

PubMed

Sense, Florian; van Rijn, Hedderik

2018-01-01

The serial reaction time task is widely used to study learning and memory. The task is traditionally administered by showing target positions on a computer screen and collecting responses using a button box or keyboard. By comparing response times to random or sequenced items or by using different transition probabilities, various forms of learning can be studied. However, this traditional laboratory setting limits the number of possible experimental manipulations. Here, we present a virtual reality version of the serial reaction time task and show that learning effects emerge as expected despite the novel way in which responses are collected. We also show that response times are distributed as expected. The current experiment was conducted in a blank virtual reality room to verify these basic principles. For future applications, the technology can be used to modify the virtual reality environment in any conceivable way, permitting a wide range of previously impossible experimental manipulations.

Extrinsic local regression on manifold-valued data

PubMed Central

Lin, Lizhen; St Thomas, Brian; Zhu, Hongtu; Dunson, David B.

2017-01-01

We propose an extrinsic regression framework for modeling data with manifold valued responses and Euclidean predictors. Regression with manifold responses has wide applications in shape analysis, neuroscience, medical imaging and many other areas. Our approach embeds the manifold where the responses lie onto a higher dimensional Euclidean space, obtains a local regression estimate in that space, and then projects this estimate back onto the image of the manifold. Outside the regression setting both intrinsic and extrinsic approaches have been proposed for modeling i.i.d manifold-valued data. However, to our knowledge our work is the first to take an extrinsic approach to the regression problem. The proposed extrinsic regression framework is general, computationally efficient and theoretically appealing. Asymptotic distributions and convergence rates of the extrinsic regression estimates are derived and a large class of examples are considered indicating the wide applicability of our approach. PMID:29225385

Summary of Terra and Aqua MODIS Long-Term Performance

NASA Technical Reports Server (NTRS)

Xiong, Xiaoxiong (Jack); Wenny, Brian N.; Angal, Amit; Barnes, William; Salomonson, Vincent

2011-01-01

Since launch in December 1999, the MODIS ProtoFlight Model (PFM) onboard the Terra spacecraft has successfully operated for more than 11 years. Its Flight Model (FM) onboard the Aqua spacecraft, launched in May 2002, has also successfully operated for over 9 years. MODIS observations are made in 36 spectral bands at three nadir spatial resolutions and are calibrated and characterized regularly by a set of on-board calibrators (OBC). Nearly 40 science products, supporting a variety of land, ocean, and atmospheric applications, are continuously derived from the calibrated reflectances and radiances of each MODIS instrument and widely distributed to the world-wide user community. Following an overview of MODIS instrument operation and calibration activities, this paper provides a summary of both Terra and Aqua MODIS long-term performance. Special considerations that are critical to maintaining MODIS data quality and beneficial for future missions are also discussed.

The wide-spread presence of rib-like patterns in basal shear of ice streams detected by surface data inversion

NASA Astrophysics Data System (ADS)

Sergienko, O. V.

2013-12-01

The direct observations of the basal conditions under continental-scale ice sheets are logistically impossible. A possible approach to estimate conditions at the ice - bed interface is from surface observations by means of inverse methods. The recent advances in remote and ground-based observations have allowed to acquire a wealth observations from Greenland and Antarctic ice sheets. Using high-resolution data sets of ice surface and bed elevations and surface velocities, inversions for basal conditions have been performed for several ice streams in Greenland and Antarctica. The inversion results reveal the wide-spread presence of rib-like spatial structures in basal shear. The analysis of the hydraulic potential distribution shows that these rib-like structures co-locate with highs of the gradient of hydraulic potential. This suggests that subglacial water plays a role in the development and evolution of the basal shear ribs.

An Information-theoretic Approach to Optimize JWST Observations and Retrievals of Transiting Exoplanet Atmospheres

NASA Astrophysics Data System (ADS)

Howe, Alex R.; Burrows, Adam; Deming, Drake

2017-01-01

We provide an example of an analysis to explore the optimization of observations of transiting hot Jupiters with the James Webb Space Telescope (JWST) to characterize their atmospheres based on a simple three-parameter forward model. We construct expansive forward model sets for 11 hot Jupiters, 10 of which are relatively well characterized, exploring a range of parameters such as equilibrium temperature and metallicity, as well as considering host stars over a wide range in brightness. We compute posterior distributions of our model parameters for each planet with all of the available JWST spectroscopic modes and several programs of combined observations and compute their effectiveness using the metric of estimated mutual information per degree of freedom. From these simulations, clear trends emerge that provide guidelines for designing a JWST observing program. We demonstrate that these guidelines apply over a wide range of planet parameters and target brightnesses for our simple forward model.

Uniform-penalty inversion of multiexponential decay data. II. Data spacing, T(2) data, systemic data errors, and diagnostics.

PubMed

Borgia, G C; Brown, R J; Fantazzini, P

2000-12-01

The basic method of UPEN (uniform penalty inversion of multiexponential decay data) is given in an earlier publication (Borgia et al., J. Magn. Reson. 132, 65-77 (1998)), which also discusses the effects of noise, constraints, and smoothing on the resolution or apparent resolution of features of a computed distribution of relaxation times. UPEN applies negative feedback to a regularization penalty, allowing stronger smoothing for a broad feature than for a sharp line. This avoids unnecessarily broadening the sharp line and/or breaking the wide peak or tail into several peaks that the relaxation data do not demand to be separate. The experimental and artificial data presented earlier were T(1) data, and all had fixed data spacings, uniform in log-time. However, for T(2) data, usually spaced uniformly in linear time, or for data spaced in any manner, we have found that the data spacing does not enter explicitly into the computation. The present work shows the extension of UPEN to T(2) data, including the averaging of data in windows and the use of the corresponding weighting factors in the computation. Measures are implemented to control portions of computed distributions extending beyond the data range. The input smoothing parameters in UPEN are normally fixed, rather than data dependent. A major problem arises, especially at high signal-to-noise ratios, when UPEN is applied to data sets with systematic errors due to instrumental nonidealities or adjustment problems. For instance, a relaxation curve for a wide line can be narrowed by an artificial downward bending of the relaxation curve. Diagnostic parameters are generated to help identify data problems, and the diagnostics are applied in several examples, with particular attention to the meaningful resolution of two closely spaced peaks in a distribution of relaxation times. Where feasible, processing with UPEN in nearly real time should help identify data problems while further instrument adjustments can still be made. The need for the nonnegative constraint is greatly reduced in UPEN, and preliminary processing without this constraint helps identify data sets for which application of the nonnegative constraint is too expensive in terms of error of fit for the data set to represent sums of decaying positive exponentials plus random noise. Copyright 2000 Academic Press.

Online cross-validation-based ensemble learning.

PubMed

Benkeser, David; Ju, Cheng; Lendle, Sam; van der Laan, Mark

2018-01-30

Online estimators update a current estimate with a new incoming batch of data without having to revisit past data thereby providing streaming estimates that are scalable to big data. We develop flexible, ensemble-based online estimators of an infinite-dimensional target parameter, such as a regression function, in the setting where data are generated sequentially by a common conditional data distribution given summary measures of the past. This setting encompasses a wide range of time-series models and, as special case, models for independent and identically distributed data. Our estimator considers a large library of candidate online estimators and uses online cross-validation to identify the algorithm with the best performance. We show that by basing estimates on the cross-validation-selected algorithm, we are asymptotically guaranteed to perform as well as the true, unknown best-performing algorithm. We provide extensions of this approach including online estimation of the optimal ensemble of candidate online estimators. We illustrate excellent performance of our methods using simulations and a real data example where we make streaming predictions of infectious disease incidence using data from a large database. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

GIS-based niche modeling for mapping species' habitats

USGS Publications Warehouse

Rotenberry, J.T.; Preston, K.L.; Knick, S.

2006-01-01

Ecological a??niche modelinga?? using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.

Comparing biomarkers as principal surrogate endpoints.

PubMed

Huang, Ying; Gilbert, Peter B

2011-12-01

Recently a new definition of surrogate endpoint, the "principal surrogate," was proposed based on causal associations between treatment effects on the biomarker and on the clinical endpoint. Despite its appealing interpretation, limited research has been conducted to evaluate principal surrogates, and existing methods focus on risk models that consider a single biomarker. How to compare principal surrogate value of biomarkers or general risk models that consider multiple biomarkers remains an open research question. We propose to characterize a marker or risk model's principal surrogate value based on the distribution of risk difference between interventions. In addition, we propose a novel summary measure (the standardized total gain) that can be used to compare markers and to assess the incremental value of a new marker. We develop a semiparametric estimated-likelihood method to estimate the joint surrogate value of multiple biomarkers. This method accommodates two-phase sampling of biomarkers and is more widely applicable than existing nonparametric methods by incorporating continuous baseline covariates to predict the biomarker(s), and is more robust than existing parametric methods by leaving the error distribution of markers unspecified. The methodology is illustrated using a simulated example set and a real data set in the context of HIV vaccine trials. © 2011, The International Biometric Society.

Measurements of normalized differential cross sections for tt ¯ production in pp collisions at √(s) =7 TeV using the ATLAS detector

NASA Astrophysics Data System (ADS)

Aad, G.; Abajyan, T.; Abbott, B.; Abdallah, J.; Abdel Khalek, S.; Abdinov, O.; Aben, R.; Abi, B.; Abolins, M.; Abouzeid, O. S.; Abramowicz, H.; Abreu, H.; Abulaiti, Y.; Acharya, B. S.; Adamczyk, L.; Adams, D. L.; Adelman, J.; Adomeit, S.; Adye, T.; Agatonovic-Jovin, T.; Aguilar-Saavedra, J. A.; Agustoni, M.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Albert, J.; Albrand, S.; Alconada Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Alimonti, G.; Alio, L.; Alison, J.; Allbrooke, B. M. M.; Allison, L. J.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alonso, F.; Alpigiani, C.; Altheimer, A.; Alvarez Gonzalez, B.; Alviggi, M. G.; Amako, K.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Ammosov, V. V.; Amor Dos Santos, S. P.; Amorim, A.; Amoroso, S.; Amram, N.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, G.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Anduaga, X. S.; Angelidakis, S.; Anger, P.; Angerami, A.; Anghinolfi, F.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonov, A.; Antos, J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Apolle, R.; Arabidze, G.; Aracena, I.; Arai, Y.; Araque, J. P.; Arce, A. T. H.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnal, V.; Arslan, O.; Artamonov, A.; Artoni, G.; Asai, S.; Asbah, N.; Ashkenazi, A.; Ask, S.; Åsman, B.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Auerbach, B.; Auge, E.; Augsten, K.; Aurousseau, M.; Avolio, G.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Bacci, C.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Backus Mayes, J.; Badescu, E.; Bagiacchi, P.; Bagnaia, P.; Bai, Y.; Bailey, D. C.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, S.; Balek, P.; Balli, F.; Banas, E.; Banerjee, Sw.; Bangert, A.; Bannoura, A. A. E.; Bansal, V.; Bansil, H. S.; Barak, L.; Baranov, S. P.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Barnovska, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Bartsch, V.; Bassalat, A.; Basye, A.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battistin, M.; Bauer, F.; Bawa, H. S.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Bechtle, P.; Beck, H. P.; Becker, K.; Becker, S.; Beckingham, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bedikian, S.; Bednyakov, V. A.; Bee, C. P.; Beemster, L. J.; Beermann, T. A.; Begel, M.; Behr, K.; Belanger-Champagne, C.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belloni, A.; Belotskiy, K.; Beltramello, O.; Benary, O.; Benchekroun, D.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez Garcia, J. A.; Benjamin, D. P.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernard, C.; Bernat, P.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertolucci, F.; Besana, M. I.; Besjes, G. J.; Bessidskaia, O.; Besson, N.; Betancourt, C.; Bethke, S.; Bhimji, W.; Bianchi, R. M.; Bianchini, L.; Bianco, M.; Biebel, O.; Bieniek, S. P.; Bierwagen, K.; Biesiada, J.; Biglietti, M.; Bilbao de Mendizabal, J.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Black, C. W.; Black, J. E.; Black, K. M.; Blackburn, D.; Blair, R. E.; Blanchard, J.-B.; Blazek, T.; Bloch, I.; Blocker, C.; Blum, W.; Blumenschein, U.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Boddy, C. R.; Boehler, M.; Boek, J.; Boek, T. T.; Bogaerts, J. A.; Bogdanchikov, A. G.; Bogouch, A.; Bohm, C.; Bohm, J.; Boisvert, V.; Bold, T.; Boldea, V.; Boldyrev, A. S.; Bolnet, N. M.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Borri, M.; Borroni, S.; Bortfeldt, J.; Bortolotto, V.; Bos, K.; Boscherini, D.; Bosman, M.; Boterenbrood, H.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Bousson, N.; Boutouil, S.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozovic-Jelisavcic, I.; Bracinik, J.; Branchini, P.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Braun, H. M.; Brazzale, S. F.; Brelier, B.; Brendlinger, K.; Brennan, A. J.; Brenner, R.; Bressler, S.; Bristow, K.; Bristow, T. M.; Britton, D.; Brochu, F. M.; Brock, I.; Brock, R.; Bromberg, C.; Bronner, J.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Brown, G.; Brown, J.; Bruckman de Renstrom, P. 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N.; Taylor, W.; Teischinger, F. A.; Teixeira Dias Castanheira, M.; Teixeira-Dias, P.; Temming, K. K.; Ten Kate, H.; Teng, P. K.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Therhaag, J.; Theveneaux-Pelzer, T.; Thoma, S.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, E. N.; Thompson, P. D.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Thomson, M.; Thong, W. M.; Thun, R. P.; Tian, F.; Tibbetts, M. J.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tiouchichine, E.; Tipton, P.; Tisserant, S.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tollefson, K.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Topilin, N. D.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Tran, H. L.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Triplett, N.; Trischuk, W.; Trocmé, B.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; True, P.; Trzebinski, M.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tua, A.; Tudorache, A.; Tudorache, V.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turecek, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Tykhonov, A.; Tylmad, M.; Tyndel, M.; Uchida, K.; Ueda, I.; Ueno, R.; Ughetto, M.; Ugland, M.; Uhlenbrock, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Urbaniec, D.; Urquijo, P.; Usai, G.; Usanova, A.; Vacavant, L.; Vacek, V.; Vachon, B.; Valencic, N.; Valentinetti, S.; Valero, A.; Valery, L.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; van der Deijl, P. C.; van der Geer, R.; van der Graaf, H.; van der Leeuw, R.; van der Ster, D.; van Eldik, N.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vanguri, R.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veloso, F.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vest, A.; Vetterli, M. C.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigne, R.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Virzi, J.; Vitells, O.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vladoiu, D.; Vlasak, M.; Vogel, A.; Vokac, P.; Volpi, G.; Volpi, M.; von der Schmitt, H.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vu Anh, T.; Vuillermet, R.; Vukotic, I.; Vykydal, Z.; Wagner, P.; Wagner, W.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Waller, P.; Walsh, B.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, K.; Wang, R.; Wang, S. M.; Wang, T.; Wang, X.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Warsinsky, M.; Washbrook, A.; Wasicki, C.; Watanabe, I.; Watkins, P. M.; Watson, A. T.; Watson, I. J.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, S.; Weber, M. S.; Weber, S. W.; Webster, J. S.; Weidberg, A. R.; Weigell, P.; Weinert, B.; Weingarten, J.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wendland, D.; Weng, Z.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Wessels, M.; Wetter, J.; Whalen, K.; White, A.; White, M. J.; White, R.; White, S.; Whiteson, D.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wijeratne, P. A.; Wildauer, A.; Wildt, M. A.; Wilkens, H. G.; Will, J. Z.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, A.; Wilson, J. A.; Wingerter-Seez, I.; Winkelmann, S.; Winklmeier, F.; Wittgen, M.; Wittig, T.; Wittkowski, J.; Wollstadt, S. J.; Wolter, M. W.; Wolters, H.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wozniak, K. W.; Wright, M.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wulf, E.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xiao, M.; Xu, D.; Xu, L.; Yabsley, B.; Yacoob, S.; Yamada, M.; Yamaguchi, H.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamanaka, T.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, U. K.; Yang, Y.; Yanush, S.; Yao, L.; Yao, W.-M.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yen, A. L.; Yildirim, E.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Yoshihara, K.; Young, C.; Young, C. J. S.; Youssef, S.; Yu, D. R.; Yu, J.; Yu, J. M.; Yu, J.; Yuan, L.; Yurkewicz, A.; Zabinski, B.; Zaidan, R.; Zaitsev, A. M.; Zaman, A.; Zambito, S.; Zanello, L.; Zanzi, D.; Zaytsev, A.; Zeitnitz, C.; Zeman, M.; Zemla, A.; Zengel, K.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zevi Della Porta, G.; Zhang, D.; Zhang, F.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, X.; Zhang, Z.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, L.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Zinonos, Z.; Ziolkowski, M.; Zitoun, R.; Zobernig, G.; Zoccoli, A.; Zur Nedden, M.; Zurzolo, G.; Zutshi, V.; Zwalinski, L.; Atlas Collaboration

2014-10-01

Measurements of normalized differential cross sections for top-quark pair production are presented as a function of the top-quark transverse momentum, and of the mass, transverse momentum, and rapidity of the tt ¯ system, in proton-proton collisions at a center-of-mass energy of √s =7 TeV. The data set corresponds to an integrated luminosity of 4.6 fb-1, recorded in 2011 with the ATLAS detector at the CERN Large Hadron Collider. Events are selected in the lepton +jets channel, requiring exactly one lepton and at least four jets with at least one of the jets tagged as originating from a b-quark. The measured spectra are corrected for detector efficiency and resolution effects and are compared to several Monte Carlo simulations and theory calculations. The results are in fair agreement with the predictions in a wide kinematic range. Nevertheless, data distributions are softer than predicted for higher values of the mass of the tt ¯ system and of the top-quark transverse momentum. The measurements can also discriminate among different sets of parton distribution functions.

Dopaminergic neurons encode a distributed, asymmetric representation of temperature in Drosophila.

PubMed

Tomchik, Seth M

2013-01-30

Dopaminergic circuits modulate a wide variety of innate and learned behaviors in animals, including olfactory associative learning, arousal, and temperature-preference behavior. It is not known whether distinct or overlapping sets of dopaminergic neurons modulate these behaviors. Here, I have functionally characterized the dopaminergic circuits innervating the Drosophila mushroom body with in vivo calcium imaging and conditional silencing of genetically defined subsets of neurons. Distinct subsets of PPL1 dopaminergic neurons innervating the vertical lobes of the mushroom body responded to decreases in temperature, but not increases, with rapidly adapting bursts of activity. PAM neurons innervating the horizontal lobes did not respond to temperature shifts. Ablation of the antennae and maxillary palps reduced, but did not eliminate, the responses. Genetic silencing of dopaminergic neurons innervating the vertical mushroom body lobes substantially reduced behavioral cold avoidance, but silencing smaller subsets of these neurons had no effect. These data demonstrate that overlapping dopaminergic circuits encode a broadly distributed, asymmetric representation of temperature that overlays regions implicated previously in learning, memory, and forgetting. Thus, diverse behaviors engage overlapping sets of dopaminergic neurons that encode multimodal stimuli and innervate a single anatomical target, the mushroom body.

A distributed-memory approximation algorithm for maximum weight perfect bipartite matching

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

Azad, Ariful; Buluc, Aydin; Li, Xiaoye S.

We design and implement an efficient parallel approximation algorithm for the problem of maximum weight perfect matching in bipartite graphs, i.e. the problem of finding a set of non-adjacent edges that covers all vertices and has maximum weight. This problem differs from the maximum weight matching problem, for which scalable approximation algorithms are known. It is primarily motivated by finding good pivots in scalable sparse direct solvers before factorization where sequential implementations of maximum weight perfect matching algorithms, such as those available in MC64, are widely used due to the lack of scalable alternatives. To overcome this limitation, we proposemore » a fully parallel distributed memory algorithm that first generates a perfect matching and then searches for weightaugmenting cycles of length four in parallel and iteratively augments the matching with a vertex disjoint set of such cycles. For most practical problems the weights of the perfect matchings generated by our algorithm are very close to the optimum. An efficient implementation of the algorithm scales up to 256 nodes (17,408 cores) on a Cray XC40 supercomputer and can solve instances that are too large to be handled by a single node using the sequential algorithm.« less

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.

The Effect of Distributed Practice in Undergraduate Statistics Homework Sets: A Randomized Trial

ERIC Educational Resources Information Center

Crissinger, Bryan R.

2015-01-01

Most homework sets in statistics courses are constructed so that students concentrate or "mass" their practice on a certain topic in one problem set. Distributed practice homework sets include review problems in each set so that practice on a topic is distributed across problem sets. There is a body of research that points to the…

C-reactive protein point-of-care testing and antibiotic prescribing for acute respiratory tract infections in rural primary health centres of North Ethiopia: a cross-sectional study.

PubMed

Yebyo, Henock; Medhanyie, Araya Abrha; Spigt, Mark; Hopstaken, Rogier

2016-01-14

Unjustified antibiotic prescribing for acute upper respiratory infections (URTIs) is probably more common in poor-resource settings where physicians are scarce. Introducing C-reactive protein (CRP) point-of-care testing in such settings could reduce the misuse of antibiotics, which could avert antibiotic resistance. However, information useful for the applicability of CRP test in resource-limited settings is lacking. This study aimed to elicit the frequency of antibiotic prescribing and distribution of CRP levels in remote, rural settings in Ethiopia. We included 414 patients with acute URTIs from four health centres. Health professionals recorded the clinical features of the patients, but the laboratory professionals measured the CRP levels of all patients at the point of care. The most prominent respiratory causes for consultation were acute URTIs combined (44.4%), and lower respiratory tract infections-pneumonia (29.71%) and acute bronchitis (25.84%). The CRP distribution was <20 mg/l, 20-99 mg/l and 100 mg/l or more in 66.6%, 27.9% and 5.5% of the patients, respectively. The CRP levels were significantly different among these clinical diagnoses (X(2)=114.3, P<0.001, d.f.=4). A wide range of antibiotics was administered for 87.8% of the patients, regardless of the diagnostic or prognostic nature of their diseases. Antibiotic prescribing for acute URTIs in the rural areas of Ethiopia is unduly high, with high proportions of mild, self-limiting illness, mostly URTIs. Implementation of CRP point-of-care testing in such resource-constrained settings, with low- or middle-grade healthcare professionals, could help reconcile the inappropriate use of antibiotics by withholding from patients who do not benefit from antibiotic treatment.

C-reactive protein point-of-care testing and antibiotic prescribing for acute respiratory tract infections in rural primary health centres of North Ethiopia: a cross-sectional study

PubMed Central

Yebyo, Henock; Medhanyie, Araya Abrha; Spigt, Mark; Hopstaken, Rogier

2016-01-01

Unjustified antibiotic prescribing for acute upper respiratory infections (URTIs) is probably more common in poor-resource settings where physicians are scarce. Introducing C-reactive protein (CRP) point-of-care testing in such settings could reduce the misuse of antibiotics, which could avert antibiotic resistance. However, information useful for the applicability of CRP test in resource-limited settings is lacking. This study aimed to elicit the frequency of antibiotic prescribing and distribution of CRP levels in remote, rural settings in Ethiopia. We included 414 patients with acute URTIs from four health centres. Health professionals recorded the clinical features of the patients, but the laboratory professionals measured the CRP levels of all patients at the point of care. The most prominent respiratory causes for consultation were acute URTIs combined (44.4%), and lower respiratory tract infections—pneumonia (29.71%) and acute bronchitis (25.84%). The CRP distribution was <20 mg/l, 20–99 mg/l and 100 mg/l or more in 66.6%, 27.9% and 5.5% of the patients, respectively. The CRP levels were significantly different among these clinical diagnoses (X2=114.3, P<0.001, d.f.=4). A wide range of antibiotics was administered for 87.8% of the patients, regardless of the diagnostic or prognostic nature of their diseases. Antibiotic prescribing for acute URTIs in the rural areas of Ethiopia is unduly high, with high proportions of mild, self-limiting illness, mostly URTIs. Implementation of CRP point-of-care testing in such resource-constrained settings, with low- or middle-grade healthcare professionals, could help reconcile the inappropriate use of antibiotics by withholding from patients who do not benefit from antibiotic treatment. PMID:26769226

Dissecting random and systematic differences between noisy composite data sets.

PubMed

Diederichs, Kay

2017-04-01

Composite data sets measured on different objects are usually affected by random errors, but may also be influenced by systematic (genuine) differences in the objects themselves, or the experimental conditions. If the individual measurements forming each data set are quantitative and approximately normally distributed, a correlation coefficient is often used to compare data sets. However, the relations between data sets are not obvious from the matrix of pairwise correlations since the numerical value of the correlation coefficient is lowered by both random and systematic differences between the data sets. This work presents a multidimensional scaling analysis of the pairwise correlation coefficients which places data sets into a unit sphere within low-dimensional space, at a position given by their CC* values [as defined by Karplus & Diederichs (2012), Science, 336, 1030-1033] in the radial direction and by their systematic differences in one or more angular directions. This dimensionality reduction can not only be used for classification purposes, but also to derive data-set relations on a continuous scale. Projecting the arrangement of data sets onto the subspace spanned by systematic differences (the surface of a unit sphere) allows, irrespective of the random-error levels, the identification of clusters of closely related data sets. The method gains power with increasing numbers of data sets. It is illustrated with an example from low signal-to-noise ratio image processing, and an application in macromolecular crystallography is shown, but the approach is completely general and thus should be widely applicable.

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

Donovan, Ellen M., E-mail: ellen.donovan@icr.ac.u; Ciurlionis, Laura; Fairfoul, Jamie

Purpose: To establish planning solutions for a concomitant three-level radiation dose distribution to the breast using linear accelerator- or tomotherapy-based intensity-modulated radiotherapy (IMRT), for the U.K. Intensity Modulated and Partial Organ (IMPORT) High trial. Methods and Materials: Computed tomography data sets for 9 patients undergoing breast conservation surgery with implanted tumor bed gold markers were used to prepare three-level dose distributions encompassing the whole breast (36 Gy), partial breast (40 Gy), and tumor bed boost (48 or 53 Gy) treated concomitantly in 15 fractions within 3 weeks. Forward and inverse planned IMRT and tomotherapy were investigated as solutions. A standardmore » electron field was compared with a photon field arrangement encompassing the tumor bed boost volume. The out-of-field doses were measured for all methods. Results: Dose-volume constraints of volume >90% receiving 32.4 Gy and volume >95% receiving 50.4 Gy for the whole breast and tumor bed were achieved. The constraint of volume >90% receiving 36 Gy for the partial breast was fulfilled in the inverse IMRT and tomotherapy plans and in 7 of 9 cases of a forward planned IMRT distribution. An electron boost to the tumor bed was inadequate in 8 of 9 cases. The IMRT methods delivered a greater whole body dose than the standard breast tangents. A contralateral lung volume >2.5 Gy was increased in the inverse IMRT and tomotherapy plans, although it did not exceed the constraint. Conclusion: We have demonstrated a set of widely applicable solutions that fulfilled the stringent clinical trial requirements for the delivery of a concomitant three-level dose distribution to the breast.« less

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Development of an objective dose distribution analysis method for OSL dating and pilot studies for planetary applications

NASA Astrophysics Data System (ADS)

Lepper, Kenneth Errol

Scope and method of study. Part I: In its simplest expression a luminescence age is the natural absorbed radiation dose (De) divided by the in-situ dose rate. The experimental techniques of Optically Stimulated Luminescence (OSL) dating have evolved to the point were hundreds of Des, and therefore depositional ages can be quickly and conveniently determined for a single sediment sample. The first major objective of this research was to develop an objective analysis method for analyzing dose distribution data and selecting an age-representative dose (Dp). The analytical method was developed based on dose data sets collected from 3 eolian and 3 fluvial sediment samples from Central Oklahoma. Findings and conclusions. Part I: An objective method of presenting the dose distribution data, and a mathematically rigorous means of determining the Dp, as well as a statistically meaningful definition of the uncertainty in Dp have been proposed. The concept of experimental error deconvolution was introduced. In addition a set of distribution shape parameters to facilitate comparison among samples have been defined. These analytical techniques hold the potential to greatly enhance the accuracy and utility of OSL dating for young fluvial sediments. Scope and method of study. Part II: The second major objective of this research was to propose the application of luminescence dating to sediments on Mars. A set of fundamental luminescence dating properties was evaluated for a martian surface materials analog and a polar deposit contextual analog. Findings and conclusions. Part II: The luminescence signals measured from the analogs were found to have a wide dynamic dose response range with no unusual or prohibitive short-term instabilities and were readily reset by exposure to sunlight. These properties form a stable base for continued investigations toward the development of luminescence dating instruments and procedures for Mars.

Wavelet and Fractal Analysis of Remotely Sensed Surface Temperature with Applications to Estimation of Surface Sensible Heat Flux Density

NASA Technical Reports Server (NTRS)

Schieldge, John

2000-01-01

Wavelet and fractal analyses have been used successfully to analyze one-dimensional data sets such as time series of financial, physical, and biological parameters. These techniques have been applied to two-dimensional problems in some instances, including the analysis of remote sensing imagery. In this respect, these techniques have not been widely used by the remote sensing community, and their overall capabilities as analytical tools for use on satellite and aircraft data sets is not well known. Wavelet and fractal analyses have the potential to provide fresh insight into the characterization of surface properties such as temperature and emissivity distributions, and surface processes such as the heat and water vapor exchange between the surface and the lower atmosphere. In particular, the variation of sensible heat flux density as a function of the change In scale of surface properties Is difficult to estimate, but - in general - wavelets and fractals have proved useful in determining the way a parameter varies with changes in scale. We present the results of a limited study on the relationship between spatial variations in surface temperature distribution and sensible heat flux distribution as determined by separate wavelet and fractal analyses. We analyzed aircraft imagery obtained in the thermal infrared (IR) bands from the multispectral TIMS and hyperspectral MASTER airborne sensors. The thermal IR data allows us to estimate the surface kinetic temperature distribution for a number of sites in the Midwestern and Southwestern United States (viz., San Pedro River Basin, Arizona; El Reno, Oklahoma; Jornada, New Mexico). The ground spatial resolution of the aircraft data varied from 5 to 15 meters. All sites were instrumented with meteorological and hydrological equipment including surface layer flux measuring stations such as Bowen Ratio systems and sonic anemometers. The ground and aircraft data sets provided the inputs for the wavelet and fractal analyses, and the validation of the results.

Availability and quality of illegitimate somatropin products obtained from the Internet.

PubMed

Vida, Róbert György; Fittler, András; Mikulka, Ivett; Ábrahám, Eszter; Sándor, Viktor; Kilár, Ferenc; Botz, Lajos

2017-02-01

Background Growth hormones are widely available on the Internet for those who want to enhance their physical performance and improve body satisfaction. Illegitimate websites market somatropin injections without medical prescription and encourage misuse. Customers potentially put their health at risk when purchasing parenteral medications online. Objective The objective of our study was to evaluate the online market of no-prescription somatropin products and to analyse and document Internet pharmacy characteristics, distribution and pharmaceutical quality. Setting Websites indexed in Google promoting somatropin for sale direct to patients. Method Websites promoting the sale of growth hormone products were identified and analysed from June to August 2014. Internet vendor sites were evaluated to identify possible patient and medication safety concerns. Website characteristics, delivery time, storage conditions, packaging and attached product information were assessed. Investigation of the somatropin content was achieved using capillary electrophoresis with UV detection and electrospray ionization mass spectrometry. Main outcome measure Accessibility and quality of somatropin injections. Results Seventeen individual Internet vendor websites distributed somatropin products directly to patients, majority (94%) did not require a valid medical prescription before dispensing the products. Majority (70%) of Internet pharmacies displayed no medical information and none (0%) of the vendors displayed any regulatory body logo. All online samples had significantly (p < 0.001) lower somatropin concentration than labelled. Conclusion Our results clearly illustrate that prescription only biologic drugs are widely available online and can be easily accessed by anyone. Unprofessional distribution and handling is likely to cause degradation and possible patient safety concerns.

Body size distribution of the dinosaurs.

PubMed

O'Gorman, Eoin J; Hone, David W E

2012-01-01

The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size.

Body Size Distribution of the Dinosaurs

PubMed Central

O’Gorman, Eoin J.; Hone, David W. E.

2012-01-01

The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size. PMID:23284818

Big biology meets microclimatology: defining thermal niches of ectotherms at landscape scales for conservation planning.

PubMed

Isaak, Daniel J; Wenger, Seth J; Young, Michael K

2017-04-01

Temperature profoundly affects ecology, a fact ever more evident as the ability to measure thermal environments increases and global changes alter these environments. The spatial structure of thermalscapes is especially relevant to the distribution and abundance of ectothermic organisms, but the ability to describe biothermal relationships at extents and grains relevant to conservation planning has been limited by small or sparse data sets. Here, we combine a large occurrence database of >23 000 aquatic species surveys with stream microclimate scenarios supported by an equally large temperature database for a 149 000-km mountain stream network to describe thermal relationships for 14 fish and amphibian species. Species occurrence probabilities peaked across a wide range of temperatures (7.0-18.8°C) but distinct warm- or cold-edge distribution boundaries were apparent for all species and represented environments where populations may be most sensitive to thermal changes. Warm-edge boundary temperatures for a native species of conservation concern were used with geospatial data sets and a habitat occupancy model to highlight subsets of the network where conservation measures could benefit local populations by maintaining cool temperatures. Linking that strategic approach to local estimates of habitat impairment remains a key challenge but is also an opportunity to build relationships and develop synergies between the research, management, and regulatory communities. As with any data mining or species distribution modeling exercise, care is required in analysis and interpretation of results, but the use of large biological data sets with accurate microclimate scenarios can provide valuable information about the thermal ecology of many ectotherms and a spatially explicit way of guiding conservation investments. © 2017 by the Ecological Society of America.

A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions.

PubMed

Gao, Xiang; Lin, Huaiying; Dong, Qunfeng

2017-01-01

Dysbiosis of microbial communities is associated with various human diseases, raising the possibility of using microbial compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling microbial compositions with Dirichlet-multinomial distributions, which are widely used to model multicategorical count data with extra variation. The parameters of the Dirichlet-multinomial distributions are estimated from training microbiome data sets based on maximum likelihood. The posterior probability of a microbiome sample belonging to a disease or healthy category is calculated based on Bayes' theorem, using the likelihood values computed from the estimated Dirichlet-multinomial distribution, as well as a prior probability estimated from the training microbiome data set or previously published information on disease prevalence. When tested on real-world microbiome data sets, our method, called DMBC (for Dirichlet-multinomial Bayes classifier), shows better classification accuracy than the only existing Bayesian microbiome classifier based on a Dirichlet-multinomial mixture model and the popular random forest method. The advantage of DMBC is its built-in automatic feature selection, capable of identifying a subset of microbial taxa with the best classification accuracy between different classes of samples based on cross-validation. This unique ability enables DMBC to maintain and even improve its accuracy at modeling species-level taxa. The R package for DMBC is freely available at https://github.com/qunfengdong/DMBC. IMPORTANCE By incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option for using microbial compositions for disease diagnosis.

An economic evaluation of home management of malaria in Uganda: an interactive Markov model.

PubMed

Lubell, Yoel; Mills, Anne J; Whitty, Christopher J M; Staedke, Sarah G

2010-08-27

Home management of malaria (HMM), promoting presumptive treatment of febrile children in the community, is advocated to improve prompt appropriate treatment of malaria in Africa. The cost-effectiveness of HMM is likely to vary widely in different settings and with the antimalarial drugs used. However, no data on the cost-effectiveness of HMM programmes are available. A Markov model was constructed to estimate the cost-effectiveness of HMM as compared to conventional care for febrile illnesses in children without HMM. The model was populated with data from Uganda, but is designed to be interactive, allowing the user to adjust certain parameters, including the antimalarials distributed. The model calculates the cost per disability adjusted life year averted and presents the incremental cost-effectiveness ratio compared to a threshold value. Model output is stratified by level of malaria transmission and the probability that a child would receive appropriate care from a health facility, to indicate the circumstances in which HMM is likely to be cost-effective. The model output suggests that the cost-effectiveness of HMM varies with malaria transmission, the probability of appropriate care, and the drug distributed. Where transmission is high and the probability of appropriate care is limited, HMM is likely to be cost-effective from a provider perspective. Even with the most effective antimalarials, HMM remains an attractive intervention only in areas of high malaria transmission and in medium transmission areas with a lower probability of appropriate care. HMM is generally not cost-effective in low transmission areas, regardless of which antimalarial is distributed. Considering the analysis from the societal perspective decreases the attractiveness of HMM. Syndromic HMM for children with fever may be a useful strategy for higher transmission settings with limited health care and diagnosis, but is not appropriate for all settings. HMM may need to be tailored to specific settings, accounting for local malaria transmission intensity and availability of health services.

WWLLN and Earth Networks new combined Global Lightning Network: First Look

NASA Astrophysics Data System (ADS)

Holzworth, R. H., II; Brundell, J. B.; Sloop, C.; Heckman, S.; Rodger, C. J.

2016-12-01

Lightning VLF sferic waveforms detected around the world by WWLLN (World Wide Lightning Location Network) and by Earth Networks WTLN receivers are being analyzed in real time to calculate the time of group arrival (TOGA) of the sferic wave packet at each station. These times (TOGAs) are then used for time-of-arrival analysis to determine the source lightning location. Beginning in 2016 we have successfully implemented the operational software to allow the incorporation of waveforms from hundreds of Earth Networks sensors into the normal WWLLN TOGA processing, resulting in a new global lightning distribution which has over twice as many stroke locations as the WWLLN-only data set. The combined global lightning network shows marked improvement over the WWLLN-only data set in regions such as central and southern Africa, and over the Indian subcontinent. As of July 2016 the new data set is typically running at about 230% of WWLLN-only in terms of total strokes, and some days over 250%, using data from 65 to 70 WWLLN stations, combined with the VLF channel from about 160 Earth Networks stations. The Earth Networks lightning network includes nearly 1000 receiving stations, so it is anticipated we will be able to further increase the total stations being used for the new combined network while still maintaining a relatively smooth global distribution of the sensors. Detailed comparisons of the new data set with WWLLN-only data, as well as with independent lightning location networks including WTLN in the CONUS and NZLDN in New Zealand will be presented.

Designing application software in wide area network settings

NASA Technical Reports Server (NTRS)

Makpangou, Mesaac; Birman, Ken

1990-01-01

Progress in methodologies for developing robust local area network software has not been matched by similar results for wide area settings. The design of application software spanning multiple local area environments is examined. For important classes of applications, simple design techniques are presented that yield fault tolerant wide area programs. An implementation of these techniques as a set of tools for use within the ISIS system is described.

Dynamic Systems for Individual Tracking via Heterogeneous Information Integration and Crowd Source Distributed Simulation

DTIC Science & Technology

2015-12-04

51   6.6   Power Consumption: Communications ...simulations executing on mobile computing platforms, an area not widely studied to date in the distributed simulation research community . A...simulation community . These initial studies focused on two conservative synchronization algorithms widely used in the distributed simulation field

Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks.

PubMed

Flassig, R J; Sundmacher, K

2012-12-01

Biochemical reaction networks in the form of coupled ordinary differential equations (ODEs) provide a powerful modeling tool for understanding the dynamics of biochemical processes. During the early phase of modeling, scientists have to deal with a large pool of competing nonlinear models. At this point, discrimination experiments can be designed and conducted to obtain optimal data for selecting the most plausible model. Since biological ODE models have widely distributed parameters due to, e.g. biologic variability or experimental variations, model responses become distributed. Therefore, a robust optimal experimental design (OED) for model discrimination can be used to discriminate models based on their response probability distribution functions (PDFs). In this work, we present an optimal control-based methodology for designing optimal stimulus experiments aimed at robust model discrimination. For estimating the time-varying model response PDF, which results from the nonlinear propagation of the parameter PDF under the ODE dynamics, we suggest using the sigma-point approach. Using the model overlap (expected likelihood) as a robust discrimination criterion to measure dissimilarities between expected model response PDFs, we benchmark the proposed nonlinear design approach against linearization with respect to prediction accuracy and design quality for two nonlinear biological reaction networks. As shown, the sigma-point outperforms the linearization approach in the case of widely distributed parameter sets and/or existing multiple steady states. Since the sigma-point approach scales linearly with the number of model parameter, it can be applied to large systems for robust experimental planning. An implementation of the method in MATLAB/AMPL is available at http://www.uni-magdeburg.de/ivt/svt/person/rf/roed.html. flassig@mpi-magdeburg.mpg.de Supplementary data are are available at Bioinformatics online.

A Distributed Energy-Aware Trust Management System for Secure Routing in Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Stelios, Yannis; Papayanoulas, Nikos; Trakadas, Panagiotis; Maniatis, Sotiris; Leligou, Helen C.; Zahariadis, Theodore

Wireless sensor networks are inherently vulnerable to security attacks, due to their wireless operation. The situation is further aggravated because they operate in an infrastructure-less environment, which mandates the cooperation among nodes for all networking tasks, including routing, i.e. all nodes act as “routers”, forwarding the packets generated by their neighbours in their way to the sink node. This implies that malicious nodes (denying their cooperation) can significantly affect the network operation. Trust management schemes provide a powerful tool for the detection of unexpected node behaviours (either faulty or malicious). Once misbehaving nodes are detected, their neighbours can use this information to avoid cooperating with them either for data forwarding, data aggregation or any other cooperative function. We propose a secure routing solution based on a novel distributed trust management system, which allows for fast detection of a wide set of attacks and also incorporates energy awareness.

bayesPop: Probabilistic Population Projections

PubMed Central

Ševčíková, Hana; Raftery, Adrian E.

2016-01-01

We describe bayesPop, an R package for producing probabilistic population projections for all countries. This uses probabilistic projections of total fertility and life expectancy generated by Bayesian hierarchical models. It produces a sample from the joint posterior predictive distribution of future age- and sex-specific population counts, fertility rates and mortality rates, as well as future numbers of births and deaths. It provides graphical ways of summarizing this information, including trajectory plots and various kinds of probabilistic population pyramids. An expression language is introduced which allows the user to produce the predictive distribution of a wide variety of derived population quantities, such as the median age or the old age dependency ratio. The package produces aggregated projections for sets of countries, such as UN regions or trading blocs. The methodology has been used by the United Nations to produce their most recent official population projections for all countries, published in the World Population Prospects. PMID:28077933

A Distributed Wireless Camera System for the Management of Parking Spaces.

PubMed

Vítek, Stanislav; Melničuk, Petr

2017-12-28

The importance of detection of parking space availability is still growing, particularly in major cities. This paper deals with the design of a distributed wireless camera system for the management of parking spaces, which can determine occupancy of the parking space based on the information from multiple cameras. The proposed system uses small camera modules based on Raspberry Pi Zero and computationally efficient algorithm for the occupancy detection based on the histogram of oriented gradients (HOG) feature descriptor and support vector machine (SVM) classifier. We have included information about the orientation of the vehicle as a supporting feature, which has enabled us to achieve better accuracy. The described solution can deliver occupancy information at the rate of 10 parking spaces per second with more than 90% accuracy in a wide range of conditions. Reliability of the implemented algorithm is evaluated with three different test sets which altogether contain over 700,000 samples of parking spaces.

SemanticOrganizer: A Customizable Semantic Repository for Distributed NASA Project Teams

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Berrios, Daniel C.; Carvalho, Robert E.; Hall, David R.; Rich, Stephen J.; Sturken, Ian B.; Swanson, Keith J.; Wolfe, Shawn R.

2004-01-01

SemanticOrganizer is a collaborative knowledge management system designed to support distributed NASA projects, including diverse teams of scientists, engineers, and accident investigators. The system provides a customizable, semantically structured information repository that stores work products relevant to multiple projects of differing types. SemanticOrganizer is one of the earliest and largest semantic web applications deployed at NASA to date, and has been used in diverse contexts ranging from the investigation of Space Shuttle Columbia's accident to the search for life on other planets. Although the underlying repository employs a single unified ontology, access control and ontology customization mechanisms make the repository contents appear different for each project team. This paper describes SemanticOrganizer, its customization facilities, and a sampling of its applications. The paper also summarizes some key lessons learned from building and fielding a successful semantic web application across a wide-ranging set of domains with diverse users.

Modeling the Distribution of Nursing Effort Using Structured Labor and Delivery Documentation

PubMed Central

Hall, Eric S.; Poynton, Mollie R.; Narus, Scott P.; Thornton, Sidney N.

2008-01-01

Our study objectives included the development and evaluation of models for representing the distribution of shared unit-wide nursing care resources among individual Labor and Delivery patients using quantified measurements of nursing care, referred to as Nursing Effort. The models were intended to enable discrimination between the amounts of care delivered to patient subsets defined by attributes such as patient acuity. For each of five proposed models, scores were generated using an analysis set of 686,402 computerized nurse-documented events associated with 1,093 patients at three hospitals during January and February 2006. Significant differences were detected in Nursing Effort scores according to patient acuity, care facility, and in scores generated during shift-change versus non shift-change hours. The development of nursing care quantification strategies proposed in this study supports outcomes analysis by establishing a foundation for measuring the effect of patient-level nursing care on individual patient outcomes. PMID:18495549

Two-sided Topp-Leone Weibull distribution

NASA Astrophysics Data System (ADS)

Podeang, Krittaya; Bodhisuwan, Winai

2017-11-01

In this paper, we introduce a general class of lifetime distributions, called the two-sided Topp-Leone generated family of distribution. A special case of new family is the two-sided Topp-Leone Weibull distribution. This distribution used the two-sided Topp-Leone distribution as a generator for the Weibull distribution. The two-sided Topp-Leone Weibull distribution is presented in several shapes of distributions such as decreasing, unimodal, and bimodal which make this distribution more than flexible than the Weibull distribution. Its quantile function is presented. The parameter estimation method by using maximum likelihood estimation is discussed. The proposed distribution is applied to the strength data set, remission times of bladder cancer patients data set and time to failure of turbocharger data set. We compare the proposed distribution to the Topp-Leone Generated Weibull distribution. In conclusion, the two-sided Topp-Leone Weibull distribution performs similarly as the Topp-Leone Generated Weibull distribution in the first and second data sets. However, the proposed distribution can perform better than fit to Topp-Leone Generated Weibull distribution for the other.

Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories

PubMed Central

2016-01-01

The analysis of amino acids in meteorites dates back over 50 years; however, it is only in recent years that research has expanded beyond investigations of a narrow set of meteorite groups (exemplified by the Murchison meteorite) into meteorites of other types and classes. These new studies have shown a wide diversity in the abundance and distribution of amino acids across carbonaceous chondrite groups, highlighting the role of parent body processes and composition in the creation, preservation, or alteration of amino acids. Although most chiral amino acids are racemic in meteorites, the enantiomeric distribution of some amino acids, particularly of the nonprotein amino acid isovaline, has also been shown to vary both within certain meteorites and across carbonaceous meteorite groups. Large l-enantiomeric excesses of some extraterrestrial protein amino acids (up to ∼60%) have also been observed in rare cases and point to nonbiological enantiomeric enrichment processes prior to the emergence of life. In this Outlook, we review these recent meteoritic analyses, focusing on variations in abundance, structural distributions, and enantiomeric distributions of amino acids and discussing possible explanations for these observations and the potential for future work. PMID:27413780

Stable Membrane-Association of mRNAs in Etiolated, Greening and Mature Plastids.

PubMed

Legen, Julia; Schmitz-Linneweber, Christian

2017-08-31

Chloroplast genes are transcribed as polycistronic precursor RNAs that give rise to a multitude of processing products down to monocistronic forms. Translation of these mRNAs is realized by bacterial type 70S ribosomes. A larger fraction of these ribosomes is attached to chloroplast membranes. This study analyzed transcriptome-wide distribution of plastid mRNAs between soluble and membrane fractions of purified plastids using microarray analyses and validating RNA gel blot hybridizations. To determine the impact of light on mRNA localization, we used etioplasts, greening plastids and mature chloroplasts from Zea mays as a source for membrane and soluble extracts. The results show that the three plastid types display an almost identical distribution of RNAs between the two organellar fractions, which is confirmed by quantitative RNA gel blot analyses. Furthermore, they reveal that different RNAs processed from polycistronic precursors show transcript-autonomous distribution between stroma and membrane fractions. Disruption of ribosomes leads to release of mRNAs from membranes, demonstrating that attachment is likely a direct consequence of translation. We conclude that plastid mRNA distribution is a stable feature of different plastid types, setting up rapid chloroplast translation in any plastid type.

Species distribution models for a migratory bird based on citizen science and satellite tracking data

USGS Publications Warehouse

Coxen, Christopher L.; Frey, Jennifer K.; Carleton, Scott A.; Collins, Daniel P.

2017-01-01

Species distribution models can provide critical baseline distribution information for the conservation of poorly understood species. Here, we compared the performance of band-tailed pigeon (Patagioenas fasciata) species distribution models created using Maxent and derived from two separate presence-only occurrence data sources in New Mexico: 1) satellite tracked birds and 2) observations reported in eBird basic data set. Both models had good accuracy (test AUC > 0.8 and True Skill Statistic > 0.4), and high overlap between suitability scores (I statistic 0.786) and suitable habitat patches (relative rank 0.639). Our results suggest that, at the state-wide level, eBird occurrence data can effectively model similar species distributions as satellite tracking data. Climate change models for the band-tailed pigeon predict a 35% loss in area of suitable climate by 2070 if CO2 emissions drop to 1990 levels by 2100, and a 45% loss by 2070 if we continue current CO2 emission levels through the end of the century. These numbers may be conservative given the predicted increase in drought, wildfire, and forest pest impacts to the coniferous forests the species inhabits in New Mexico. The northern portion of the species’ range in New Mexico is predicted to be the most viable through time.

Using patient lists to add value to integrated data repositories.

PubMed

Wade, Ted D; Zelarney, Pearlanne T; Hum, Richard C; McGee, Sylvia; Batson, Deborah H

2014-12-01

Patient lists are project-specific sets of patients that can be queried in integrated data repositories (IDR's). By allowing a set of patients to be an addition to the qualifying conditions of a query, returned results will refer to, and only to, that set of patients. We report a variety of use cases for such lists, including: restricting retrospective chart review to a defined set of patients; following a set of patients for practice management purposes; distributing "honest-brokered" (deidentified) data; adding phenotypes to biosamples; and enhancing the content of study or registry data. Among the capabilities needed to implement patient lists in an IDR are: capture of patient identifiers from a query and feedback of these into the IDR; the existence of a permanent internal identifier in the IDR that is mappable to external identifiers; the ability to add queryable attributes to the IDR; the ability to merge data from multiple queries; and suitable control over user access and de-identification of results. We implemented patient lists in a custom IDR of our own design. We reviewed capabilities of other published IDRs for focusing on sets of patients. The widely used i2b2 IDR platform has various ways to address patient sets, and it could be modified to add the low-overhead version of patient lists that we describe. Copyright © 2014 Elsevier Inc. All rights reserved.

Defining the ecologically relevant mixed-layer depth for Antarctica's coastal seas

NASA Astrophysics Data System (ADS)

Carvalho, Filipa; Kohut, Josh; Oliver, Matthew J.; Schofield, Oscar

2017-01-01

Mixed-layer depth (MLD) has been widely linked to phytoplankton dynamics in Antarctica's coastal regions; however, inconsistent definitions have made intercomparisons among region-specific studies difficult. Using a data set with over 20,000 water column profiles corresponding to 32 Slocum glider deployments in three coastal Antarctic regions (Ross Sea, Amundsen Sea, and West Antarctic Peninsula), we evaluated the relationship between MLD and phytoplankton vertical distribution. Comparisons of these MLD estimates to an applied definition of phytoplankton bloom depth, as defined by the deepest inflection point in the chlorophyll profile, show that the maximum of buoyancy frequency is a good proxy for an ecologically relevant MLD. A quality index is used to filter profiles where MLD is not determined. Despite the different regional physical settings, we found that the MLD definition based on the maximum of buoyancy frequency best describes the depth to which phytoplankton can be mixed in Antarctica's coastal seas.

Correlation of microphotoluminescence spectroscopy, scanning transmission electron microscopy, and atom probe tomography on a single nano-object containing an InGaN/GaN multiquantum well system.

PubMed

Rigutti, Lorenzo; Blum, Ivan; Shinde, Deodatta; Hernández-Maldonado, David; Lefebvre, Williams; Houard, Jonathan; Vurpillot, François; Vella, Angela; Tchernycheva, Maria; Durand, Christophe; Eymery, Joël; Deconihout, Bernard

2014-01-08

A single nanoscale object containing a set of InGaN/GaN nonpolar multiple-quantum wells has been analyzed by microphotoluminescence spectroscopy (μPL), high-resolution scanning transmission electron microscopy (HR-STEM) and atom probe tomography (APT). The correlated measurements constitute a rich and coherent set of data supporting the interpretation that the observed μPL narrow emission lines, polarized perpendicularly to the crystal c-axis and with energies in the interval 2.9-3.3 eV, are related to exciton states localized in potential minima induced by the irregular 3D In distribution within the quantum well (QW) planes. This novel method opens up interesting perspectives, as it will be possible to apply it on a wide class of quantum confining emitters and nano-objects.

[Not Available].

PubMed

Mokeddem, Diab; Khellaf, Abdelhafid

2009-01-01

Optimal design problem are widely known by their multiple performance measures that are often competing with each other. In this paper, an optimal multiproduct batch chemical plant design is presented. The design is firstly formulated as a multiobjective optimization problem, to be solved using the well suited non dominating sorting genetic algorithm (NSGA-II). The NSGA-II have capability to achieve fine tuning of variables in determining a set of non dominating solutions distributed along the Pareto front in a single run of the algorithm. The NSGA-II ability to identify a set of optimal solutions provides the decision-maker DM with a complete picture of the optimal solution space to gain better and appropriate choices. Then an outranking with PROMETHEE II helps the decision-maker to finalize the selection of a best compromise. The effectiveness of NSGA-II method with multiojective optimization problem is illustrated through two carefully referenced examples.

SMART-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios

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

Hodge, Bri-Mathias; Palmintier, Bryan

This presentation provides an overview of full-scale, high-quality, synthetic distribution system data set(s) for testing distribution automation algorithms, distributed control approaches, ADMS capabilities, and other emerging distribution technologies.

snpGeneSets: An R Package for Genome-Wide Study Annotation

PubMed Central

Mei, Hao; Li, Lianna; Jiang, Fan; Simino, Jeannette; Griswold, Michael; Mosley, Thomas; Liu, Shijian

2016-01-01

Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/. PMID:27807048

ZERODUR strength modeling with Weibull statistical distributions

NASA Astrophysics Data System (ADS)

Hartmann, Peter

2016-07-01

The decisive influence on breakage strength of brittle materials such as the low expansion glass ceramic ZERODUR is the surface condition. For polished or etched surfaces it is essential if micro cracks are present and how deep they are. Ground surfaces have many micro cracks caused by the generation process. Here only the depths of the micro cracks are relevant. In any case presence and depths of micro cracks are statistical by nature. The Weibull distribution is the model used traditionally for the representation of such data sets. It is based on the weakest link ansatz. The use of the two or three parameter Weibull distribution for data representation and reliability prediction depends on the underlying crack generation mechanisms. Before choosing the model for a specific evaluation, some checks should be done. Is there only one mechanism present or is it to be expected that an additional mechanism might contribute deviating results? For ground surfaces the main mechanism is the diamond grains' action on the surface. However, grains breaking from their bonding might be moved by the tool across the surface introducing a slightly deeper crack. It is not to be expected that these scratches follow the same statistical distribution as the grinding process. Hence, their description with the same distribution parameters is not adequate. Before including them a dedicated discussion should be performed. If there is additional information available influencing the selection of the model, for example the existence of a maximum crack depth, this should be taken into account also. Micro cracks introduced by small diamond grains on tools working with limited forces cannot be arbitrarily deep. For data obtained with such surfaces the existence of a threshold breakage stress should be part of the hypothesis. This leads to the use of the three parameter Weibull distribution. A differentiation based on the data set alone without preexisting information is possible but requires a large data set. With only 20 specimens per sample such differentiation is not possible. This requires 100 specimens per set, the more the better. The validity of the statistical evaluation methods is discussed with several examples. These considerations are of special importance because of their consequences on the prognosis methods and results. Especially the use of the two parameter Weibull distribution for high strength surfaces has led to non-realistic results. Extrapolation down to low acceptable probability of failure covers a wide range without data points existing and is mainly influenced by the slope determined by the high strength specimens. In the past this misconception has prevented the use of brittle materials for stress loads, which they could have endured easily.

Alternative Setting-Wide Positive Behavior Support

ERIC Educational Resources Information Center

Simonsen, Brandi; Jeffrey-Pearsall, Jennifer; Sugai, George; McCurdy, Barry

2011-01-01

School-wide positive behavior support (SWPBS) has an established evidence base in general education settings, and emerging evidence suggests that SWPBS may be effective in alternative settings (e.g., alternative, residential, or hospital schools; psychiatric hospitals). Given the intense educational and behavioral needs of students typically…

Mapping of Boulder Ejecta around Late Amazonian Impact Craters on Mars

NASA Astrophysics Data System (ADS)

Hood, D.; Karunatillake, S.; Fassett, C.

2017-12-01

Detailed mapping of boulders in Martian crater ejecta is lacking due to the large burden of manual boulder counting. Using a newly-developed boulder recognition algorithm, we map the ejected blocks of four Late Amazonian craters. These four craters: Tomini B (125° E, 15° N), Zumba (227° E, -9° N), Gratteri (200° E, -18° N), and an unnamed crater at 230° E, -23° N, have crater ages spanning from as young as 200 ka to as old as 17 Ma [Hartmann et al., 2010; Schon and Head, 2012]. Both Zumba and the unnamed crater are in Daedalia Planum but have very distinct ages making these ideal targets to examine boulder distribution variability within the same target material. Gratteri and Tomini B, by contrast, are in less distinct geologic settings with the impacted material being of mixed fluvial-volcanic origin. For these craters we locate and measure all meter-scale boulders outside of the crater rim and up to 3 crater radii away. Following the method described by Krishna and Kumar [Krishna and Kumar, 2016], we divide the area outside the crater basin into 36 angular sectors, each being 10° wide, and 30 radial sectors 1/10 crater radii wide up to 3 crater radii from the rim. These divisions enable investigation into the distribution of ejected boulders as a function of both direction and distance. We compute the cumulative size-frequency distribution, normalized to the surface area of the observed region, using an exponential fit, as N(a) = Ce-ab, where C is a constant equaling the total number of distinct boulders, a is the average diameter of each boulder, N(a) is the number of boulders of size not less than a, and b is the fit parameter (e.g.[Golombek and Rapp, 1997]). In addition, we also compute the spatial distribution of boulder shapes quantified as elongation: 1-width/height. With the distributions well-described, we compare the spatial distribution of boulders around these four craters to understand how target lithology and age affect the observed distributions.

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

PubMed Central

Holt, Carson; Campbell, Michael; Keays, David A.; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; T. Domyan, Eric; Suh, Alexander; Warren, Wesley C.; Yandell, Mark; Gilbert, M. Thomas P.; Shapiro, Michael D.

2018-01-01

The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general. PMID:29519939

Strategic positioning for nursing excellence in health systems: insights from chief nursing executives.

PubMed

Arnold, Lauren; Drenkard, Karen; Ela, Sue; Goedken, Jolene; Hamilton, Connie; Harris, Carla; Holecek, Nancy; White, Maureen

2006-01-01

The emergence of health systems as a dominant structure for organizing healthcare has stimulated the development of health system chief nursing executive (CNE) positions. These positions have large spans of control, requiring CNEs to balance a wide range of responsibilities, making them accountable for fiscal management, quality of care, compliance, and contributing to organizational growth. As such the CNE is required to use principles of distributive justice to guide priority setting and decision making. This review addresses important questions about CNE system integration strategies, strategic priorities, and organizational positioning as they attempt to fulfill their ethical responsibilities to patients and the nurses they serve.

A pricing rule for affiliate transactions: Room for consensus

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

Costello, K.W.

1998-12-01

Because it conforms to politically acceptable notions of fairness, state and federal regulators have relied heavily on the concept of fully distributed cost to govern affiliate transactions. This should be leavened by alternative transfer-pricing measures to balance the goals of economic efficiency and fairness. This discussion, particularly the principles set down, although focusing on products or services, is also relevant to the outright sale of assets by a utility to an affiliate or vice versa. The author also proposes language for the pricing of affiliate transactions that attempts to accommodate the widely divergent positions currently being debated in the regulatorymore » arena.« less

The mechanical behavior of metal alloys with grain size distribution in a wide range of strain rates

NASA Astrophysics Data System (ADS)

Skripnyak, V. A.; Skripnyak, V. V.; Skripnyak, E. G.

2017-12-01

The paper discusses a multiscale simulation approach for the construction of grain structure of metals and alloys, providing high tensile strength with ductility. This work compares the mechanical behavior of light alloys and the influence of the grain size distribution in a wide range of strain rates. The influence of the grain size distribution on the inelastic deformation and fracture of aluminium and magnesium alloys is investigated by computer simulations in a wide range of strain rates. It is shown that the yield stress depends on the logarithm of the normalized strain rate for light alloys with a bimodal grain distribution and coarse-grained structure.

“Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups

PubMed Central

Cantinelli, Thomas; Chenal-Francisque, Viviane; Diancourt, Laure; Frezal, Lise; Leclercq, Alexandre; Wirth, Thierry

2013-01-01

The food-borne pathogen Listeria monocytogenes is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how “epidemic clones” should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define L. monocytogenes clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the “epidemic clone” denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space. PMID:24006010

Toward a panoramic perspective of the association between environmental factors and cardiovascular disease: An environment-wide association study from National Health and Nutrition Examination Survey 1999-2014.

PubMed

Zhuang, Xiaodong; Guo, Yue; Ni, Ao; Yang, Daya; Liao, Lizhen; Zhang, Shaozhao; Zhou, Huimin; Sun, Xiuting; Wang, Lichun; Wang, Xueqin; Liao, Xinxue

2018-06-04

An environment-wide association study (EWAS) may be useful to comprehensively test and validate associations between environmental factors and cardiovascular disease (CVD) in an unbiased manner. Data from National Health and Nutrition Examination Survey (1999-2014) were randomly 50:50 spilt into training set and testing set. CVD was ascertained by a self-reported diagnosis of myocardial infarction, coronary heart disease or stroke. We performed multiple linear regression analyses associating 203 environmental factors and 132 clinical phenotypes with CVD in training set (false discovery rate < 5%) and significant factors were validated in the testing set (P < 0.05). Random forest (RF) model was used for multicollinearity elimination and variable importance ranking. Discriminative power of factors for CVD was calculated by area under the receiver operating characteristic (AUROC). Overall, 43,568 participants with 4084 (9.4%) CVD were included. After adjusting for age, sex, race, body mass index, blood pressure and socio-economic level, we identified 5 environmental variables and 19 clinical phenotypes associated with CVD in training and testing dataset. Top five factors in RF importance ranking were: waist, glucose, uric acid, and red cell distribution width and glycated hemoglobin. AUROC of the RF model was 0.816 (top 5 factors) and 0.819 (full model). Sensitivity analyses reveal no specific moderators of the associations. Our systematic evaluation provides new knowledge on the complex array of environmental correlates of CVD. These identified correlates may serve as a complementary approach to CVD risk assessment. Our findings need to be probed in further observational and interventional studies. Copyright © 2018. Published by Elsevier Ltd.

Global Conservation Priorities for Marine Turtles

PubMed Central

Wallace, Bryan P.; DiMatteo, Andrew D.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Mortimer, Jeanne A.; Seminoff, Jeffrey A.; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jérôme; Bowen, Brian W.; Briseño Dueñas, Raquel; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Finkbeiner, Elena M.; Girard, Alexandre; Girondot, Marc; Hamann, Mark; Hurley, Brendan J.; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

2011-01-01

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a “conservation priorities portfolio” system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa. PMID:21969858

Transverse momentum dependent (TMD) parton distribution functions generated in the modified DGLAP formalism based on the valence-like distributions

NASA Astrophysics Data System (ADS)

Hosseinkhani, H.; Modarres, M.; Olanj, N.

2017-07-01

Transverse momentum dependent (TMD) parton distributions, also referred to as unintegrated parton distribution functions (UPDFs), are produced via the Kimber-Martin-Ryskin (KMR) prescription. The GJR08 set of parton distribution functions (PDFs) which are based on the valence-like distributions is used, at the leading order (LO) and the next-to-leading order (NLO) approximations, as inputs of the KMR formalism. The general and the relative behaviors of the generated TMD PDFs at LO and NLO and their ratios in a wide range of the transverse momentum values, i.e. kt2 = 10, 102, 104 and 108GeV2 are investigated. It is shown that the properties of the parent valence-like PDFs are imprinted on the daughter TMD PDFs. Imposing the angular ordering constraint (AOC) leads to the dynamical variable limits on the integrals which in turn increase the contributions from the lower scales at lower kt2. The results are compared with our previous studies based on the MSTW2008 input PDFs and it is shown that the present calculation gives flatter TMD PDFs. Finally, a comparison of longitudinal structure function (FL) is made by using the produced TMD PDFs and those that were generated through the MSTW2008-LO PDF from our previous work and the corresponding data from H1 and ZEUS collaborations and a reasonable agreement is found.

Universal Distribution of Litter Decay Rates

NASA Astrophysics Data System (ADS)

Forney, D. C.; Rothman, D. H.

2008-12-01

Degradation of litter is the result of many physical, chemical and biological processes. The high variability of these processes likely accounts for the progressive slowdown of decay with litter age. This age dependence is commonly thought to result from the superposition of processes with different decay rates k. Here we assume an underlying continuous yet unknown distribution p(k) of decay rates [1]. To seek its form, we analyze the mass-time history of 70 LIDET [2] litter data sets obtained under widely varying conditions. We construct a regularized inversion procedure to find the best fitting distribution p(k) with the least degrees of freedom. We find that the resulting p(k) is universally consistent with a lognormal distribution, i.e.~a Gaussian distribution of log k, characterized by a dataset-dependent mean and variance of log k. This result is supported by a recurring observation that microbial populations on leaves are log-normally distributed [3]. Simple biological processes cause the frequent appearance of the log-normal distribution in ecology [4]. Environmental factors, such as soil nitrate, soil aggregate size, soil hydraulic conductivity, total soil nitrogen, soil denitrification, soil respiration have been all observed to be log-normally distributed [5]. Litter degradation rates depend on many coupled, multiplicative factors, which provides a fundamental basis for the lognormal distribution. Using this insight, we systematically estimated the mean and variance of log k for 512 data sets from the LIDET study. We find the mean strongly correlates with temperature and precipitation, while the variance appears to be uncorrelated with main environmental factors and is thus likely more correlated with chemical composition and/or ecology. Results indicate the possibility that the distribution in rates reflects, at least in part, the distribution of microbial niches. [1] B. P. Boudreau, B.~R. Ruddick, American Journal of Science,291, 507, (1991). [2] M. Harmon, Forest Science Data Bank: TD023 [Database]. LTER Intersite Fine Litter Decomposition Experiment (LIDET): Long-Term Ecological Research, (2007). [3] G.~A. Beattie, S.~E. Lindow, Phytopathology 89, 353 (1999). [4] R.~A. May, Ecology and Evolution of Communities/, A pattern of Species Abundance and Diversity, 81 (1975). [5] T.~B. Parkin, J.~A. Robinson, Advances in Soil Science 20, Analysis of Lognormal Data, 194 (1992).

The distribution of hot spots

NASA Technical Reports Server (NTRS)

Stefanick, M.; Jurdy, D. M.

1984-01-01

Statistical analyses are compared for two published hot spot data sets, one minimal set of 42 and another larger set of 117, using three different approaches. First, the earths surface is divided into 16 equal-area fractions and the observed distribution of hot spots among them is analyzed using chi-square tests. Second, cumulative distributions about the principal axes of the hot spot inertia tensor are used to describe hot spot distribution. Finally, a hot spot density function is constructed for each of the two hot spot data sets. The methods all indicate that hot spots have a nonuniform distribution, even when statistical fluctuations are considered. To the first order, hot spots are concentrated on one half of of the earth's surface area; within that portion, the distribution is consistent with a uniform distribution. The observed hot spot densities for neither data set are explained solely by plate speed.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

PubMed Central

Vergara, María; Basto, Mafalda P.; Madeira, María José; Gómez-Moliner, Benjamín J.; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species. PMID:26222680

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

PubMed

Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Software architecture for a distributed real-time system in Ada, with application to telerobotics

NASA Technical Reports Server (NTRS)

Olsen, Douglas R.; Messiora, Steve; Leake, Stephen

1992-01-01

The architecture structure and software design methodology presented is described in the context of telerobotic application in Ada, specifically the Engineering Test Bed (ETB), which was developed to support the Flight Telerobotic Servicer (FTS) Program at GSFC. However, the nature of the architecture is such that it has applications to any multiprocessor distributed real-time system. The ETB architecture, which is a derivation of the NASA/NBS Standard Reference Model (NASREM), defines a hierarchy for representing a telerobot system. Within this hierarchy, a module is a logical entity consisting of the software associated with a set of related hardware components in the robot system. A module is comprised of submodules, which are cyclically executing processes that each perform a specific set of functions. The submodules in a module can run on separate processors. The submodules in the system communicate via command/status (C/S) interface channels, which are used to send commands down and relay status back up the system hierarchy. Submodules also communicate via setpoint data links, which are used to transfer control data from one submodule to another. A submodule invokes submodule algorithms (SMA's) to perform algorithmic operations. Data that describe or models a physical component of the system are stored as objects in the World Model (WM). The WM is a system-wide distributed database that is accessible to submodules in all modules of the system for creating, reading, and writing objects.

Confounding adjustment in comparative effectiveness research conducted within distributed research networks.

PubMed

Toh, Sengwee; Gagne, Joshua J; Rassen, Jeremy A; Fireman, Bruce H; Kulldorff, Martin; Brown, Jeffrey S

2013-08-01

A distributed research network (DRN) of electronic health care databases, in which data reside behind the firewall of each data partner, can support a wide range of comparative effectiveness research (CER) activities. An essential component of a fully functional DRN is the capability to perform robust statistical analyses to produce valid, actionable evidence without compromising patient privacy, data security, or proprietary interests. We describe the strengths and limitations of different confounding adjustment approaches that can be considered in observational CER studies conducted within DRNs, and the theoretical and practical issues to consider when selecting among them in various study settings. Several methods can be used to adjust for multiple confounders simultaneously, either as individual covariates or as confounder summary scores (eg, propensity scores and disease risk scores), including: (1) centralized analysis of patient-level data, (2) case-centered logistic regression of risk set data, (3) stratified or matched analysis of aggregated data, (4) distributed regression analysis, and (5) meta-analysis of site-specific effect estimates. These methods require different granularities of information be shared across sites and afford investigators different levels of analytic flexibility. DRNs are growing in use and sharing of highly detailed patient-level information is not always feasible in DRNs. Methods that incorporate confounder summary scores allow investigators to adjust for a large number of confounding factors without the need to transfer potentially identifiable information in DRNs. They have the potential to let investigators perform many analyses traditionally conducted through a centralized dataset with detailed patient-level information.

Seascape models reveal places to focus coastal fisheries management.

PubMed

Stamoulis, Kostantinos A; Delevaux, Jade M S; Williams, Ivor D; Poti, Matthew; Lecky, Joey; Costa, Bryan; Kendall, Matthew S; Pittman, Simon J; Donovan, Mary K; Wedding, Lisa M; Friedlander, Alan M

2018-06-01

To design effective marine reserves and support fisheries, more information on fishing patterns and impacts for targeted species is needed, as well as better understanding of their key habitats. However, fishing impacts vary geographically and are difficult to disentangle from other factors that influence targeted fish distributions. We developed a set of fishing effort and habitat layers at high resolution and employed machine learning techniques to create regional-scale seascape models and predictive maps of biomass and body length of targeted reef fishes for the main Hawaiian Islands. Spatial patterns of fishing effort were shown to be highly variable and seascape models indicated a low threshold beyond which targeted fish assemblages were severely impacted. Topographic complexity, exposure, depth, and wave power were identified as key habitat variables that influenced targeted fish distributions and defined productive habitats for reef fisheries. High targeted reef fish biomass and body length were found in areas not easily accessed by humans, while model predictions when fishing effort was set to zero showed these high values to be more widely dispersed among suitable habitats. By comparing current targeted fish distributions with those predicted when fishing effort was removed, areas with high recovery potential on each island were revealed, with average biomass recovery of 517% and mean body length increases of 59% on Oahu, the most heavily fished island. Spatial protection of these areas would aid recovery of nearshore coral reef fisheries. © 2018 by the Ecological Society of America.

Ecological distribution and population physiology defined by proteomics in a natural microbial community

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

Muller, R; Denef, Vincent; Kalnejals, Linda

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism smore » metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ« less

On the improvement for charging large-scale flexible electrostatic actuators

NASA Astrophysics Data System (ADS)

Liao, Hsu-Ching; Chen, Han-Long; Su, Yu-Hao; Chen, Yu-Chi; Ko, Wen-Ching; Liou, Chang-Ho; Wu, Wen-Jong; Lee, Chih-Kung

2011-04-01

Recently, the development of flexible electret based electrostatic actuator has been widely discussed. The devices was shown to have high sound quality, energy saving, flexible structure and can be cut to any shape. However, achieving uniform charge on the electret diaphragm is one of the most critical processes needed to have the speaker ready for large-scale production. In this paper, corona discharge equipment contains multi-corona probes and grid bias was set up to inject spatial charges within the electret diaphragm. The optimal multi-corona probes system was adjusted to achieve uniform charge distribution of electret diaphragm. The processing conditions include the distance between the corona probes, the voltages of corona probe and grid bias, etc. We assembled the flexible electret loudspeakers first and then measured their sound pressure and beam pattern. The uniform charge distribution within the electret diaphragm based flexible electret loudspeaker provided us with the opportunity to shape the loudspeaker arbitrarily and to tailor the sound distribution per specifications request. Some of the potential futuristic applications for this device such as sound poster, smart clothes, and sound wallpaper, etc. were discussed as well.

Ionization competition effects on population distribution and radiative opacity of mixture plasmas

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

Li, Yongjun; Gao, Cheng; Tian, Qinyun

2015-11-15

Ionization competition arising from the electronic shell structures of various atomic species in the mixture plasmas was investigated, taking SiO{sub 2} as an example. Using a detailed-level-accounting approximation, we studied the competition effects on the charge state population distribution and spectrally resolved and Planck and Rosseland mean radiative opacities of mixture plasmas. A set of coupled equations for ionization equilibria that include all components of the mixture plasmas are solved to determine the population distributions. For a given plasma density, competition effects are found at three distinct temperature ranges, corresponding to the ionization of M-, L-, and K-shell electrons ofmore » Si. Taking the effects into account, the spectrally resolved and Planck and Rosseland mean opacities are systematically investigated over a wide range of plasma densities and temperatures. For a given mass density, the Rosseland mean decreases monotonically with plasma temperature, whereas Planck mean does not. Although the overall trend is a decrease, the Planck mean increases over a finite intermediate temperature regime. A comparison with the available experimental and theoretical results is made.« less

Ecological distribution and population physiology defined by proteomics in a natural microbial community

USGS Publications Warehouse

Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

2010-01-01

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

The effect of signal variability on the histograms of anthropomorphic channel outputs: factors resulting in non-normally distributed data

NASA Astrophysics Data System (ADS)

Elshahaby, Fatma E. A.; Ghaly, Michael; Jha, Abhinav K.; Frey, Eric C.

2015-03-01

Model Observers are widely used in medical imaging for the optimization and evaluation of instrumentation, acquisition parameters and image reconstruction and processing methods. The channelized Hotelling observer (CHO) is a commonly used model observer in nuclear medicine and has seen increasing use in other modalities. An anthropmorphic CHO consists of a set of channels that model some aspects of the human visual system and the Hotelling Observer, which is the optimal linear discriminant. The optimality of the CHO is based on the assumption that the channel outputs for data with and without the signal present have a multivariate normal distribution with equal class covariance matrices. The channel outputs result from the dot product of channel templates with input images and are thus the sum of a large number of random variables. The central limit theorem is thus often used to justify the assumption that the channel outputs are normally distributed. In this work, we aim to examine this assumption for realistically simulated nuclear medicine images when various types of signal variability are present.

Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti.

PubMed

Rašić, Gordana; Filipović, Igor; Weeks, Andrew R; Hoffmann, Ary A

2014-04-11

Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. In particular, the delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). We aimed to characterize the new SNP set and to test the resolution against previously described microsatellite markers in detecting broad and fine-scale genetic patterns in Ae. aegypti. We developed bioinformatics tools that support the customization of restriction enzyme-based protocols for SNP discovery. We showed that our approach for RAD library construction achieves unbiased genome representation that reflects true evolutionary processes. In Ae. aegypti samples from three continents we identified more than 18,000 putative SNPs. They were widely distributed across the three Ae. aegypti chromosomes, with 47.9% found in intergenic regions and 17.8% in exons of over 2,300 genes. Pattern of their imputed effects in ORFs and UTRs were consistent with those found in a recent transcriptome study. We demonstrated that individual mosquitoes from Indonesia, Australia, Vietnam and Brazil can be assigned with a very high degree of confidence to their region of origin using a large SNP panel. We also showed that familial relatedness of samples from a 0.4 km2 area could be confidently established with a subset of SNPs. Using a cost-effective customized RAD sequencing approach supported by our bioinformatics tools, we characterized over 18,000 SNPs in field samples of the dengue fever mosquito Ae. aegypti. The variants were annotated and positioned onto the three Ae. aegypti chromosomes. The new SNP set provided much greater resolution in detecting population structure and estimating fine-scale relatedness than a set of polymorphic microsatellites. RAD-based markers demonstrate great potential to advance our understanding of mosquito population processes, critical for implementing new control measures against this major disease vector.

Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis

PubMed Central

Hill, Andrew; Loh, Po-Ru; Bharadwaj, Ragu B.; Pons, Pascal; Shang, Jingbo; Guinan, Eva; Lakhani, Karim; Kilty, Iain

2017-01-01

Abstract Background: The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. Results: Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project. Conclusions: Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics. PMID:28327993

Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.

PubMed

Hill, Andrew; Loh, Po-Ru; Bharadwaj, Ragu B; Pons, Pascal; Shang, Jingbo; Guinan, Eva; Lakhani, Karim; Kilty, Iain; Jelinsky, Scott A

2017-05-01

The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project. Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics. © The Author 2017. Published by Oxford University Press.

Efficient Use of Distributed Systems for Scientific Applications

NASA Technical Reports Server (NTRS)

Taylor, Valerie; Chen, Jian; Canfield, Thomas; Richard, Jacques

2000-01-01

Distributed computing has been regarded as the future of high performance computing. Nationwide high speed networks such as vBNS are becoming widely available to interconnect high-speed computers, virtual environments, scientific instruments and large data sets. One of the major issues to be addressed with distributed systems is the development of computational tools that facilitate the efficient execution of parallel applications on such systems. These tools must exploit the heterogeneous resources (networks and compute nodes) in distributed systems. This paper presents a tool, called PART, which addresses this issue for mesh partitioning. PART takes advantage of the following heterogeneous system features: (1) processor speed; (2) number of processors; (3) local network performance; and (4) wide area network performance. Further, different finite element applications under consideration may have different computational complexities, different communication patterns, and different element types, which also must be taken into consideration when partitioning. PART uses parallel simulated annealing to partition the domain, taking into consideration network and processor heterogeneity. The results of using PART for an explicit finite element application executing on two IBM SPs (located at Argonne National Laboratory and the San Diego Supercomputer Center) indicate an increase in efficiency by up to 36% as compared to METIS, a widely used mesh partitioning tool. The input to METIS was modified to take into consideration heterogeneous processor performance; METIS does not take into consideration heterogeneous networks. The execution times for these applications were reduced by up to 30% as compared to METIS. These results are given in Figure 1 for four irregular meshes with number of elements ranging from 30,269 elements for the Barth5 mesh to 11,451 elements for the Barth4 mesh. Future work with PART entails using the tool with an integrated application requiring distributed systems. In particular this application, illustrated in the document entails an integration of finite element and fluid dynamic simulations to address the cooling of turbine blades of a gas turbine engine design. It is not uncommon to encounter high-temperature, film-cooled turbine airfoils with 1,000,000s of degrees of freedom. This results because of the complexity of the various components of the airfoils, requiring fine-grain meshing for accuracy. Additional information is contained in the original.

A Reexamination of the Psychometric Properties of the "School-Wide Evaluation Tool" (SET)

ERIC Educational Resources Information Center

Vincent, Claudia; Spaulding, Scott; Tobin, Tary Jeanne

2010-01-01

As a follow-up to Horner et al., this study focuses on the internal consistency and validity of the School-wide Evaluation Tool (SET) at all school levels. Analyzing SET data from 833 elementary, 264 middle, and 93 high schools, the authors focused on (a) describing commonalities and differences in SET data across the school levels, (b) assessing…

Earth Science Data Archive and Access at the NASA/Goddard Space Flight Center Distributed Active Archive Center (DAAC)

NASA Technical Reports Server (NTRS)

Leptoukh, Gregory

1999-01-01

The Goddard Distributed Active Archive Center (DAAC), as an integral part of the Earth Observing System Data and Information System (EOSDIS), is the official source of data for several important earth remote sensing missions. These include the Sea-viewing Wide-Field-of-view Sensor (SeaWiFS) launched in August 1997, the Tropical Rainfall Measuring Mission (TRMM) launched in November 1997, and the Moderate Resolution Imaging Spectroradiometer (MODIS) scheduled for launch in mid 1999 as part of the EOS AM-1 instrumentation package. The data generated from these missions supports a host of users in the hydrological, land biosphere and oceanographic research and applications communities. The volume and nature of the data present unique challenges to an Earth science data archive and distribution system such as the DAAC. The DAAC system receives, archives and distributes a large number of standard data products on a daily basis, including data files that have been reprocessed with updated calibration data or improved analytical algorithms. A World Wide Web interface is provided allowing interactive data selection and automatic data subscriptions as distribution options. The DAAC also creates customized and value-added data products, which allow additional user flexibility and reduced data volume. Another significant part of our overall mission is to provide ancillary data support services and archive support for worldwide field campaigns designed to validate the results from the various satellite-derived measurements. In addition to direct data services, accompanying documentation, WWW links to related resources, support for EOSDIS data formats, and informed response to inquiries are routinely provided to users. The current GDAAC WWW search and order system is being restructured to provide users with a simplified, hierarchical access to data. Data Browsers have been developed for several data sets to aid users in ordering data. These Browsers allow users to specify spatial, temporal, and other parameter criteria in searching for and previewing data.

Study of Parameters Affecting the Level of Ultrasound Exposure with In Vitro Set-Ups

NASA Astrophysics Data System (ADS)

Leskinen, Jarkko J.; Hynynen, Kullervo

2010-03-01

Ultrasound (US) exposures are widely used with in vitro cell systems e.g. in stem cell and tissue engineering research. However, without the knowledge of factors affecting the level of US exposure, the outcome of the biological result may vary from test to test or even be misinterpreted. Thereby, some of the factors affecting in vitro US exposures were studied. The level of US exposure was characterized in standard commercial cell culturing plates. The temperature distributions were measured inside the wells using infrared camera and fine wire thermocouples, and pressure and intensity distributions using a laser vibrometer and a schlieren system. The measurements were made at operating frequency of around 1 MHz with varying temporal parameters and powers (up to 2 W of acoustic power). Heat accumulation between the wells varied up to 40-50% depending on the location of the well on the plate. This well-to-well variation was be linked to the activity of reporter plasmid on osteoblastic cells. Similar temperature variations within the wells were also measured. Small sub-wavelength change in the exposure distance or, respectively, liquid volume inside the well was found to alter the acoustic field in both magnitude and shape due the standing waves. The gathered data reveals the complexity of the acoustic field in a typical in vitro set-up and gives new information about the environment of the in vitro cells during US exposures. This data may be especially useful when US set-ups are designed or characterized.

Achnanthidium minutissimum (Bacillariophyta) valve deformities as indicators of metal enrichment in diverse widely-distributed freshwater habitats.

PubMed

Cantonati, Marco; Angeli, Nicola; Virtanen, Laura; Wojtal, Agata Z; Gabrieli, Jacopo; Falasco, Elisa; Lavoie, Isabelle; Morin, Soizic; Marchetto, Aldo; Fortin, Claude; Smirnova, Svetlana

2014-03-15

In the presence of different environmental stressors, diatoms can produce frustules presenting different types of deformities. Metals and trace elements are among the most common causes of these teratological forms. Metal enrichment in water bodies can be attributed to the geological setting of the area or to pollution. The widespread benthic diatom Achnanthidium minutissimum (ADMI) is one of the most metal-tolerant species. In the present study, ADMI teratologies were defined from samples taken from eight very diverse, widely-distributed inland-water habitats: streams affected by active and abandoned mining areas, a metal-contaminated stream, a spring in an old chalcopyrite mine, a mineral-water fountain, and a sediment core taken from a lake affected by metal contamination in the past. Deformed frustules of ADMI were characterised mainly by one (sometimes two) more or less bent off ending, conferring to the specimens a cymbelloid outline (cymbelliclinum-like teratology, CLT). Marked teratologies were distinguished from slight deformities. Hydrochemical analyses, including metals and trace elements, were carried out and enrichment factors (EF) relative to average crustal composition were calculated. To improve our knowledge on the potential of different metals and trace elements to trigger the occurrence of ADMI CLT, we carefully selected 15 springs out of 110 (CRENODAT dataset) where both ADMI and above-average metal or metalloid concentrations occurred, and re-analysed these samples. The results from the eight widely-distributed core sites as well as from the 15 selected CRENODAT springs led to the hypothesis that two metals (copper and zinc) and a metalloid (antimony) were the most likely triggers of ADMI CLT formation. From a quantitative point of view, it is worth noting that the lowest concentrations triggering ADMI CLT can be fairly low, particularly in the case of copper contamination. The antimony-rich site was characterised by a marked-teratology variant where both ends of ADMI were bent off. © 2013 Elsevier B.V. All rights reserved.

Comparison of low-altitude wind-shear statistics derived from measured and proposed standard wind profiles

NASA Technical Reports Server (NTRS)

Usry, J. W.

1983-01-01

Wind shear statistics were calculated for a simulated set of wind profiles based on a proposed standard wind field data base. Wind shears were grouped in altitude in altitude bands of 100 ft between 100 and 1400 ft and in wind shear increments of 0.025 knot/ft. Frequency distributions, means, and standard deviations for each altitude band were derived for the total sample were derived for both sets. It was found that frequency distributions in each altitude band for the simulated data set were more dispersed below 800 ft and less dispersed above 900 ft than those for the measured data set. Total sample frequency of occurrence for the two data sets was about equal for wind shear values between +0.075 knot/ft, but the simulated data set had significantly larger values for all wind shears outside these boundaries. It is shown that normal distribution in both data sets neither data set was normally distributed; similar results are observed from the cumulative frequency distributions.

Adaptive Set-Based Methods for Association Testing.

PubMed

Su, Yu-Chen; Gauderman, William James; Berhane, Kiros; Lewinger, Juan Pablo

2016-02-01

With a typical sample size of a few thousand subjects, a single genome-wide association study (GWAS) using traditional one single nucleotide polymorphism (SNP)-at-a-time methods can only detect genetic variants conferring a sizable effect on disease risk. Set-based methods, which analyze sets of SNPs jointly, can detect variants with smaller effects acting within a gene, a pathway, or other biologically relevant sets. Although self-contained set-based methods (those that test sets of variants without regard to variants not in the set) are generally more powerful than competitive set-based approaches (those that rely on comparison of variants in the set of interest with variants not in the set), there is no consensus as to which self-contained methods are best. In particular, several self-contained set tests have been proposed to directly or indirectly "adapt" to the a priori unknown proportion and distribution of effects of the truly associated SNPs in the set, which is a major determinant of their power. A popular adaptive set-based test is the adaptive rank truncated product (ARTP), which seeks the set of SNPs that yields the best-combined evidence of association. We compared the standard ARTP, several ARTP variations we introduced, and other adaptive methods in a comprehensive simulation study to evaluate their performance. We used permutations to assess significance for all the methods and thus provide a level playing field for comparison. We found the standard ARTP test to have the highest power across our simulations followed closely by the global model of random effects (GMRE) and a least absolute shrinkage and selection operator (LASSO)-based test. © 2015 WILEY PERIODICALS, INC.

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories

Treesearch

Mark J. Statham; James Murdoch; Jan Janecka; Keith B. Aubry; Ceiridwen J. Edwards; Carl D. Soulsbury; Oliver Berry; Zhenghuan Wang; David Harrison; Malcolm Pearch; Louise Tomsett; Judith Chupasko; Benjamin N. Sacks

2014-01-01

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world’s most widely distributed wild terrestrial carnivore. Analyses of 697 bp of...

Species Distribution Modelling of Aedes aegypti in two dengue-endemic regions of Pakistan.

PubMed

Fatima, Syeda Hira; Atif, Salman; Rasheed, Syed Basit; Zaidi, Farrah; Hussain, Ejaz

2016-03-01

Statistical tools are effectively used to determine the distribution of mosquitoes and to make ecological inferences about the vector-borne disease dynamics. In this study, we utilised species distribution models to understand spatial patterns of Aedes aegypti in two dengue-prevalent regions of Pakistan, Lahore and Swat. Species distribution models can potentially indicate the probability of suitability of Ae. aegypti once introduced to new regions like Swat, where invasion of this species is a recent phenomenon. The distribution of Ae. aegypti was determined by applying the MaxEnt algorithm on a set of potential environmental factors and species sample records. The ecological dependency of species on each environmental variable was analysed using response curves. We quantified the statistical performance of the models based on accuracy assessment and spatial predictions. Our results suggest that Ae. aegypti is widely distributed in Lahore. Human population density and urban infrastructure are primarily responsible for greater probability of mosquito occurrence in this region. In Swat, Ae. aegypti has clumped distribution, where urban patches provide refuge to the species in an otherwise hostile heterogeneous environment and road networks are assumed to have facilitated in passive-mediated dispersal of species. In Pakistan, Ae. aegypti is expanding its range northwards; this could be associated with rapid urbanisation, trade and travel. The main implication of this expansion is that more people are at risk of dengue fever in the northern highlands of Pakistan. © 2016 John Wiley & Sons Ltd.

Using sparse photometric data sets for asteroid lightcurve studies

NASA Astrophysics Data System (ADS)

Warner, Brian D.; Harris, Alan W.

2011-12-01

With the advent of wide-field imagers, it has become possible to conduct a photometric lightcurve survey of many asteroids simultaneously, either for that single purpose (e.g., Dermawan, B., Nakamura, T., Yoshida, F. [2011]. Publ. Astron. Soc. Japan 63, S555-S576; Masiero, J., Jedicke, R., Ďurech, J., Gwyn, S., Denneau, L., Larsen, J. [2009]. Icarus 204, 145-171), or as a part of a multipurpose survey (e.g., Pan-STARRS, LSST). Such surveys promise to yield photometric data for many thousands of asteroids, but these data sets will be “sparse” compared to most of those taken in a “targeted” mode directed to one asteroid at a time. We consider the potential limitations of sparse data sets using different sampling rates with respect to specific research questions that might be addressed with lightcurve data. For our study we created synthetic sparse data sets similar to those from wide-field surveys by generating more than 380,000 individual lightcurves that were combined into more than 47,000 composite lightcurves. The variables in generating the data included the number of observations per night, number of nights, noise, and the intervals between observations and nights, in addition to periods ranging from 0.1 to 400 h and amplitudes ranging from 0.1 to 2.0 mag. A Fourier analysis pipeline was used to find the period for each composite lightcurve and then review the derived period and period spectrum to gauge how well an automated analysis of sparse data sets would perform in finding the true period. For this part of the analysis, a normally distributed noise level of 0.03 mag was added to the data, regardless of amplitude, thus simulating a relatively high SNR for the observations. For the second part of the analysis, a smaller set of composite curves was generated with fixed core parameters of eight observations per night, 8 nights within a 14-day span, periods ranging from 2 to 6 h, and an amplitude of either 0.3 mag or 0.4 mag. Individual data sets using these fixed parameters added normally-distributed noise of 0.05, 0.1, or 0.2 mag. The analysis examined the success rates for finding the true period as the noise increased towards levels simulating data for objects close to sky background levels. After applying a filter to remove highly-ambiguous solution sets, the best chance for success was found to be when the true period was in the range of P ≈ 2-5 h and amplitudes were A ⩾ 0.5 mag. The solution sets for lightcurves with low amplitude, long periods, and/or those that were sampled too sparsely in comparison to the period were often too ambiguous to be considered reliable for statistical rotation studies. Analysis of slow rotators (P > 24 h) found that somewhat reasonable solutions of P < 6 h could be found for about 15-20% of those objects, even at higher amplitudes, indicating that the Fourier analysis had locked onto the noise in the data. Efforts to produce an automated pipeline to help determine an unambiguous (or nearly so) solution based on the period spectrum from the Fourier analysis were made. These proved unsuccessful because of the number of parameters that must be considered and the difficulties in assigning an objective weight to each one in finding a final result. Despite this initial failure, further attempts will be made to quantify the U rating system. Comparison of the synthetic data analysis results to those from two actual surveys shows a reasonable agreement between the two. A review of the pros and cons of sparse versus dense data sets shows that each has a significant role in future studies and that it will be critical to establish open lines of communications and data exchange between the deep wide-field sparse data surveys and dense data programs.

Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

PubMed Central

Bennett, Kristin P.

2014-01-01

We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

Port-O-Sim Object Simulation Application

NASA Technical Reports Server (NTRS)

Lanzi, Raymond J.

2009-01-01

Port-O-Sim is a software application that supports engineering modeling and simulation of launch-range systems and subsystems, as well as the vehicles that operate on them. It is flexible, distributed, object-oriented, and realtime. A scripting language is used to configure an array of simulation objects and link them together. The script is contained in a text file, but executed and controlled using a graphical user interface. A set of modules is defined, each with input variables, output variables, and settings. These engineering models can be either linked to each other or run as standalone. The settings can be modified during execution. Since 2001, this application has been used for pre-mission failure mode training for many Range Safety Scenarios. It contains range asset link analysis, develops look-angle data, supports sky-screen site selection, drives GPS (Global Positioning System) and IMU (Inertial Measurement Unit) simulators, and can support conceptual design efforts for multiple flight programs with its capacity for rapid six-degrees-of-freedom model development. Due to the assembly of various object types into one application, the application is applicable across a wide variety of launch range problem domains.

Worldwide Historical Estimates of Leaf Area Index, 1932-2000

NASA Technical Reports Server (NTRS)

Scurlock, J. M. O.; Asner, G. P.; Gower, S. T.

2001-01-01

Approximately 1000 published estimates of leaf area index (LAI) from nearly 400 unique field sites, covering the period 1932-2000, have been compiled into a single data set. LA1 is a key parameter for global and regional models of biosphere/atmosphere exchange of carbon dioxide, water vapor, and other materials. It also plays an integral role in determining the energy balance of the land surface. This data set provides a benchmark of typical values and ranges of LA1 for a variety of biomes and land cover types, in support of model development and validation of satellite-derived remote sensing estimates of LA1 and other vegetation parameters. The LA1 data are linked to a bibliography of over 300 originalsource references.This report documents the development of this data set, its contents, and its availability on the Internet from the Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics. Caution is advised in using these data, which were collected using a wide range of methodologies and assumptions that may not allow comparisons among sites.

A genome-wide association study identifies multiple loci associated with mathematics ability and disability

PubMed Central

Docherty, S J; Davis, O S P; Kovas, Y; Meaburn, E L; Dale, P S; Petrill, S A; Schalkwyk, L C; Plomin, R

2010-01-01

Numeracy is as important as literacy and exhibits a similar frequency of disability. Although its etiology is relatively poorly understood, quantitative genetic research has demonstrated mathematical ability to be moderately heritable. In this first genome-wide association study (GWAS) of mathematical ability and disability, 10 out of 43 single nucleotide polymorphism (SNP) associations nominated from two high- vs. low-ability (n = 600 10-year-olds each) scans of pooled DNA were validated (P < 0.05) in an individually genotyped sample of *2356 individuals spanning the entire distribution of mathematical ability, as assessed by teacher reports and online tests. Although the effects are of the modest sizes now expected for complex traits and require further replication, interesting candidate genes are implicated such as NRCAM which encodes a neuronal cell adhesion molecule. When combined into a set, the 10 SNPs account for 2.9% (F = 56.85; df = 1 and 1881; P = 7.277e–14) of the phenotypic variance. The association is linear across the distribution consistent with a quantitative trait locus (QTL) hypothesis; the third of children in our sample who harbour 10 or more of the 20 risk alleles identified are nearly twice as likely (OR = 1.96; df = 1; P = 3.696e–07) to be in the lowest performing 15% of the distribution. Our results correspond with those of quantitative genetic research in indicating that mathematical ability and disability are influenced by many genes generating small effects across the entire spectrum of ability, implying that more highly powered studies will be needed to detect and replicate these QTL associations. PMID:20039944

Insights into mountain precipitation and snowpack from a basin-scale wireless-sensor network

NASA Astrophysics Data System (ADS)

Zhang, Z.; Glaser, S.; Bales, R.; Conklin, M.; Rice, R.; Marks, D.

2017-08-01

A spatially distributed wireless-sensor network, installed across the 2154 km2 portion of the 5311 km2 American River basin above 1500 m elevation, provided spatial measurements of temperature, relative humidity, and snow depth in the Sierra Nevada, California. The network consisted of 10 sensor clusters, each with 10 measurement nodes, distributed to capture the variability in topography and vegetation cover. The sensor network captured significant spatial heterogeneity in rain versus snow precipitation for water-year 2014, variability that was not apparent in the more limited operational data. Using daily dew-point temperature to track temporal elevational changes in the rain-snow transition, the amount of snow accumulation at each node was used to estimate the fraction of rain versus snow. This resulted in an underestimate of total precipitation below the 0°C dew-point elevation, which averaged 1730 m across 10 precipitation events, indicating that measuring snow does not capture total precipitation. We suggest blending lower elevation rain gauge data with higher-elevation sensor-node data for each event to estimate total precipitation. Blended estimates were on average 15-30% higher than using either set of measurements alone. Using data from the current operational snow-pillow sites gives even lower estimates of basin-wide precipitation. Given the increasing importance of liquid precipitation in a warming climate, a strategy that blends distributed measurements of both liquid and solid precipitation will provide more accurate basin-wide precipitation estimates, plus spatial and temporal patters of snow accumulation and melt in a basin.

A genome-wide association study identifies multiple loci associated with mathematics ability and disability.

PubMed

Docherty, S J; Davis, O S P; Kovas, Y; Meaburn, E L; Dale, P S; Petrill, S A; Schalkwyk, L C; Plomin, R

2010-03-01

Numeracy is as important as literacy and exhibits a similar frequency of disability. Although its etiology is relatively poorly understood, quantitative genetic research has demonstrated mathematical ability to be moderately heritable. In this first genome-wide association study (GWAS) of mathematical ability and disability, 10 out of 43 single nucleotide polymorphism (SNP) associations nominated from two high- vs. low-ability (n = 600 10-year-olds each) scans of pooled DNA were validated (P < 0.05) in an individually genotyped sample of (*)2356 individuals spanning the entire distribution of mathematical ability, as assessed by teacher reports and online tests. Although the effects are of the modest sizes now expected for complex traits and require further replication, interesting candidate genes are implicated such as NRCAM which encodes a neuronal cell adhesion molecule. When combined into a set, the 10 SNPs account for 2.9% (F = 56.85; df = 1 and 1881; P = 7.277e-14) of the phenotypic variance. The association is linear across the distribution consistent with a quantitative trait locus (QTL) hypothesis; the third of children in our sample who harbour 10 or more of the 20 risk alleles identified are nearly twice as likely (OR = 1.96; df = 1; P = 3.696e-07) to be in the lowest performing 15% of the distribution. Our results correspond with those of quantitative genetic research in indicating that mathematical ability and disability are influenced by many genes generating small effects across the entire spectrum of ability, implying that more highly powered studies will be needed to detect and replicate these QTL associations.

Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters.

PubMed

Harrison, Luke B; Larsson, Hans C E

2015-03-01

Likelihood-based methods are commonplace in phylogenetic systematics. Although much effort has been directed toward likelihood-based models for molecular data, comparatively less work has addressed models for discrete morphological character (DMC) data. Among-character rate variation (ACRV) may confound phylogenetic analysis, but there have been few analyses of the magnitude and distribution of rate heterogeneity among DMCs. Using 76 data sets covering a range of plants, invertebrate, and vertebrate animals, we used a modified version of MrBayes to test equal, gamma-distributed and lognormally distributed models of ACRV, integrating across phylogenetic uncertainty using Bayesian model selection. We found that in approximately 80% of data sets, unequal-rates models outperformed equal-rates models, especially among larger data sets. Moreover, although most data sets were equivocal, more data sets favored the lognormal rate distribution relative to the gamma rate distribution, lending some support for more complex character correlations than in molecular data. Parsimony estimation of the underlying rate distributions in several data sets suggests that the lognormal distribution is preferred when there are many slowly evolving characters and fewer quickly evolving characters. The commonly adopted four rate category discrete approximation used for molecular data was found to be sufficient to approximate a gamma rate distribution with discrete characters. However, among the two data sets tested that favored a lognormal rate distribution, the continuous distribution was better approximated with at least eight discrete rate categories. Although the effect of rate model on the estimation of topology was difficult to assess across all data sets, it appeared relatively minor between the unequal-rates models for the one data set examined carefully. As in molecular analyses, we argue that researchers should test and adopt the most appropriate model of rate variation for the data set in question. As discrete characters are increasingly used in more sophisticated likelihood-based phylogenetic analyses, it is important that these studies be built on the most appropriate and carefully selected underlying models of evolution. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

PubMed Central

Chagné, David; Crowhurst, Ross N.; Troggio, Michela; Davey, Mark W.; Gilmore, Barbara; Lawley, Cindy; Vanderzande, Stijn; Hellens, Roger P.; Kumar, Satish; Cestaro, Alessandro; Velasco, Riccardo; Main, Dorrie; Rees, Jasper D.; Iezzoni, Amy; Mockler, Todd; Wilhelm, Larry; Van de Weg, Eric; Gardiner, Susan E.; Bassil, Nahla; Peace, Cameron

2012-01-01

As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple. PMID:22363718

Skewness and kurtosis analysis for non-Gaussian distributions

NASA Astrophysics Data System (ADS)

Celikoglu, Ahmet; Tirnakli, Ugur

2018-06-01

In this paper we address a number of pitfalls regarding the use of kurtosis as a measure of deviations from the Gaussian. We treat kurtosis in both its standard definition and that which arises in q-statistics, namely q-kurtosis. We have recently shown that the relation proposed by Cristelli et al. (2012) between skewness and kurtosis can only be verified for relatively small data sets, independently of the type of statistics chosen; however it fails for sufficiently large data sets, if the fourth moment of the distribution is finite. For infinite fourth moments, kurtosis is not defined as the size of the data set tends to infinity. For distributions with finite fourth moments, the size, N, of the data set for which the standard kurtosis saturates to a fixed value, depends on the deviation of the original distribution from the Gaussian. Nevertheless, using kurtosis as a criterion for deciding which distribution deviates further from the Gaussian can be misleading for small data sets, even for finite fourth moment distributions. Going over to q-statistics, we find that although the value of q-kurtosis is finite in the range of 0 < q < 3, this quantity is not useful for comparing different non-Gaussian distributed data sets, unless the appropriate q value, which truly characterizes the data set of interest, is chosen. Finally, we propose a method to determine the correct q value and thereby to compute the q-kurtosis of q-Gaussian distributed data sets.

Measurements of normalized differential cross sections for t t ¯ production in p p collisions at ( s ) = 7     TeV using the ATLAS detector

DOE PAGES

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

2014-10-13

We present measurements of normalized differential cross sections for top-quark pair production as a function of the top-quark transverse momentum, and of the mass, transverse momentum, and rapidity of the t¯t system, in proton–proton collisions at a center-of-mass energy of √ s=7 TeV. The data set corresponds to an integrated luminosity of 4.6 fb ₋1, recorded in 2011 with the ATLAS detector at the CERN Large Hadron Collider. Events are selected in the lepton + jets channel, requiring exactly one lepton and at least four jets with at least one of the jets tagged as originating from a b-quark. Themore » measured spectra are corrected for detector efficiency and resolution effects and are compared to several Monte Carlo simulations and theory calculations. The results are in fair agreement with the predictions in a wide kinematic range. Nevertheless, data distributions are softer than predicted for higher values of the mass of the t¯t system and of the top-quark transverse momentum. Lastly, the measurements can also discriminate among different sets of parton distribution functions.« less

Determining Boundary Layer Mixing State based on NASA DISCOVER-AQ Airborne Soundings over the Baltimore/Washington Area

NASA Astrophysics Data System (ADS)

Chen, G.; Crawford, J. H.; Silverman, M. L.; Anderson, B. E.; Barrick, J. D.; Diskin, G. S.; Fried, A.; Yang, M. M.; Weinheimer, A. J.; Lenschow, D. H.

2012-12-01

The DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) mission conducted its first field deployment in the Washington D.C./Baltimore region during July 2011. The overarching goal is to better understand how remotely-sensed column measurements can be used to diagnose near-surface air quality. To achieve this objective, the DISCOVER-AQ sampling strategy requires extensive probing of the vertical structure of the lower troposphere as it relates to both trace gases and aerosols. This strategy was implemented by using the NASA P-3B aircraft to spiral from 0.3 to ~3 km over 6 MDE (Maryland Department of the Environment) ground monitoring sites. A total of 254 spirals were flown which generated detailed vertical distributions for a large variety of trace gases, aerosol properties, and meteorological variables. This data set allows a detailed assessment of vertical mixing state, which can be estimated by the changes of the measured variables with height within the boundary layer. The data set was further filtered to minimize the influence of the horizontal inhomogeneity. To be presented are cases under different atmospheric stability classes to show the actual observed atmospheric structure and vertical distributions of the aerosols and trace gases which have a wide range of lifetimes.

A model for AGN variability on multiple time-scales

NASA Astrophysics Data System (ADS)

Sartori, Lia F.; Schawinski, Kevin; Trakhtenbrot, Benny; Caplar, Neven; Treister, Ezequiel; Koss, Michael J.; Urry, C. Megan; Zhang, C. E.

2018-05-01

We present a framework to link and describe active galactic nuclei (AGN) variability on a wide range of time-scales, from days to billions of years. In particular, we concentrate on the AGN variability features related to changes in black hole fuelling and accretion rate. In our framework, the variability features observed in different AGN at different time-scales may be explained as realisations of the same underlying statistical properties. In this context, we propose a model to simulate the evolution of AGN light curves with time based on the probability density function (PDF) and power spectral density (PSD) of the Eddington ratio (L/LEdd) distribution. Motivated by general galaxy population properties, we propose that the PDF may be inspired by the L/LEdd distribution function (ERDF), and that a single (or limited number of) ERDF+PSD set may explain all observed variability features. After outlining the framework and the model, we compile a set of variability measurements in terms of structure function (SF) and magnitude difference. We then combine the variability measurements on a SF plot ranging from days to Gyr. The proposed framework enables constraints on the underlying PSD and the ability to link AGN variability on different time-scales, therefore providing new insights into AGN variability and black hole growth phenomena.

Dynamic Uncertain Causality Graph for Knowledge Representation and Probabilistic Reasoning: Directed Cyclic Graph and Joint Probability Distribution.

PubMed

Zhang, Qin

2015-07-01

Probabilistic graphical models (PGMs) such as Bayesian network (BN) have been widely applied in uncertain causality representation and probabilistic reasoning. Dynamic uncertain causality graph (DUCG) is a newly presented model of PGMs, which can be applied to fault diagnosis of large and complex industrial systems, disease diagnosis, and so on. The basic methodology of DUCG has been previously presented, in which only the directed acyclic graph (DAG) was addressed. However, the mathematical meaning of DUCG was not discussed. In this paper, the DUCG with directed cyclic graphs (DCGs) is addressed. In contrast, BN does not allow DCGs, as otherwise the conditional independence will not be satisfied. The inference algorithm for the DUCG with DCGs is presented, which not only extends the capabilities of DUCG from DAGs to DCGs but also enables users to decompose a large and complex DUCG into a set of small, simple sub-DUCGs, so that a large and complex knowledge base can be easily constructed, understood, and maintained. The basic mathematical definition of a complete DUCG with or without DCGs is proved to be a joint probability distribution (JPD) over a set of random variables. The incomplete DUCG as a part of a complete DUCG may represent a part of JPD. Examples are provided to illustrate the methodology.

Distributing Congestion Management System Information Using the World Wide Web

DOT National Transportation Integrated Search

1997-01-01

The Internet is a unique medium for the distribution of information, and it provides a tremendous opportunity to take advantage of peoples innate interest in transportation issues as they relate to their own lives. In particular, the World Wide Web (...

Analysis on the Utility of Satellite Imagery for Detection of Agricultural Facility

NASA Astrophysics Data System (ADS)

Kang, J.-M.; Baek, S.-H.; Jung, K.-Y.

2012-07-01

Now that the agricultural facilities are being increase owing to development of technology and diversification of agriculture and the ratio of garden crops that are imported a lot and the crops cultivated in facilities are raised in Korea, the number of vinyl greenhouses is tending upward. So, it is important to grasp the distribution of vinyl greenhouses as much as that of rice fields, dry fields and orchards, but it is difficult to collect the information of wide areas economically and correctly. Remote sensing using satellite imagery is able to obtain data of wide area at the same time, quickly and cost-effectively collect, monitor and analyze information from every object on earth. In this study, in order to analyze the utilization of satellite imagery at detection of agricultural facility, image classification was performed about the agricultural facility, vinyl greenhouse using Formosat-2 satellite imagery. The training set of sea, vegetation, building, bare ground and vinyl greenhouse was set to monitor the agricultural facilities of the object area and the training set for the vinyl greenhouses that are main monitoring object was classified and set again into 3 types according the spectral characteristics. The image classification using 4 kinds of supervise classification methods applied by the same training set were carried out to grasp the image classification method which is effective for monitoring agricultural facilities. And, in order to minimize the misclassification appeared in the classification using the spectral information, the accuracy of classification was intended to be raised by adding texture information. The results of classification were analyzed regarding the accuracy comparing with that of naked-eyed detection. As the results of classification, the method of Mahalanobis distance was shown as more efficient than other methods and the accuracy of classification was higher when adding texture information. Hence the more effective monitoring of agricultural facilities is expected to be available if the characteristics such as texture information including satellite images or spatial pattern are studied in detail.

Partial Least Squares Regression Can Aid in Detecting Differential Abundance of Multiple Features in Sets of Metagenomic Samples

PubMed Central

Libiger, Ondrej; Schork, Nicholas J.

2015-01-01

It is now feasible to examine the composition and diversity of microbial communities (i.e., “microbiomes”) that populate different human organs and orifices using DNA sequencing and related technologies. To explore the potential links between changes in microbial communities and various diseases in the human body, it is essential to test associations involving different species within and across microbiomes, environmental settings and disease states. Although a number of statistical techniques exist for carrying out relevant analyses, it is unclear which of these techniques exhibit the greatest statistical power to detect associations given the complexity of most microbiome datasets. We compared the statistical power of principal component regression, partial least squares regression, regularized regression, distance-based regression, Hill's diversity measures, and a modified test implemented in the popular and widely used microbiome analysis methodology “Metastats” across a wide range of simulated scenarios involving changes in feature abundance between two sets of metagenomic samples. For this purpose, simulation studies were used to change the abundance of microbial species in a real dataset from a published study examining human hands. Each technique was applied to the same data, and its ability to detect the simulated change in abundance was assessed. We hypothesized that a small subset of methods would outperform the rest in terms of the statistical power. Indeed, we found that the Metastats technique modified to accommodate multivariate analysis and partial least squares regression yielded high power under the models and data sets we studied. The statistical power of diversity measure-based tests, distance-based regression and regularized regression was significantly lower. Our results provide insight into powerful analysis strategies that utilize information on species counts from large microbiome data sets exhibiting skewed frequency distributions obtained on a small to moderate number of samples. PMID:26734061

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

PubMed Central

2013-01-01

Background High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to exploit this feature and distinguish expression profiles with higher resolution. RNA-seq data analysis methods so far have been mostly applied to data sets with few replicates and their default settings try to provide the best performance under this constraint. These methods are based on two well-known count data distributions: the Poisson and the negative binomial. The way to properly calibrate them with large RNA-seq data sets is not trivial for the non-expert bioinformatics user. Results Here we show that expression profiles produced by extensively-replicated RNA-seq experiments lead to a rich diversity of count data distributions beyond the Poisson and the negative binomial, such as Poisson-Inverse Gaussian or Pólya-Aeppli, which can be captured by a more general family of count data distributions called the Poisson-Tweedie. The flexibility of the Poisson-Tweedie family enables a direct fitting of emerging features of large expression profiles, such as heavy-tails or zero-inflation, without the need to alter a single configuration parameter. We provide a software package for R called tweeDEseq implementing a new test for differential expression based on the Poisson-Tweedie family. Using simulations on synthetic and real RNA-seq data we show that tweeDEseq yields P-values that are equally or more accurate than competing methods under different configuration parameters. By surveying the tiny fraction of sex-specific gene expression changes in human lymphoblastoid cell lines, we also show that tweeDEseq accurately detects differentially expressed genes in a real large RNA-seq data set with improved performance and reproducibility over the previously compared methodologies. Finally, we compared the results with those obtained from microarrays in order to check for reproducibility. Conclusions RNA-seq data with many replicates leads to a handful of count data distributions which can be accurately estimated with the statistical model illustrated in this paper. This method provides a better fit to the underlying biological variability; this may be critical when comparing groups of RNA-seq samples with markedly different count data distributions. The tweeDEseq package forms part of the Bioconductor project and it is available for download at http://www.bioconductor.org. PMID:23965047

Re-evaluating the functional landscape of the cardiovascular system during development

PubMed Central

Takada, Norio; Omae, Madoka; Sagawa, Fumihiko; Chi, Neil C.; Endo, Satsuki; Kozawa, Satoshi

2017-01-01

ABSTRACT The cardiovascular system facilitates body-wide distribution of oxygen, a vital process for the development and survival of virtually all vertebrates. However, the zebrafish, a vertebrate model organism, appears to form organs and survive mid-larval periods without a functional cardiovascular system. Despite such dispensability, it is the first organ to develop. Such enigma prompted us to hypothesize other cardiovascular functions that are important for developmental and/or physiological processes. Hence, systematic cellular ablations and functional perturbations were performed on the zebrafish cardiovascular system to gain comprehensive and body-wide understanding of such functions and to elucidate the underlying mechanisms. This approach identifies a set of organ-specific genes, each implicated for important functions. The study also unveils distinct cardiovascular mechanisms, each differentially regulating their expressions in organ-specific and oxygen-independent manners. Such mechanisms are mediated by organ-vessel interactions, circulation-dependent signals, and circulation-independent beating-heart-derived signals. A comprehensive and body-wide functional landscape of the cardiovascular system reported herein may provide clues as to why it is the first organ to develop. Furthermore, these data could serve as a resource for the study of organ development and function. PMID:28982700

VARED: Verification and Analysis of Requirements and Early Designs

NASA Technical Reports Server (NTRS)

Badger, Julia; Throop, David; Claunch, Charles

2014-01-01

Requirements are a part of every project life cycle; everything going forward in a project depends on them. Good requirements are hard to write, there are few useful tools to test, verify, or check them, and it is difficult to properly marry them to the subsequent design, especially if the requirements are written in natural language. In fact, the inconsistencies and errors in the requirements along with the difficulty in finding these errors contribute greatly to the cost of the testing and verification stage of flight software projects [1]. Large projects tend to have several thousand requirements written at various levels by different groups of people. The design process is distributed and a lack of widely accepted standards for requirements often results in a product that varies widely in style and quality. A simple way to improve this would be to standardize the design process using a set of tools and widely accepted requirements design constraints. The difficulty with this approach is finding the appropriate constraints and tools. Common complaints against the tools available include ease of use, functionality, and available features. Also, although preferable, it is rare that these tools are capable of testing the quality of the requirements.

Re-evaluating the functional landscape of the cardiovascular system during development.

PubMed

Takada, Norio; Omae, Madoka; Sagawa, Fumihiko; Chi, Neil C; Endo, Satsuki; Kozawa, Satoshi; Sato, Thomas N

2017-11-15

The cardiovascular system facilitates body-wide distribution of oxygen, a vital process for the development and survival of virtually all vertebrates. However, the zebrafish, a vertebrate model organism, appears to form organs and survive mid-larval periods without a functional cardiovascular system. Despite such dispensability, it is the first organ to develop. Such enigma prompted us to hypothesize other cardiovascular functions that are important for developmental and/or physiological processes. Hence, systematic cellular ablations and functional perturbations were performed on the zebrafish cardiovascular system to gain comprehensive and body-wide understanding of such functions and to elucidate the underlying mechanisms. This approach identifies a set of organ-specific genes, each implicated for important functions. The study also unveils distinct cardiovascular mechanisms, each differentially regulating their expressions in organ-specific and oxygen-independent manners. Such mechanisms are mediated by organ-vessel interactions, circulation-dependent signals, and circulation-independent beating-heart-derived signals. A comprehensive and body-wide functional landscape of the cardiovascular system reported herein may provide clues as to why it is the first organ to develop. Furthermore, these data could serve as a resource for the study of organ development and function. © 2017. Published by The Company of Biologists Ltd.

Lead-free hunting rifle ammunition: product availability, price, effectiveness, and role in global wildlife conservation.

PubMed

Thomas, Vernon George

2013-10-01

Proposals to end the use of lead hunting ammunition because of the established risks of lead exposure to wildlife and humans are impeded by concerns about the availability, price, and effectiveness of substitutes. The product availability and retail prices of different calibers of lead-free bullets and center-fire rifle ammunition were assessed for ammunition sold in the USA and Europe. Lead-free bullets are made in 35 calibers and 51 rifle cartridge designations. Thirty-seven companies distribute internationally ammunition made with lead-free bullets. There is no major difference in the retail price of equivalent lead-free and lead-core ammunition for most popular calibers. Lead-free ammunition has set bench-mark standards for accuracy, lethality, and safety. Given the demonstrated wide product availability, comparable prices, and the effectiveness of high-quality lead-free ammunition, it is possible to phase out the use of lead hunting ammunition world-wide, based on progressive policy and enforceable legislation.

AN INFORMATION-THEORETIC APPROACH TO OPTIMIZE JWST OBSERVATIONS AND RETRIEVALS OF TRANSITING EXOPLANET ATMOSPHERES

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

Howe, Alex R.; Burrows, Adam; Deming, Drake, E-mail: arhowe@umich.edu, E-mail: burrows@astro.princeton.edu, E-mail: ddeming@astro.umd.edu

We provide an example of an analysis to explore the optimization of observations of transiting hot Jupiters with the James Webb Space Telescope ( JWST ) to characterize their atmospheres based on a simple three-parameter forward model. We construct expansive forward model sets for 11 hot Jupiters, 10 of which are relatively well characterized, exploring a range of parameters such as equilibrium temperature and metallicity, as well as considering host stars over a wide range in brightness. We compute posterior distributions of our model parameters for each planet with all of the available JWST spectroscopic modes and several programs ofmore » combined observations and compute their effectiveness using the metric of estimated mutual information per degree of freedom. From these simulations, clear trends emerge that provide guidelines for designing a JWST observing program. We demonstrate that these guidelines apply over a wide range of planet parameters and target brightnesses for our simple forward model.« less

Screening of short- and medium-chain chlorinated paraffins in selected riverine sediments and sludge from the Czech Republic.

PubMed

Pribylová, Petra; Klánová, Jana; Holoubek, Ivan

2006-11-01

Wide distribution of chlorinated paraffins in the environment has already been demonstrated in several studies; however, information about their levels in the Central Europe is still very limited. First study focused on the SCCP contamination of the Czech aquatic environment have been performed recently, and its results motivated the authors to analyze sediments from a wide set of the Czech rivers in order to obtain more detailed information. Thirty-six sediment samples from eleven rivers and five drainage vents neighboring the chemical factories were analyzed; special attention was paid to the industrial areas. For the first time in the Czech Republic, medium-chain in addition to short-chain chlorinated paraffins were analyzed using GC-ECNI-MS. Chlorinated paraffins were detected in sediment samples on the concentration levels up to 347 ngg(-1) for short-chain chlorinated paraffins, and 5575 ngg(-1) for medium-chain chlorinated paraffins. Average chlorination degree of SCCPs was 65%.

Gene set analysis using variance component tests.

PubMed

Huang, Yen-Tsung; Lin, Xihong

2013-06-28

Gene set analyses have become increasingly important in genomic research, as many complex diseases are contributed jointly by alterations of numerous genes. Genes often coordinate together as a functional repertoire, e.g., a biological pathway/network and are highly correlated. However, most of the existing gene set analysis methods do not fully account for the correlation among the genes. Here we propose to tackle this important feature of a gene set to improve statistical power in gene set analyses. We propose to model the effects of an independent variable, e.g., exposure/biological status (yes/no), on multiple gene expression values in a gene set using a multivariate linear regression model, where the correlation among the genes is explicitly modeled using a working covariance matrix. We develop TEGS (Test for the Effect of a Gene Set), a variance component test for the gene set effects by assuming a common distribution for regression coefficients in multivariate linear regression models, and calculate the p-values using permutation and a scaled chi-square approximation. We show using simulations that type I error is protected under different choices of working covariance matrices and power is improved as the working covariance approaches the true covariance. The global test is a special case of TEGS when correlation among genes in a gene set is ignored. Using both simulation data and a published diabetes dataset, we show that our test outperforms the commonly used approaches, the global test and gene set enrichment analysis (GSEA). We develop a gene set analyses method (TEGS) under the multivariate regression framework, which directly models the interdependence of the expression values in a gene set using a working covariance. TEGS outperforms two widely used methods, GSEA and global test in both simulation and a diabetes microarray data.

Development and Evaluation of a Multistatic Ultrawideband Random Noise Radar

DTIC Science & Technology

2010-03-01

noncoherent MIMO investigates 13 a statistical diversity gain available to systems with widely separated antennas per- forming a distributed detection...design. When widely distributed antenna are operating as a MIMO radar system, research shows a noncoherent signal gain is realized, if there exists

Perceptions and use of iPad technology by pharmacy practice faculty members.

PubMed

DiVall, Margarita V; Zgarrick, David P

2014-04-17

To explore the potential of tablet technology to address the specific workload challenges of pharmacy practice faculty members and to evaluate tablet usage after a department-wide iPad initiative. After conducting a needs assessment to determine pharmacy faculty attitudes towards tablet technology and to identify potential usage scenarios, all faculty members in a department of pharmacy practice received an iPad. After iPad distribution, training sessions and virtual tutorials were provided. An anonymous survey was administered to evaluate the pilot. The needs assessment survey revealed positive attitudes towards iPad technology, identified use scenarios, and led to a department-wide iPad pilot program. Most faculty members used iPads for connectivity with students (86%), paper/project annotation (68%), assessment (57%), and demonstration of tools used in practice (36%). For teaching, 61% of faculty members used iPads in seminars/laboratories, 57% used iPads in the experiential setting, and 43% used iPads in the classroom. Use of iPads for patient-care activities varied and depended on site support for mobile technology. The 23 faculty members with external practice sites used iPads to a greater extent and had more positive attitudes towards this technology compared with campus-based faculty members. Integration of tablet technology into the pharmacy education setting resulted in faculty-reported increased productivity and decreased paper waste. It also allowed faculty members to experiment with new teaching strategies in the classroom and experiential setting. Administrators at institutions exploring the use of tablet technology should allocate resources based on faculty needs and usage patterns.

Local and Widely Distributed EEG Activity in Schizophrenia With Prevalence of Negative Symptoms.

PubMed

Grin-Yatsenko, Vera A; Ponomarev, Valery A; Pronina, Marina V; Poliakov, Yury I; Plotnikova, Irina V; Kropotov, Juri D

2017-09-01

We evaluated EEG frequency abnormalities in resting state (eyes closed and eyes open) EEG in a group of chronic schizophrenia patients as compared with healthy subjects. The study included 3 methods of analysis of deviation of EEG characteristics: genuine EEG, current source density (CSD), and group independent component (gIC). All 3 methods have shown that the EEG in schizophrenia patients is characterized by enhanced low-frequency (delta and theta) and high-frequency (beta) activity in comparison with the control group. However, the spatial pattern of differences was dependent on the type of method used. Comparative analysis has shown that increased EEG power in schizophrenia patients apparently concerns both widely spatially distributed components and local components of signal. Furthermore, the observed differences in the delta and theta range can be described mainly by the local components, and those in the beta range mostly by spatially widely distributed ones. The possible nature of the widely distributed activity is discussed.

Cerebro-Oculo-Facio-Skeletal Syndrome (COFS)

MedlinePlus

... clenched fists, wide-set nipples, vision impairments, involuntary eye movements, and impaired cognitive development, which can be moderate ... clenched fists, wide-set nipples, vision impairments, involuntary eye movements, and impaired cognitive development, which can be moderate ...

Understanding feedback report uptake: process evaluation findings from a 13-month feedback intervention in long-term care settings.

PubMed

Sales, Anne E; Fraser, Kimberly; Baylon, Melba Andrea B; O'Rourke, Hannah M; Gao, Gloria; Bucknall, Tracey; Maisey, Suzanne

2015-02-12

Long-term care settings provide care to a large proportion of predominantly older, highly disabled adults across the United States and Canada. Managing and improving quality of care is challenging, in part because staffing is highly dependent on relatively non-professional health care aides and resources are limited. Feedback interventions in these settings are relatively rare, and there has been little published information about the process of feedback intervention. Our objectives were to describe the key components of uptake of the feedback reports, as well as other indicators of participant response to the intervention. We conducted this project in nine long-term care units in four facilities in Edmonton, Canada. We used mixed methods, including observations during a 13-month feedback report intervention with nine post-feedback survey cycles, to conduct a process evaluation of a feedback report intervention in these units. We included all facility-based direct care providers (staff) in the feedback report distribution and survey administration. We conducted descriptive analyses of the data from observations and surveys, presenting this in tabular and graphic form. We constructed a short scale to measure uptake of the feedback reports. Our analysis evaluated feedback report uptake by provider type over the 13 months of the intervention. We received a total of 1,080 survey responses over the period of the intervention, which varied by type of provider, facility, and survey month. Total number of reports distributed ranged from 103 in cycle 12 to 229 in cycle 3, although the method of delivery varied widely across the period, from 12% to 65% delivered directly to individuals and 15% to 84% left for later distribution. The key elements of feedback uptake, including receiving, reading, understanding, discussing, and reporting a perception that the reports were useful, varied by survey cycle and provider type, as well as by facility. Uptake, as we measured it, was consistently high overall, but varied widely by provider type and time period. We report detailed process data describing the aspects of uptake of a feedback report during an intensive, longitudinal feedback intervention in long-term care facilities. Uptake is a complex process for which we used multiple measures. We demonstrate the feasibility of conducting a complex longitudinal feedback intervention in relatively resource-poor long-term care facilities to a wider range of provider types than have been included in prior feedback interventions.

A parallel algorithm for 2D visco-acoustic frequency-domain full-waveform inversion: application to a dense OBS data set

NASA Astrophysics Data System (ADS)

Sourbier, F.; Operto, S.; Virieux, J.

2006-12-01

We present a distributed-memory parallel algorithm for 2D visco-acoustic full-waveform inversion of wide-angle seismic data. Our code is written in fortran90 and use MPI for parallelism. The algorithm was applied to real wide-angle data set recorded by 100 OBSs with a 1-km spacing in the eastern-Nankai trough (Japan) to image the deep structure of the subduction zone. Full-waveform inversion is applied sequentially to discrete frequencies by proceeding from the low to the high frequencies. The inverse problem is solved with a classic gradient method. Full-waveform modeling is performed with a frequency-domain finite-difference method. In the frequency-domain, solving the wave equation requires resolution of a large unsymmetric system of linear equations. We use the massively parallel direct solver MUMPS (http://www.enseeiht.fr/irit/apo/MUMPS) for distributed-memory computer to solve this system. The MUMPS solver is based on a multifrontal method for the parallel factorization. The MUMPS algorithm is subdivided in 3 main steps: a symbolic analysis step that performs re-ordering of the matrix coefficients to minimize the fill-in of the matrix during the subsequent factorization and an estimation of the assembly tree of the matrix. Second, the factorization is performed with dynamic scheduling to accomodate numerical pivoting and provides the LU factors distributed over all the processors. Third, the resolution is performed for multiple sources. To compute the gradient of the cost function, 2 simulations per shot are required (one to compute the forward wavefield and one to back-propagate residuals). The multi-source resolutions can be performed in parallel with MUMPS. In the end, each processor stores in core a sub-domain of all the solutions. These distributed solutions can be exploited to compute in parallel the gradient of the cost function. Since the gradient of the cost function is a weighted stack of the shot and residual solutions of MUMPS, each processor computes the corresponding sub-domain of the gradient. In the end, the gradient is centralized on the master processor using a collective communation. The gradient is scaled by the diagonal elements of the Hessian matrix. This scaling is computed only once per frequency before the first iteration of the inversion. Estimation of the diagonal terms of the Hessian requires performing one simulation per non redondant shot and receiver position. The same strategy that the one used for the gradient is used to compute the diagonal Hessian in parallel. This algorithm was applied to a dense wide-angle data set recorded by 100 OBSs in the eastern Nankai trough, offshore Japan. Thirteen frequencies ranging from 3 and 15 Hz were inverted. Tweny iterations per frequency were computed leading to 260 tomographic velocity models of increasing resolution. The velocity model dimensions are 105 km x 25 km corresponding to a finite-difference grid of 4201 x 1001 grid with a 25-m grid interval. The number of shot was 1005 and the number of inverted OBS gathers was 93. The inversion requires 20 days on 6 32-bits bi-processor nodes with 4 Gbytes of RAM memory per node when only the LU factorization is performed in parallel. Preliminary estimations of the time required to perform the inversion with the fully-parallelized code is 6 and 4 days using 20 and 50 processors respectively.

Class imbalance in unsupervised change detection - A diagnostic analysis from urban remote sensing

NASA Astrophysics Data System (ADS)

Leichtle, Tobias; Geiß, Christian; Lakes, Tobia; Taubenböck, Hannes

2017-08-01

Automatic monitoring of changes on the Earth's surface is an intrinsic capability and simultaneously a persistent methodological challenge in remote sensing, especially regarding imagery with very-high spatial resolution (VHR) and complex urban environments. In order to enable a high level of automatization, the change detection problem is solved in an unsupervised way to alleviate efforts associated with collection of properly encoded prior knowledge. In this context, this paper systematically investigates the nature and effects of class distribution and class imbalance in an unsupervised binary change detection application based on VHR imagery over urban areas. For this purpose, a diagnostic framework for sensitivity analysis of a large range of possible degrees of class imbalance is presented, which is of particular importance with respect to unsupervised approaches where the content of images and thus the occurrence and the distribution of classes are generally unknown a priori. Furthermore, this framework can serve as a general technique to evaluate model transferability in any two-class classification problem. The applied change detection approach is based on object-based difference features calculated from VHR imagery and subsequent unsupervised two-class clustering using k-means, genetic k-means and self-organizing map (SOM) clustering. The results from two test sites with different structural characteristics of the built environment demonstrated that classification performance is generally worse in imbalanced class distribution settings while best results were reached in balanced or close to balanced situations. Regarding suitable accuracy measures for evaluating model performance in imbalanced settings, this study revealed that the Kappa statistics show significant response to class distribution while the true skill statistic was widely insensitive to imbalanced classes. In general, the genetic k-means clustering algorithm achieved the most robust results with respect to class imbalance while the SOM clustering exhibited a distinct optimization towards a balanced distribution of classes.

Evaluation of SCS-CN method using a fully distributed physically based coupled surface-subsurface flow model

NASA Astrophysics Data System (ADS)

Shokri, Ali

2017-04-01

The hydrological cycle contains a wide range of linked surface and subsurface flow processes. In spite of natural connections between surface water and groundwater, historically, these processes have been studied separately. The current trend in hydrological distributed physically based model development is to combine distributed surface water models with distributed subsurface flow models. This combination results in a better estimation of the temporal and spatial variability of the interaction between surface and subsurface flow. On the other hand, simple lumped models such as the Soil Conservation Service Curve Number (SCS-CN) are still quite common because of their simplicity. In spite of the popularity of the SCS-CN method, there have always been concerns about the ambiguity of the SCS-CN method in explaining physical mechanism of rainfall-runoff processes. The aim of this study is to minimize these ambiguity by establishing a method to find an equivalence of the SCS-CN solution to the DrainFlow model, which is a fully distributed physically based coupled surface-subsurface flow model. In this paper, two hypothetical v-catchment tests are designed and the direct runoff from a storm event are calculated by both SCS-CN and DrainFlow models. To find a comparable solution to runoff prediction through the SCS-CN and DrainFlow, the variance between runoff predictions by the two models are minimized by changing Curve Number (CN) and initial abstraction (Ia) values. Results of this study have led to a set of lumped model parameters (CN and Ia) for each catchment that is comparable to a set of physically based parameters including hydraulic conductivity, Manning roughness coefficient, ground surface slope, and specific storage. Considering the lack of physical interpretation in CN and Ia is often argued as a weakness of SCS-CN method, the novel method in this paper gives a physical explanation to CN and Ia.

Independent variable complexity for regional regression of the flow duration curve in ungauged basins

NASA Astrophysics Data System (ADS)

Fouad, Geoffrey; Skupin, André; Hope, Allen

2016-04-01

The flow duration curve (FDC) is one of the most widely used tools to quantify streamflow. Its percentile flows are often required for water resource applications, but these values must be predicted for ungauged basins with insufficient or no streamflow data. Regional regression is a commonly used approach for predicting percentile flows that involves identifying hydrologic regions and calibrating regression models to each region. The independent variables used to describe the physiographic and climatic setting of the basins are a critical component of regional regression, yet few studies have investigated their effect on resulting predictions. In this study, the complexity of the independent variables needed for regional regression is investigated. Different levels of variable complexity are applied for a regional regression consisting of 918 basins in the US. Both the hydrologic regions and regression models are determined according to the different sets of variables, and the accuracy of resulting predictions is assessed. The different sets of variables include (1) a simple set of three variables strongly tied to the FDC (mean annual precipitation, potential evapotranspiration, and baseflow index), (2) a traditional set of variables describing the average physiographic and climatic conditions of the basins, and (3) a more complex set of variables extending the traditional variables to include statistics describing the distribution of physiographic data and temporal components of climatic data. The latter set of variables is not typically used in regional regression, and is evaluated for its potential to predict percentile flows. The simplest set of only three variables performed similarly to the other more complex sets of variables. Traditional variables used to describe climate, topography, and soil offered little more to the predictions, and the experimental set of variables describing the distribution of basin data in more detail did not improve predictions. These results are largely reflective of cross-correlation existing in hydrologic datasets, and highlight the limited predictive power of many traditionally used variables for regional regression. A parsimonious approach including fewer variables chosen based on their connection to streamflow may be more efficient than a data mining approach including many different variables. Future regional regression studies may benefit from having a hydrologic rationale for including different variables and attempting to create new variables related to streamflow.

Millimeter-wave Line Ratios and Sub-beam Volume Density Distributions

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

Leroy, Adam K.; Gallagher, Molly; Usero, Antonio

We explore the use of mm-wave emission line ratios to trace molecular gas density when observations integrate over a wide range of volume densities within a single telescope beam. For observations targeting external galaxies, this case is unavoidable. Using a framework similar to that of Krumholz and Thompson, we model emission for a set of common extragalactic lines from lognormal and power law density distributions. We consider the median density of gas that produces emission and the ability to predict density variations from observed line ratios. We emphasize line ratio variations because these do not require us to know themore » absolute abundance of our tracers. Patterns of line ratio variations have the potential to illuminate the high-end shape of the density distribution, and to capture changes in the dense gas fraction and median volume density. Our results with and without a high-density power law tail differ appreciably; we highlight better knowledge of the probability density function (PDF) shape as an important area. We also show the implications of sub-beam density distributions for isotopologue studies targeting dense gas tracers. Differential excitation often implies a significant correction to the naive case. We provide tabulated versions of many of our results, which can be used to interpret changes in mm-wave line ratios in terms of adjustments to the underlying density distributions.« less

Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index.

PubMed

Carugo, Oliviero

2017-12-01

Amino acids and their properties are variably distributed in proteins and different compositions determine all protein features, ranging from solubility to stability and functionality. Gini index, a tool to estimate distribution uniformity, is widely used in macroeconomics and has numerous statistical applications. Here, Gini index is used to analyze the distribution of hydrophobicity in proteins and to compare hydrophobicity distribution in globular and intrinsically disordered proteins. Based on the analysis of carefully selected high-quality data sets of proteins extracted from the Protein Data Bank (http://www.rcsb.org) and from the DisProt database (http://www.disprot.org/), it is observed that hydrophobicity is distributed in a more diverse way in intrinsically disordered proteins than in folded and soluble globular proteins. This correlates with the observation that the amino acid composition deviates from the uniformity (estimate with the Shannon and the Gini-Simpson indices) more in intrinsically disordered proteins than in globular and soluble proteins. Although statistical tools tike the Gini index have received little attention in molecular biology, these results show that they allow one to estimate sequence diversity and that they are useful to delineate trends that can hardly be described, otherwise, in simple and concise ways. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Provenance-aware optimization of workload for distributed data production

NASA Astrophysics Data System (ADS)

Makatun, Dzmitry; Lauret, Jérôme; Rudová, Hana; Šumbera, Michal

2017-10-01

Distributed data processing in High Energy and Nuclear Physics (HENP) is a prominent example of big data analysis. Having petabytes of data being processed at tens of computational sites with thousands of CPUs, standard job scheduling approaches either do not address well the problem complexity or are dedicated to one specific aspect of the problem only (CPU, network or storage). Previously we have developed a new job scheduling approach dedicated to distributed data production - an essential part of data processing in HENP (preprocessing in big data terminology). In this contribution, we discuss the load balancing with multiple data sources and data replication, present recent improvements made to our planner and provide results of simulations which demonstrate the advantage against standard scheduling policies for the new use case. Multi-source or provenance is common in computing models of many applications whereas the data may be copied to several destinations. The initial input data set would hence be already partially replicated to multiple locations and the task of the scheduler is to maximize overall computational throughput considering possible data movements and CPU allocation. The studies have shown that our approach can provide a significant gain in overall computational performance in a wide scope of simulations considering realistic size of computational Grid and various input data distribution.

Anopheles plumbeus (Diptera: Culicidae) in Germany: updated geographic distribution and public health impact of a nuisance and vector mosquito.

PubMed

Heym, Eva C; Kampen, Helge; Fahle, Marcus; Hohenbrink, Tobias L; Schäfer, Mandy; Scheuch, Dorothee E; Walther, Doreen

2017-01-01

The aim of this study was to map the current spatial distribution of Anopheles plumbeus in Germany, a potential vector of malaria parasites and West Nile virus. Reports of mass occurrence and nuisance connected with artificial breeding site usage by this species were analysed. Distribution data were collected from 2011 to 2014 mainly through trapping and submissions of adult mosquito specimens to a citizen science project. In the framework of the latter, additional information was gathered on recent nuisance incidents caused by An. plumbeus, including a longitudinal analysis of mosquito occurrence and the impact of management measures at a nuisance site in south-western Germany. Based on the most comprehensive set of collection data obtained during the last decades, An. plumbeus is shown to be widely distributed over Germany. The data also indicate a continuing extension of the breeding site repertoire of the species from natural to artificial habitats that facilitate mass development. Increasing incidents of persistent nuisance suggest that this mosquito species is rarely diagnosed correctly and managed adequately. As An. plumbeus is both a serious nuisance pest and a potential vector species, awareness of this species and the public health problems linked to it should be raised among pest managers and public health personnel. © 2016 John Wiley & Sons Ltd.

Small-scale geochemical cycles and the distribution of uranium in central and north Florida organic deposits

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

Bond, P.A.

1993-03-01

The global geochemical cycle for an element tracks its path from its various sources to its sinks via processes of weathering and transportation. The cycle may then be quantified in a necessarily approximate manner. The geochemical cycle (thus quantified) reveals constraints (known and unknown) on an element's behavior imposed by the various processes which act on it. In the context of a global geochemical cycle, a continent becomes essentially a source term. If, however, an element's behavior is examined in a local or regional context, sources and their related sinks may be identified. This suggests that small-scale geochemical cycles maymore » be superimposed on global geochemical cycles. Definition of such sub-cycles may clarify the distribution of an element in the earth's near-surface environment. In Florida, phosphate minerals of the Hawthorn Group act as a widely distributed source of uranium. Uranium is transported by surface- and ground-waters. Florida is the site of extensive wetlands and peatlands. The organic matter associated with these deposits adsorbs uranium and may act as a local sink depending on its hydrogeologic setting. This work examines the role of organic matter in the distribution of uranium in the surface and shallow subsurface environments of central and north Florida.« less

Predicting the geographic distribution of a species from presence-only data subject to detection errors

USGS Publications Warehouse

Dorazio, Robert M.

2012-01-01

Several models have been developed to predict the geographic distribution of a species by combining measurements of covariates of occurrence at locations where the species is known to be present with measurements of the same covariates at other locations where species occurrence status (presence or absence) is unknown. In the absence of species detection errors, spatial point-process models and binary-regression models for case-augmented surveys provide consistent estimators of a species’ geographic distribution without prior knowledge of species prevalence. In addition, these regression models can be modified to produce estimators of species abundance that are asymptotically equivalent to those of the spatial point-process models. However, if species presence locations are subject to detection errors, neither class of models provides a consistent estimator of covariate effects unless the covariates of species abundance are distinct and independently distributed from the covariates of species detection probability. These analytical results are illustrated using simulation studies of data sets that contain a wide range of presence-only sample sizes. Analyses of presence-only data of three avian species observed in a survey of landbirds in western Montana and northern Idaho are compared with site-occupancy analyses of detections and nondetections of these species.

Confining the angular distribution of terrestrial gamma ray flash emission

NASA Astrophysics Data System (ADS)

Gjesteland, T.; Østgaard, N.; Collier, A. B.; Carlson, B. E.; Cohen, M. B.; Lehtinen, N. G.

2011-11-01

Terrestrial gamma ray flashes (TGFs) are bremsstrahlung emissions from relativistic electrons accelerated in electric fields associated with thunder storms, with photon energies up to at least 40 MeV, which sets the lowest estimate of the total potential of 40 MV. The electric field that produces TGFs will be reflected by the initial angular distribution of the TGF emission. Here we present the first constraints on the TGF emission cone based on accurately geolocated TGFs. The source lightning discharges associated with TGFs detected by RHESSI are determined from the Atmospheric Weather Electromagnetic System for Observation, Modeling, and Education (AWESOME) network and the World Wide Lightning Location Network (WWLLN). The distribution of the observation angles for 106 TGFs are compared to Monte Carlo simulations. We find that TGF emissions within a half angle >30° are consistent with the distributions of observation angle derived from the networks. In addition, 36 events occurring before 2006 are used for spectral analysis. The energy spectra are binned according to observation angle. The result is a significant softening of the TGF energy spectrum for large (>40°) observation angles, which is consistent with a TGF emission half angle (<40°). The softening is due to Compton scattering which reduces the photon energies.

A compositional reservoir simulator on distributed memory parallel computers

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

Rame, M.; Delshad, M.

1995-12-31

This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. Amore » portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented.« less

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia).

PubMed

Holt, Carson; Campbell, Michael; Keays, David A; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; T Domyan, Eric; Suh, Alexander; Warren, Wesley C; Yandell, Mark; Gilbert, M Thomas P; Shapiro, Michael D

2018-05-04

The domestic rock pigeon ( Columba livia ) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general. Copyright © 2018 Holt et al.

Solar Astronomy Data Base: Packaged Information on Diskette

NASA Technical Reports Server (NTRS)

Mckinnon, John A.

1990-01-01

In its role as a library, the National Geophysical Data Center has transferred to diskette a collection of small, digital files of routinely measured solar indices for use on an IBM-compatible desktop computer. Recording these observations on diskette allows the distribution of specialized information to researchers with a wide range of expertise in computer science and solar astronomy. Every data set was made self-contained by including formats, extraction utilities, and plain-language descriptive text. Moreover, for several archives, two versions of the observations are provided - one suitable for display, the other for analysis with popular software packages. Since the files contain no control characters, each one can be modified with any text editor.

Emerging arboviruses and public health challenges in Brazil

PubMed Central

Lima-Camara, Tamara Nunes

2016-01-01

ABSTRACT Environmental modification by anthropogenic actions, disordered urban growth, globalization of international exchange and climate change are some factors that help the emergence and dissemination of human infectious diseases transmitted by vectors. This review discusses the recent entry of three arboviruses in Brazil: Chikungunya, West Nile, and Zika virus, focusing on the challenges for the Country’s public health. The Brazilian population is exposed to infections caused by these three arboviruses widely distributed on the national territory and associated with humans. Without effective vaccine and specific treatment, the maintainance and integration of a continuos entomological and epidemiological surveillance are important so we can set methods to control and prevent these arboviruses in the Country. PMID:27355468

A Web-based system for the intelligent management of diabetic patients.

PubMed

Riva, A; Bellazzi, R; Stefanelli, M

1997-01-01

We describe the design and implementation of a distributed computer-based system for the management of insulin-dependent diabetes mellitus. The goal of the system is to support the normal activities of the physicians and patients involved in the care of diabetes by providing them with a set of automated services ranging from data collection and transmission to data analysis and decision support. The system is highly integrated with current practices in the management of diabetes, and it uses Internet technology to achieve high availability and ease of use. In particular, the user interaction takes place through dynamically generated World Wide Web pages, so that all the system's functions share an intuitive graphic user interface.

On the relation between fluvio-deltaic flood basin geomorphology and the wide-spread occurrence of arsenic pollution in shallow aquifers.

PubMed

Donselaar, Marinus E; Bhatt, Ajay G; Ghosh, Ashok K

2017-01-01

Pollution of groundwater with natural (geogenic) arsenic occurs on an enormous, world-wide scale, and causes wide-spread, serious health risks for an estimated more than hundred million people who depend on the use of shallow aquifers for drinking and irrigation water. A literature review of key studies on arsenic concentration levels yields that Holocene fluvial and deltaic flood basins are the hotspots of arsenic pollution, and that the dominant geomorphological setting of the arsenic-polluted areas consists of shallow-depth meandering-river deposits with sand-prone fluvial point-bar deposits surrounded by clay-filled (clay plug) abandoned meander bends (oxbow lakes). Analysis of the lithofacies distribution and related permeability contrasts of the geomorphological elements in two cored wells in a point bar and adjacent clay plug along the Ganges River, in combination with data of arsenic concentrations and organic matter content reveals that the low-permeable clay-plug deposits have a high organic matter content and the adjacent permeable point-bar sands show high but spatially very variable arsenic concentrations. On the basis of the geomorphological juxtaposition, the analysis of fluvial depositional processes and lithofacies characteristics, inherent permeability distribution and the omnipresence of the two geomorphological elements in Holocene flood basins around the world, a generic model is presented for the wide-spread arsenic occurrence. The anoxic deeper part (hypolimnion) of the oxbow lake, and the clay plugs are identified as the loci of reactive organic carbon and microbial respiration in an anoxic environment that triggers the reductive dissolution of iron oxy-hydroxides and the release of arsenic on the scale of entire fluvial floodplains and deltaic basins. The adjacent permeable point-bar sands are identified as the effective trap for the dissolved arsenic, and the internal permeability heterogeneity is the cause for aquifer compartmentalization, with large arsenic concentration differences between neighboring compartments. Copyright © 2016 Elsevier B.V. All rights reserved.

Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs).

PubMed

Terai, Yohey; Takezaki, Naoko; Mayer, Werner E; Tichy, Herbert; Takahata, Naoyuki; Klein, Jan; Okada, Norihiro

2004-01-01

Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.

Geographic distribution of the invasive cattle tick Rhipicephalus microplus, a country-wide survey in Benin.

PubMed

De Clercq, E M; Vanwambeke, S O; Sungirai, M; Adehan, S; Lokossou, R; Madder, M

2012-12-01

The cattle tick Rhipicephalus microplus is currently invading the West African region, and little information is available on the spread of this exotic tick in this region. We set out a country-wide field survey to determine its current distribution in Benin. Ticks were collected on cattle from 106 farms selected by random sampling covering all regions of the country. Rhipicephalus annulatus was found on 70 % of all farms, R. decoloratus on 42 %, R. geigyi on 58 %, and R. microplus on 49 %. There is a clear geographic separation between the indigenous Rhipicephalus species and R. microplus. Rhipicephalus annulatus occurs mainly in the northern departments, but it was also observed in lower numbers in locations in the south. The presence of R. decoloratus is limited to the northern region, and in most locations, this tick makes up a small proportion of the collected ticks. The tick R. geigyi tends to be dominant, but occurs only in the four northern departments. The observations concerning R. microplus are entirely different, this species occurs in the southern and central region. The results of this survey confirm the invasive character and displacement properties of R. microplus, since in less than a decade it has colonized more than half of the country and has displaced indigenous ticks of the same genus in many of the sampled locations.

Development of the first georeferenced map of Rhipicephalus (Boophilus) spp. in Mexico from 1970 to date and prediction of its spatial distribution.

PubMed

Alcala-Canto, Yazmin; Figueroa-Castillo, Juan Antonio; Ibarra-Velarde, Froylán; Vera-Montenegro, Yolanda; Cervantes-Valencia, María Eugenia; Salem, Abdelfattah Z M; Cuéllar-Ordaz, Jorge Alfredo

2018-05-07

The tick genus Ripicephalus (Boophilus), particularly R. microplus, is one of the most important ectoparasites that affects livestock health and considered an epidemiological risk because it causes significant economic losses due, mainly, to restrictions in the export of infested animals to several countries. Its spatial distribution has been tied to environmental factors, mainly warm temperatures and high relative humidity. In this work, we integrated a dataset consisting of 5843 records of Rhipicephalus spp., in Mexico covering close to 50 years to know which environmental variables mostly influence this ticks' distribution. Occurrences were georeferenced using the software DIVA-GIS and the potential current distribution was modelled using the maximum entropy method (Maxent). The algorithm generated a map of high predictive capability (Area under the curve = 0.942), providing the various contribution and permutation importance of the tested variables. Precipitation seasonality, particularly in March, and isothermality were found to be the most significant climate variables in determining the probability of spatial distribution of Rhipicephalus spp. in Mexico (15.7%, 36.0% and 11.1%, respectively). Our findings demonstrate that Rhipicephalus has colonized Mexico widely, including areas characterized by different types of climate. We conclude that the Maxent distribution model using Rhipicephalus records and a set of environmental variables can predict the extent of the tick range in this country, information that should support the development of integrated control strategies.

Transit-time and age distributions for nonlinear time-dependent compartmental systems.

PubMed

Metzler, Holger; Müller, Markus; Sierra, Carlos A

2018-02-06

Many processes in nature are modeled using compartmental systems (reservoir/pool/box systems). Usually, they are expressed as a set of first-order differential equations describing the transfer of matter across a network of compartments. The concepts of age of matter in compartments and the time required for particles to transit the system are important diagnostics of these models with applications to a wide range of scientific questions. Until now, explicit formulas for transit-time and age distributions of nonlinear time-dependent compartmental systems were not available. We compute densities for these types of systems under the assumption of well-mixed compartments. Assuming that a solution of the nonlinear system is available at least numerically, we show how to construct a linear time-dependent system with the same solution trajectory. We demonstrate how to exploit this solution to compute transit-time and age distributions in dependence on given start values and initial age distributions. Furthermore, we derive equations for the time evolution of quantiles and moments of the age distributions. Our results generalize available density formulas for the linear time-independent case and mean-age formulas for the linear time-dependent case. As an example, we apply our formulas to a nonlinear and a linear version of a simple global carbon cycle model driven by a time-dependent input signal which represents fossil fuel additions. We derive time-dependent age distributions for all compartments and calculate the time it takes to remove fossil carbon in a business-as-usual scenario.

Quantitative evaluation of potential irradiation geometries for carbon-ion beam grid therapy.

PubMed

Tsubouchi, Toshiro; Henry, Thomas; Ureba, Ana; Valdman, Alexander; Bassler, Niels; Siegbahn, Albert

2018-03-01

Radiotherapy using grids containing cm-wide beam elements has been carried out sporadically for more than a century. During the past two decades, preclinical research on radiotherapy with grids containing small beam elements, 25 μm-0.7 mm wide, has been performed. Grid therapy with larger beam elements is technically easier to implement, but the normal tissue tolerance to the treatment is decreasing. In this work, a new approach in grid therapy, based on irradiations with grids containing narrow carbon-ion beam elements was evaluated dosimetrically. The aim formulated for the suggested treatment was to obtain a uniform target dose combined with well-defined grids in the irradiated normal tissue. The gain, obtained by crossfiring the carbon-ion beam grids over a simulated target volume, was quantitatively evaluated. The dose distributions produced by narrow rectangular carbon-ion beams in a water phantom were simulated with the PHITS Monte Carlo code. The beam-element height was set to 2.0 cm in the simulations, while the widths varied from 0.5 to 10.0 mm. A spread-out Bragg peak (SOBP) was then created for each beam element in the grid, to cover the target volume with dose in the depth direction. The dose distributions produced by the beam-grid irradiations were thereafter constructed by adding the dose profiles simulated for single beam elements. The variation of the valley-to-peak dose ratio (VPDR) with depth in water was thereafter evaluated. The separation of the beam elements inside the grids were determined for different irradiation geometries with a selection criterion. The simulated carbon-ion beams remained narrow down to the depths of the Bragg peaks. With the formulated selection criterion, a beam-element separation which was close to the beam-element width was found optimal for grids containing 3.0-mm-wide beam elements, while a separation which was considerably larger than the beam-element width was found advantageous for grids containing 0.5-mm-wide beam elements. With the single-grid irradiation setup, the VPDRs were close to 1.0 already at a distance of several cm from the target. The valley doses given to the normal tissue at 0.5 cm distance from the target volume could be limited to less than 10% of the mean target dose if a crossfiring setup with four interlaced grids was used. The dose distributions produced by grids containing 0.5- and 3.0-mm wide beam elements had characteristics which could be useful for grid therapy. Grids containing mm-wide carbon-ion beam elements could be advantageous due to the technical ease with which these beams can be produced and delivered, despite the reduced threshold doses observed for early and late responding normal tissue for beams of millimeter width, compared to submillimetric beams. The treatment simulations showed that nearly homogeneous dose distributions could be created inside the target volumes, combined with low valley doses in the normal tissue located close to the target volume, if the carbon-ion beam grids were crossfired in an interlaced manner with optimally selected beam-element separations. The formulated selection criterion was found useful for the quantitative evaluation of the dose distributions produced by the different irradiation setups. © 2018 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Phenomenology of leading nucleon production in e p collisions at HERA in the framework of fracture functions

NASA Astrophysics Data System (ADS)

Shoeibi, Samira; Taghavi-Shahri, F.; Khanpour, Hamzeh; Javidan, Kurosh

2018-04-01

In recent years, several experiments at the e-p collider HERA have collected high precision deep-inelastic scattering (DIS) data on the spectrum of leading nucleon carrying a large fraction of the proton's energy. In this paper, we have analyzed recent experimental data on the production of forward protons and neutrons in DIS at HERA in the framework of a perturbative QCD. We propose a technique based on the fractures functions framework, and extract the nucleon fracture functions (FFs) M2(n /p )(x ,Q2;xL) from global QCD analysis of DIS data measured by the ZEUS Collaboration at HERA. We have shown that an approach based on the fracture functions formalism allows us to phenomenologically parametrize the nucleon FFs. Considering both leading neutron as well as leading proton production data at HERA, we present the results for the separate parton distributions for all parton species, including valence quark densities, the antiquark densities, the strange sea distribution, and the gluon distribution functions. We proposed several parametrizations for the nucleon FFs and open the possibility of these asymmetries. The obtained optimum set of nucleon FFs is accompanied by Hessian uncertainty sets which allow one to propagate uncertainties to other observables interest. The extracted results for the t -integrated leading neutron F2LN (3 )(x ,Q2;xL) and leading proton F2LP (3 )(x ,Q2;xL) structure functions are in good agreement with all data analyzed, for a wide range of fractional momentum variable x as well as the longitudinal momentum fraction xL.

The role of hydrodynamic processes on anchovy eggs and larvae distribution in the sicily channel (mediterranean sea): a case study for the 2004 data set.

PubMed

Falcini, Federico; Palatella, Luigi; Cuttitta, Angela; Buongiorno Nardelli, Bruno; Lacorata, Guglielmo; Lanotte, Alessandra S; Patti, Bernardino; Santoleri, Rosalia

2015-01-01

Knowledge of the link between ocean hydrodynamics and distribution of small pelagic fish species is fundamental for the sustainable management of fishery resources. Both commercial and scientific communities are indeed seeking to provide services that could "connect the dots" among in situ and remote observations, numerical ocean modelling, and fisheries. In the Mediterranean Sea and, in particular, in the Sicily Channel the reproductive strategy of the European Anchovy (Engraulis encrasicolus) is strongly influenced by the oceanographic patterns, which are often visible in sea surface temperature satellite data. Based on these experimental evidences, we propose here a more general approach where the role of ocean currents, wind effects, and mesoscale activity are tied together. To investigate how these features affect anchovy larvae distribution, we pair ichthyoplankton observations to a wide remote sensing data set, and to Lagrangian numerical simulations for larval transport. Our analysis shows that while the wind-induced coastal current is able to transport anchovy larvae from spawning areas to the recruiting area off the Sicilian south-eastern tip, significant cross-shore transport due to the combination of strong northwesterly mistral winds and topographic effects delivers larvae away from the coastal conveyor belt. We then use a potential vorticity approach to describe the occurrence of larvae cross-shore transport. We conclude that monitoring and quantifying the upwelling on the southern Sicilian coast during the spawning season allows to estimate the cross-shore transport of larvae and the consequent decrease of individuals within the recruiting area.

Three-dimensional lattice Boltzmann model for compressible flows.

PubMed

Sun, Chenghai; Hsu, Andrew T

2003-07-01

A three-dimensional compressible lattice Boltzmann model is formulated on a cubic lattice. A very large particle-velocity set is incorporated in order to enable a greater variation in the mean velocity. Meanwhile, the support set of the equilibrium distribution has only six directions. Therefore, this model can efficiently handle flows over a wide range of Mach numbers and capture shock waves. Due to the simple form of the equilibrium distribution, the fourth-order velocity tensors are not involved in the formulation. Unlike the standard lattice Boltzmann model, no special treatment is required for the homogeneity of fourth-order velocity tensors on square lattices. The Navier-Stokes equations were recovered, using the Chapman-Enskog method from the Bhatnagar-Gross-Krook (BGK) lattice Boltzmann equation. The second-order discretization error of the fluctuation velocity in the macroscopic conservation equation was eliminated by means of a modified collision invariant. The model is suitable for both viscous and inviscid compressible flows with or without shocks. Since the present scheme deals only with the equilibrium distribution that depends only on fluid density, velocity, and internal energy, boundary conditions on curved wall are easily implemented by an extrapolation of macroscopic variables. To verify the scheme for inviscid flows, we have successfully simulated a three-dimensional shock-wave propagation in a box and a normal shock of Mach number 10 over a wedge. As an application to viscous flows, we have simulated a flat plate boundary layer flow, flow over a cylinder, and a transonic flow over a NACA0012 airfoil cascade.

Areas of potential suitability and survival of Dendroctonus valens in China under extreme climate warming scenario.

PubMed

He, S Y; Ge, X Z; Wang, T; Wen, J B; Zong, S X

2015-08-01

The areas in China with climates suitable for the potential distribution of the pest species red turpentine beetle (RTB) Dendroctonus valens LeConte (Coleoptera: Scolytidae) were predicted by CLIMEX based on historical climate data and future climate data with warming estimated. The model used a historical climate data set (1971-2000) and a simulated climate data set (2010-2039) provided by the Tyndall Centre for Climate Change (TYN SC 2.0). Based on the historical climate data, a wide area was available in China with a suitable climate for the beetle in which every province might contain suitable habitats for this pest, particularly all of the southern provinces. The northern limit of the distribution of the beetle was predicted to reach Yakeshi and Elunchun in Inner Mongolia, and the western boundary would reach to Keerkezi in Xinjiang Province. Based on a global-warming scenario, the area with a potential climate suited to RTB in the next 30 years (2010-2039) may extend further to the northeast. The northern limit of the distribution could reach most parts of south Heilongjiang Province, whereas the western limit would remain unchanged. Combined with the tendency for RTB to spread, the variation in suitable habitats within the scenario of extreme climate warming and the multiple geographical elements of China led us to assume that, within the next 30 years, RTB would spread towards the northeast, northwest, and central regions of China and could be a potentially serious problem for the forests of China.

The Role of Hydrodynamic Processes on Anchovy Eggs and Larvae Distribution in the Sicily Channel (Mediterranean Sea): A Case Study for the 2004 Data Set

PubMed Central

Falcini, Federico; Palatella, Luigi; Cuttitta, Angela; Buongiorno Nardelli, Bruno; Lacorata, Guglielmo; Lanotte, Alessandra S.; Patti, Bernardino; Santoleri, Rosalia

2015-01-01

Knowledge of the link between ocean hydrodynamics and distribution of small pelagic fish species is fundamental for the sustainable management of fishery resources. Both commercial and scientific communities are indeed seeking to provide services that could “connect the dots” among in situ and remote observations, numerical ocean modelling, and fisheries. In the Mediterranean Sea and, in particular, in the Sicily Channel the reproductive strategy of the European Anchovy (Engraulis encrasicolus) is strongly influenced by the oceanographic patterns, which are often visible in sea surface temperature satellite data. Based on these experimental evidences, we propose here a more general approach where the role of ocean currents, wind effects, and mesoscale activity are tied together. To investigate how these features affect anchovy larvae distribution, we pair ichthyoplankton observations to a wide remote sensing data set, and to Lagrangian numerical simulations for larval transport. Our analysis shows that while the wind-induced coastal current is able to transport anchovy larvae from spawning areas to the recruiting area off the Sicilian south-eastern tip, significant cross-shore transport due to the combination of strong northwesterly mistral winds and topographic effects delivers larvae away from the coastal conveyor belt. We then use a potential vorticity approach to describe the occurrence of larvae cross-shore transport. We conclude that monitoring and quantifying the upwelling on the southern Sicilian coast during the spawning season allows to estimate the cross-shore transport of larvae and the consequent decrease of individuals within the recruiting area. PMID:25915489

Using a higher criticism statistic to detect modest effects in a genome-wide study of rheumatoid arthritis

PubMed Central

2009-01-01

In high-dimensional studies such as genome-wide association studies, the correction for multiple testing in order to control total type I error results in decreased power to detect modest effects. We present a new analytical approach based on the higher criticism statistic that allows identification of the presence of modest effects. We apply our method to the genome-wide study of rheumatoid arthritis provided in the Genetic Analysis Workshop 16 Problem 1 data set. There is evidence for unknown bias in this study that could be explained by the presence of undetected modest effects. We compared the asymptotic and empirical thresholds for the higher criticism statistic. Using the asymptotic threshold we detected the presence of modest effects genome-wide. We also detected modest effects using 90th percentile of the empirical null distribution as a threshold; however, there is no such evidence when the 95th and 99th percentiles were used. While the higher criticism method suggests that there is some evidence for modest effects, interpreting individual single-nucleotide polymorphisms with significant higher criticism statistics is of undermined value. The goal of higher criticism is to alert the researcher that genetic effects remain to be discovered and to promote the use of more targeted and powerful studies to detect the remaining effects. PMID:20018032

Stepwise inference of likely dynamic flux distributions from metabolic time series data.

PubMed

Faraji, Mojdeh; Voit, Eberhard O

2017-07-15

Most metabolic pathways contain more reactions than metabolites and therefore have a wide stoichiometric matrix that corresponds to infinitely many possible flux distributions that are perfectly compatible with the dynamics of the metabolites in a given dataset. This under-determinedness poses a challenge for the quantitative characterization of flux distributions from time series data and thus for the design of adequate, predictive models. Here we propose a method that reduces the degrees of freedom in a stepwise manner and leads to a dynamic flux distribution that is, in a statistical sense, likely to be close to the true distribution. We applied the proposed method to the lignin biosynthesis pathway in switchgrass. The system consists of 16 metabolites and 23 enzymatic reactions. It has seven degrees of freedom and therefore admits a large space of dynamic flux distributions that all fit a set of metabolic time series data equally well. The proposed method reduces this space in a systematic and biologically reasonable manner and converges to a likely dynamic flux distribution in just a few iterations. The estimated solution and the true flux distribution, which is known in this case, show excellent agreement and thereby lend support to the method. The computational model was implemented in MATLAB (version R2014a, The MathWorks, Natick, MA). The source code is available at https://github.gatech.edu/VoitLab/Stepwise-Inference-of-Likely-Dynamic-Flux-Distributions and www.bst.bme.gatech.edu/research.php . mojdeh@gatech.edu or eberhard.voit@bme.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Predicting the spatial and temporal distributions of marine fish species utilizing earth system data in a MaxEnt model framework

NASA Astrophysics Data System (ADS)

Wang, L.; Kerr, L. A.; Bridger, E.

2016-02-01

Changes in species distributions have been widely associated with climate change. Understanding how ocean temperatures influence species distributions is critical for elucidating the role of climate in ecosystem change as well as for forecasting how species may be distributed in the future. As such, species distribution modeling (SDM) is increasingly useful in marine ecosystems research, as it can enable estimation of the likelihood of encountering marine fish in space or time as a function of a set of environmental and ecosystem conditions. Many traditional SDM approaches are applied to species data collected through standardized methods that include both presence and absence records, but are incapable of using presence-only data, such as those collected from fisheries or through citizen science programs. Maximum entropy (MaxEnt) models provide promising tools as they can predict species distributions from incomplete information (presence-only data). We developed a MaxEnt framework to relate the occurrence records of several marine fish species (e.g. Atlantic herring, Atlantic mackerel, and butterfish) to environmental conditions. Environmental variables derived from remote sensing, such as monthly average sea surface temperature (SST), are matched with fish species data, and model results indicate the relative occurrence rate of the species as a function of the environmental variables. The results can be used to provide hindcasts of where species might have been in the past in relation to historical environmental conditions, nowcasts in relation to current conditions, and forecasts of future species distributions. In this presentation, we will assess the relative influence of several environmental factors on marine fish species distributions, and evaluate the effects of data coverage on these presence-only models. We will also discuss how the information from species distribution forecasts can support climate adaptation planning in marine fisheries.

Response Grids: Practical Ways to Display Large Data Sets with High Visual Impact

ERIC Educational Resources Information Center

Gates, Simon

2013-01-01

Spreadsheets are useful for large data sets but they may be too wide or too long to print as conventional tables. Response grids offer solutions to the challenges posed by any large data set. They have wide application throughout science and for every subject and context where visual data displays are designed, within education and elsewhere.…

Age gradients in the stellar populations of massive star forming regions based on a new stellar chronometer

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

Getman, Konstantin V.; Feigelson, Eric D.; Kuhn, Michael A.

2014-06-01

A major impediment to understanding star formation in massive star-forming regions (MSFRs) is the absence of a reliable stellar chronometer to unravel their complex star formation histories. We present a new estimation of stellar ages using a new method that employs near-infrared (NIR) and X-ray photometry, Age {sub JX} . Stellar masses are derived from X-ray luminosities using the L{sub X} -M relation from the Taurus cloud. J-band luminosities are compared to mass-dependent pre-main-sequence (PMS) evolutionary models to estimate ages. Age {sub JX} is sensitive to a wide range of evolutionary stages, from disk-bearing stars embedded in a cloud tomore » widely dispersed older PMS stars. The Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) project characterizes 20 OB-dominated MSFRs using X-ray, mid-infrared, and NIR catalogs. The Age {sub JX} method has been applied to 5525 out of 31,784 MYStIX Probable Complex Members. We provide a homogeneous set of median ages for over 100 subclusters in 15 MSFRs; median subcluster ages range between 0.5 Myr and 5 Myr. The important science result is the discovery of age gradients across MYStIX regions. The wide MSFR age distribution appears as spatially segregated structures with different ages. The Age {sub JX} ages are youngest in obscured locations in molecular clouds, intermediate in revealed stellar clusters, and oldest in distributed populations. The NIR color index J – H, a surrogate measure of extinction, can serve as an approximate age predictor for young embedded clusters.« less

The ambient dose equivalent at flight altitudes: a fit to a large set of data using a Bayesian approach.

PubMed

Wissmann, F; Reginatto, M; Möller, T

2010-09-01

The problem of finding a simple, generally applicable description of worldwide measured ambient dose equivalent rates at aviation altitudes between 8 and 12 km is difficult to solve due to the large variety of functional forms and parametrisations that are possible. We present an approach that uses Bayesian statistics and Monte Carlo methods to fit mathematical models to a large set of data and to compare the different models. About 2500 data points measured in the periods 1997-1999 and 2003-2006 were used. Since the data cover wide ranges of barometric altitude, vertical cut-off rigidity and phases in the solar cycle 23, we developed functions which depend on these three variables. Whereas the dependence on the vertical cut-off rigidity is described by an exponential, the dependences on barometric altitude and solar activity may be approximated by linear functions in the ranges under consideration. Therefore, a simple Taylor expansion was used to define different models and to investigate the relevance of the different expansion coefficients. With the method presented here, it is possible to obtain probability distributions for each expansion coefficient and thus to extract reliable uncertainties even for the dose rate evaluated. The resulting function agrees well with new measurements made at fixed geographic positions and during long haul flights covering a wide range of latitudes.

Modelling large scale human activity in San Francisco

NASA Astrophysics Data System (ADS)

Gonzalez, Marta

2010-03-01

Diverse group of people with a wide variety of schedules, activities and travel needs compose our cities nowadays. This represents a big challenge for modeling travel behaviors in urban environments; those models are of crucial interest for a wide variety of applications such as traffic forecasting, spreading of viruses, or measuring human exposure to air pollutants. The traditional means to obtain knowledge about travel behavior is limited to surveys on travel journeys. The obtained information is based in questionnaires that are usually costly to implement and with intrinsic limitations to cover large number of individuals and some problems of reliability. Using mobile phone data, we explore the basic characteristics of a model of human travel: The distribution of agents is proportional to the population density of a given region, and each agent has a characteristic trajectory size contain information on frequency of visits to different locations. Additionally we use a complementary data set given by smart subway fare cards offering us information about the exact time of each passenger getting in or getting out of the subway station and the coordinates of it. This allows us to uncover the temporal aspects of the mobility. Since we have the actual time and place of individual's origin and destination we can understand the temporal patterns in each visited location with further details. Integrating two described data set we provide a dynamical model of human travels that incorporates different aspects observed empirically.

Surface Mass Balance of the Columbia Glacier, Alaska, 1978 and 2010 Balance Years

USGS Publications Warehouse

O'Neel, Shad

2012-01-01

Although Columbia Glacier is one of the largest sources of glacier mass loss in Alaska, surface mass balance measurements are sparse, with only a single data set available from 1978. The dearth of surface mass-balance data prohibits partitioning of the total mass losses between dynamics and surface forcing; however, the accurate inclusion of calving glaciers into predictive models requires both dynamic and climatic forcing of total mass balance. During 2010, the U.S. Geological Survey collected surface balance data at several locations distributed over the surface of Columbia Glacier to estimate the glacier-wide annual balance for balance year 2010 using the 2007 area-altitude distribution. This report also summarizes data collected in 1978, calculates the 1978 annual surface balance, and uses these observations to constrain the 2010 values, particularly the shape of the balance profile. Both years exhibit balances indicative of near-equilibrium surface mass-balance conditions, and demonstrate the importance of dynamic processes during the rapid retreat.

A Distributed Wireless Camera System for the Management of Parking Spaces

PubMed Central

Melničuk, Petr

2017-01-01

The importance of detection of parking space availability is still growing, particularly in major cities. This paper deals with the design of a distributed wireless camera system for the management of parking spaces, which can determine occupancy of the parking space based on the information from multiple cameras. The proposed system uses small camera modules based on Raspberry Pi Zero and computationally efficient algorithm for the occupancy detection based on the histogram of oriented gradients (HOG) feature descriptor and support vector machine (SVM) classifier. We have included information about the orientation of the vehicle as a supporting feature, which has enabled us to achieve better accuracy. The described solution can deliver occupancy information at the rate of 10 parking spaces per second with more than 90% accuracy in a wide range of conditions. Reliability of the implemented algorithm is evaluated with three different test sets which altogether contain over 700,000 samples of parking spaces. PMID:29283371

[Research of regional medical consumables reagent logistics system in the modern hospital].

PubMed

Wu, Jingjiong; Zhang, Yanwen; Luo, Xiaochen; Zhang, Qing; Zhu, Jianxin

2013-09-01

To explore the modern hospital and regional medical consumable reagents logistics system management. The characteristics of regional logistics, through cooperation between medical institutions within the region, and organize a wide range of special logistics activities, to make reasonable of the regional medical consumable reagents logistics. To set the regional management system, dynamic management systems, supply chain information management system, after-sales service system and assessment system. By the research of existing medical market and medical resources, to establish the regional medical supplies reagents directory and the initial data. The emphasis is centralized dispatch of medical supplies reagents, to introduce qualified logistics company for dispatching, to improve the modern hospital management efficiency, to costs down. Regional medical center and regional community health service centers constitute a regional logistics network, the introduction of medical consumable reagents logistics services, fully embodies integrity level, relevance, purpose, environmental adaptability of characteristics by the medical consumable reagents regional logistics distribution. Modern logistics distribution systems can increase the area of medical consumables reagent management efficiency and reduce costs.

Deriving photometric redshifts using fuzzy archetypes and self-organizing maps - I. Methodology

NASA Astrophysics Data System (ADS)

Speagle, Joshua S.; Eisenstein, Daniel J.

2017-07-01

We propose a method to substantially increase the flexibility and power of template fitting-based photometric redshifts by transforming a large number of galaxy spectral templates into a corresponding collection of 'fuzzy archetypes' using a suitable set of perturbative priors designed to account for empirical variation in dust attenuation and emission-line strengths. To bypass widely separated degeneracies in parameter space (e.g. the redshift-reddening degeneracy), we train self-organizing maps (SOMs) on large 'model catalogues' generated from Monte Carlo sampling of our fuzzy archetypes to cluster the predicted observables in a topologically smooth fashion. Subsequent sampling over the SOM then allows full reconstruction of the relevant probability distribution functions (PDFs). This combined approach enables the multimodal exploration of known variation among galaxy spectral energy distributions with minimal modelling assumptions. We demonstrate the power of this approach to recover full redshift PDFs using discrete Markov chain Monte Carlo sampling methods combined with SOMs constructed from Large Synoptic Survey Telescope ugrizY and Euclid YJH mock photometry.

The imaging node for the Planetary Data System

USGS Publications Warehouse

Eliason, E.M.; LaVoie, S.K.; Soderblom, L.A.

1996-01-01

The Planetary Data System Imaging Node maintains and distributes the archives of planetary image data acquired from NASA's flight projects with the primary goal of enabling the science community to perform image processing and analysis on the data. The Node provides direct and easy access to the digital image archives through wide distribution of the data on CD-ROM media and on-line remote-access tools by way of Internet services. The Node provides digital image processing tools and the expertise and guidance necessary to understand the image collections. The data collections, now approaching one terabyte in volume, provide a foundation for remote sensing studies for virtually all the planetary systems in our solar system (except for Pluto). The Node is responsible for restoring data sets from past missions in danger of being lost. The Node works with active flight projects to assist in the creation of their archive products and to ensure that their products and data catalogs become an integral part of the Node's data collections.

Direct and full-scale experimental verifications towards ground-satellite quantum key distribution

NASA Astrophysics Data System (ADS)

Wang, Jian-Yu; Yang, Bin; Liao, Sheng-Kai; Zhang, Liang; Shen, Qi; Hu, Xiao-Fang; Wu, Jin-Cai; Yang, Shi-Ji; Jiang, Hao; Tang, Yan-Lin; Zhong, Bo; Liang, Hao; Liu, Wei-Yue; Hu, Yi-Hua; Huang, Yong-Mei; Qi, Bo; Ren, Ji-Gang; Pan, Ge-Sheng; Yin, Juan; Jia, Jian-Jun; Chen, Yu-Ao; Chen, Kai; Peng, Cheng-Zhi; Pan, Jian-Wei

2013-05-01

Quantum key distribution (QKD) provides the only intrinsically unconditional secure method for communication based on the principle of quantum mechanics. Compared with fibre-based demonstrations, free-space links could provide the most appealing solution for communication over much larger distances. Despite significant efforts, all realizations to date rely on stationary sites. Experimental verifications are therefore extremely crucial for applications to a typical low Earth orbit satellite. To achieve direct and full-scale verifications of our set-up, we have carried out three independent experiments with a decoy-state QKD system, and overcome all conditions. The system is operated on a moving platform (using a turntable), on a floating platform (using a hot-air balloon), and with a high-loss channel to demonstrate performances under conditions of rapid motion, attitude change, vibration, random movement of satellites, and a high-loss regime. The experiments address wide ranges of all leading parameters relevant to low Earth orbit satellites. Our results pave the way towards ground-satellite QKD and a global quantum communication network.

Clear and Measurable Signature of Modified Gravity in the Galaxy Velocity Field

NASA Astrophysics Data System (ADS)

Hellwing, Wojciech A.; Barreira, Alexandre; Frenk, Carlos S.; Li, Baojiu; Cole, Shaun

2014-06-01

The velocity field of dark matter and galaxies reflects the continued action of gravity throughout cosmic history. We show that the low-order moments of the pairwise velocity distribution v12 are a powerful diagnostic of the laws of gravity on cosmological scales. In particular, the projected line-of-sight galaxy pairwise velocity dispersion σ12(r) is very sensitive to the presence of modified gravity. Using a set of high-resolution N-body simulations, we compute the pairwise velocity distribution and its projected line-of-sight dispersion for a class of modified gravity theories: the chameleon f(R) gravity and Galileon gravity (cubic and quartic). The velocities of dark matter halos with a wide range of masses would exhibit deviations from general relativity at the (5-10)σ level. We examine strategies for detecting these deviations in galaxy redshift and peculiar velocity surveys. If detected, this signature would be a "smoking gun" for modified gravity.

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.

Liquid chromatographic determination of minocycline in brain-to-plasma distribution studies in the rat.

PubMed

Colovic, Milena; Caccia, Silvio

2003-07-05

An isocratic reversed-phase high-performance liquid chromatographic procedure was developed for the determination of minocycline in rat plasma and brain and applied to brain-to-blood (plasma) distribution studies. The procedure is based on isolation of the compound and the internal standard (either demeclocycline or tetracycline may be used) from plasma and brain constituents using the Oasis HLB cartridge, with satisfactory recovery and specificity, and separation on a Symmetry Shield RP8 (15 cm x 4.6 mm, 3.5 microm) column coupled with a UV detector set at 350 nm. The assay was linear over a wide range, with a lower limit of quantification of 50 ng ml(-1) or g(-1), using 0.2 ml of plasma and about 200 mg of brain tissue. Precision and accuracy were acceptable. In the rat minocycline crossed the blood-brain barrier slowly, achieving mean brain concentrations between 30 and 40% of the equivalent systemic exposure, regardless of the dose and route of administration.

PARALLEL HOP: A SCALABLE HALO FINDER FOR MASSIVE COSMOLOGICAL DATA SETS

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

Skory, Stephen; Turk, Matthew J.; Norman, Michael L.

2010-11-15

Modern N-body cosmological simulations contain billions (10{sup 9}) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly employed halo finders, suchmore » that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here, we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes message passing interface and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger data sets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit {sup yt}, an analysis toolkit for adaptive mesh refinement data that include complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and data sets in excess of 2000{sup 3} particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.« less

COMPARATIVE ASSESSMENT OF THE COMPOSITION AND CHARGE STATE OF NITROGENASE FeMo-COFACTOR

PubMed Central

Harris, Travis V.; Szilagyi, Robert K.

2011-01-01

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed the exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional and basis set. Overall, we found that a more oxidized [MoIV-2FeII-5FeIII-9S2−-C4−] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria, and is thus favored over the currently preferred composition of [MoIV-4FeII-3FeIII-9S2−-N3−] from the literature. PMID:21545160

Multiwaveguide implantable probe for light delivery to sets of distributed brain targets.

PubMed

Zorzos, Anthony N; Boyden, Edward S; Fonstad, Clifton G

2010-12-15

Optical fibers are commonly inserted into living tissues such as the brain in order to deliver light to deep targets for neuroscientific and neuroengineering applications such as optogenetics, in which light is used to activate or silence neurons expressing specific photosensitive proteins. However, an optical fiber is limited to delivering light to a single target within the three-dimensional structure of the brain. We here demonstrate a multiwaveguide probe capable of independently delivering light to multiple targets along the probe axis, thus enabling versatile optical control of sets of distributed brain targets. The 1.45-cm-long probe is microfabricated in the form of a 360-μm-wide array of 12 parallel silicon oxynitride (SiON) multimode waveguides clad with SiO(2) and coated with aluminum; probes of custom dimensions are easily created as well. The waveguide array accepts light from a set of sources at the input end and guides the light down each waveguide to an aluminum corner mirror that efficiently deflects light away from the probe axis. Light losses at each stage are small (input coupling loss, 0.4 ± 0.3 dB; bend loss, negligible; propagation loss, 3.1 ± 1 dB/cm using the outscattering method and 3.2 ± 0.4 dB/cm using the cutback method; corner mirror loss, 1.5 ± 0.4 dB); a waveguide coupled, for example, to a 5 mW source will deliver over 1.5 mW to a target at a depth of 1 cm.

Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR.

PubMed

Jahn, Michael; Vorpahl, Carsten; Hübschmann, Thomas; Harms, Hauke; Müller, Susann

2016-12-19

Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells.

Modeling natural wetlands: A new global framework built on wetland observations

NASA Astrophysics Data System (ADS)

Matthews, E.; Romanski, J.; Olefeldt, D.

2015-12-01

Natural wetlands are the world's largest methane (CH4) source, and their distribution and CH4 fluxes are sensitive to interannual and longer-term climate variations. Wetland distributions used in wetland-CH4 models diverge widely, and these geographic differences contribute substantially to large variations in magnitude, seasonality and distribution of modeled methane fluxes. Modeling wetland type and distribution—closely tied to simulating CH4 emissions—is a high priority, particularly for studies of wetlands and CH4 dynamics under past and future climates. Methane-wetland models either prescribe or simulate methane-producing areas (aka wetlands) and both approaches result in predictable over- and under-estimates. 1) Monthly satellite-derived inundation data include flooded areas that are not wetlands (e.g., lakes, reservoirs, and rivers), and do not identify non-flooded wetlands. 2) Models simulating methane-producing areas overwhelmingly rely on modeled soil moisture, systematically over-estimating total global area, with regional over- and under-estimates, while schemes to model soil-moisture typically cannot account for positive water tables (i.e., flooding). Interestingly, while these distinct hydrological approaches to identify wetlands are complementary, merging them does not provide critical data needed to model wetlands for methane studies. We present a new integrated framework for modeling wetlands, and ultimately their methane emissions, that exploits the extensive body of data and information on wetlands. The foundation of the approach is an existing global gridded data set comprising all and only wetlands, including vegetation information. This data set is augmented with data inter alia on climate, inundation dynamics, soil type and soil carbon, permafrost, active-layer depth, growth form, and species composition. We investigate this enhanced wetland data set to identify which variables best explain occurrence and characteristics of observed wetland ecosystems. The novelty of the new approach is that it starts from what we know about wetlands, builds ecosystem-specific models from these observations, and avoids known biases in current hydrology-based approaches to wetland definition in methane models.

Selection of organisms for the co-evolution-based study of protein interactions.

PubMed

Herman, Dorota; Ochoa, David; Juan, David; Lopez, Daniel; Valencia, Alfonso; Pazos, Florencio

2011-09-12

The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.

Parallel Clustering Algorithm for Large-Scale Biological Data Sets

PubMed Central

Wang, Minchao; Zhang, Wu; Ding, Wang; Dai, Dongbo; Zhang, Huiran; Xie, Hao; Chen, Luonan; Guo, Yike; Xie, Jiang

2014-01-01

Backgrounds Recent explosion of biological data brings a great challenge for the traditional clustering algorithms. With increasing scale of data sets, much larger memory and longer runtime are required for the cluster identification problems. The affinity propagation algorithm outperforms many other classical clustering algorithms and is widely applied into the biological researches. However, the time and space complexity become a great bottleneck when handling the large-scale data sets. Moreover, the similarity matrix, whose constructing procedure takes long runtime, is required before running the affinity propagation algorithm, since the algorithm clusters data sets based on the similarities between data pairs. Methods Two types of parallel architectures are proposed in this paper to accelerate the similarity matrix constructing procedure and the affinity propagation algorithm. The memory-shared architecture is used to construct the similarity matrix, and the distributed system is taken for the affinity propagation algorithm, because of its large memory size and great computing capacity. An appropriate way of data partition and reduction is designed in our method, in order to minimize the global communication cost among processes. Result A speedup of 100 is gained with 128 cores. The runtime is reduced from serval hours to a few seconds, which indicates that parallel algorithm is capable of handling large-scale data sets effectively. The parallel affinity propagation also achieves a good performance when clustering large-scale gene data (microarray) and detecting families in large protein superfamilies. PMID:24705246

Contrasting bee pollination in two co-occurring distylic species of Cordia (Cordiaceae, Boraginales) in the Brazilian semi-arid Caatinga: generalist in C. globosa vs. specialist in C. leucocephala.

PubMed

Machado, Isabel C; Lopes, Ariadna V; Sazima, Marlies

2010-12-01

In this study we compare the reproductive biology of Cordia globosa and C. leucocephala (Cordiaceae, Boraginales; formerly referred to Boraginaceae) to understand the functioning of the floral morphs and the relations with their effective pollinators. The species are synchronopatric, distylic, and self-incompatible. Though they share melittophilous traits, the main visitor and pollinator of C. globosa was the generalist and exotic bee Apis mellifera, while the only one of C. leucocephala was the oligoletic bee Ceblurgus longipalpis. These two latter species are restricted to the Caatinga of NE Brazil, contrasting with the wide distribution of Cordia globosa. While the fruit-set for C. globosa was high, independently if the pollen donor/stigma receptor was a pin (long-styled) or thrum (short-styled) individual, in C. leucocephala the fruit-set was low and occurred only when a thrum individual was the pollen donor. This raises the possibility of this species moving towards dioecy. The high natural fruit-set of C. globosa confirms the generalist bee as its effective pollinator. The low fruit-set after manual crosses in C. leucocephala may be due to low pollen viability. Additionally, the low natural fruit-set (two times lower than after crosses) may be related with the foraging behavior of the specialist pollinator.

Selection of organisms for the co-evolution-based study of protein interactions

PubMed Central

2011-01-01

Background The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. Results We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. Conclusions In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest. PMID:21910884

Prediction of vein connectivity using the percolation approach: model test with field data

NASA Astrophysics Data System (ADS)

Belayneh, M.; Masihi, M.; Matthäi, S. K.; King, P. R.

2006-09-01

Evaluating the uncertainty in fracture connectivity and its effect on the flow behaviour of natural fracture networks formed under in situ conditions is an extremely difficult task. One widely used probabilistic approach is to use percolation theory, which is well adapted to estimate the connectivity and conductivity of geometrical objects near the percolation threshold. In this paper, we apply scaling laws from percolation theory to predict the connectivity of vein sets exposed on the southern margin of the Bristol Channel Basin. Two vein sets in a limestone bed interbedded with shales on the limb of a rollover fold were analysed for length, spacing and aperture distributions. Eight scan lines, low-level aerial photographs and mosaics of photographs taken with a tripod were used. The analysed veins formed contemporaneously with the rollover fold during basin subsidence on the hanging wall of a listric normal fault. The first vein set, V1, is fold axis-parallel (i.e. striking ~100°) and normal to bedding. The second vein set, V2, strikes 140° and crosscuts V1. We find a close agreement in connectivity between our predictions using the percolation approach and the field data. The implication is that reasonable predictions of vein connectivity can be made from sparse data obtained from boreholes or (limited) sporadic outcrop.

Using multifractal modeling as a standard tool in geochemical exploration for predicting mineralized areas

NASA Astrophysics Data System (ADS)

Gonçalves, Mario A.

2015-04-01

It has been 20 years since the pioneering work of Cheng et al (1994) first proposed a quantitative relationship for the areas enclosing concentration values of an element above given thresholds and their distribution in the field, known as concentration-area (CA) method, which is based in multifractal theory. The method allows the definition of geochemical anomalies in wide set of geological backgrounds but it took nearly 15 years before it became a widely used methodology for mineral exploration. The method was also extended to 1D and 3D data sets. It is worth noting the variety of methods that spanned from the theory of fractals. Building on previous models, including multiplicative cascades and size-grade relationships, increasing evidence points to the powerful tools of fractal theory to describe and model ore deposit distribution and formation. However, while much of these approaches become complex and not easy to use, the CA method is remarkable for its utter simplicity and disarming results obtained when confronted with the geological reality in the field. This is most valued by companies and professionals undertaking geochemical exploration surveys for the characterization or refining of potential ore targets or known mineralized areas. Several approaches have combined the CA method with geostatistic modeling and simulation and other established statistical techniques in order to enhance anomalous threshold identification. Examples are not restricted to geochemical exploration alone, other applications being studies on environmental change. Some of these examples will be addressed as they have been applied to different regions in the world, but particular emphasis will be put on geochemical exploration surveys in different geotectonic units of the Variscan basement in the Iberian Peninsula. These include quartz-vein gold mineralization in Northern Portugal and several surveys for base metals over two wide areas, which served to re-evaluate much of the scattered geochemical data sets that have been accumulating for decades of mining exploration in Southern Portugal. The studied zones include: the tectonic controlled quartz-vein Au-Sb mineralizations, the gabbroic and ultramafic complex of the southern border of the Ossa-Morena Zone, and the rocks belonging to the World-class massive sulfide province, the Iberian Pyrite Belt (IPB). The methodology used the CA method but also variogram analysis and modelling to outline and classify different sets of mineral deposits before confirmation in the field. This diversity of geologic contexts serves to show how effective and powerful the CA method can be, since it not only enhances already known mineralizations, it allowed the screening and identification of several new mineralized spots that have been previously overlooked. This has been of particularly economic importance because a major re-analysis of data and new exploration campaigns are currently under way for the next years in the IPB, with the potential for opening a new paradigm in the exploration for massive sulfide deposits in the region. Cheng et al, 1994, J. Geochem. Explor., 51, 109.

Calibrated tree priors for relaxed phylogenetics and divergence time estimation.

PubMed

Heled, Joseph; Drummond, Alexei J

2012-01-01

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.

Strategies for lidar characterization of particulates from point and area sources

NASA Astrophysics Data System (ADS)

Wojcik, Michael D.; Moore, Kori D.; Martin, Randal S.; Hatfield, Jerry

2010-10-01

Use of ground based remote sensing technologies such as scanning lidar systems (light detection and ranging) has gained traction in characterizing ambient aerosols due to some key advantages such as wide area of regard (10 km2), fast response time, high spatial resolution (<10 m) and high sensitivity. Energy Dynamics Laboratory and Utah State University, in conjunction with the USDA-ARS, has developed a three-wavelength scanning lidar system called Aglite that has been successfully deployed to characterize particle motion, concentration, and size distribution at both point and diffuse area sources in agricultural and industrial settings. A suite of massbased and size distribution point sensors are used to locally calibrate the lidar. Generating meaningful particle size distribution, mass concentration, and emission rate results based on lidar data is dependent on strategic onsite deployment of these point sensors with successful local meteorological measurements. Deployment strategies learned from field use of this entire measurement system over five years include the characterization of local meteorology and its predictability prior to deployment, the placement of point sensors to prevent contamination and overloading, the positioning of the lidar and beam plane to avoid hard target interferences, and the usefulness of photographic and written observational data.

Electronic Structure of Fullerene Acceptors in Organic Bulk-Heterojunctions. A Combined EPR and DFT Study

DOE PAGES

Mardis, Kristy L.; Webb, J.; Holloway, Tarita; ...

2015-12-03

Organic photovoltaic (OPV) devices are a promising alternative energy source. Attempts to improve their performance have focused on the optimization of electron-donating polymers, while electron-accepting fullerenes have received less attention. Here, we report an electronic structure study of the widely used soluble fullerene derivatives PC61BM and PC71BM in their singly reduced state, that are generated in the polymer:fullerene blends upon light-induced charge separation. Density functional theory (DFT) calculations characterize the electronic structures of the fullerene radical anions through spin density distributions and magnetic resonance parameters. The good agreement of the calculated magnetic resonance parameters with those determined experimentally by advancedmore » electron paramagnetic resonance (EPR) allows the validation of the DFT calculations. Thus, for the first time, the complete set of magnetic resonance parameters including directions of the principal g-tensor axes were determined. For both molecules, no spin density is present on the PCBM side chain, and the axis of the largest g-value lies along the PCBM molecular axis. While the spin density distribution is largely uniform for PC61BM, it is not evenly distributed for PC71BM.« less

An overview of the EOSDIS V0 information management system: Lessons learned from the implementation of a distributed data system

NASA Technical Reports Server (NTRS)

Ryan, Patrick M.

1994-01-01

The EOSDIS Version 0 system, released in July, 1994, is a working prototype of a distributed data system. One of the purposes of the V0 project is to take several existing data systems and coordinate them into one system while maintaining the independent nature of the original systems. The project is a learning experience and the lessons are being passed on to the architects of the system which will distribute the data received from the planned EOS satellites. In the V0 system, the data resides on heterogeneous systems across the globe but users are presented with a single, integrated interface. This interface allows users to query the participating data centers based on a wide set of criteria. Because this system is a prototype, we used many novel approaches in trying to connect a diverse group of users with the huge amount of available data. Some of these methods worked and others did not. Now that V0 has been released to the public, we can look back at the design and implementation of the system and also consider some possible future directions for the next generation of EOSDIS.

Joint probabilistic determination of earthquake location and velocity structure: application to local and regional events

NASA Astrophysics Data System (ADS)

Beucler, E.; Haugmard, M.; Mocquet, A.

2016-12-01

The most widely used inversion schemes to locate earthquakes are based on iterative linearized least-squares algorithms and using an a priori knowledge of the propagation medium. When a small amount of observations is available for moderate events for instance, these methods may lead to large trade-offs between outputs and both the velocity model and the initial set of hypocentral parameters. We present a joint structure-source determination approach using Bayesian inferences. Monte-Carlo continuous samplings, using Markov chains, generate models within a broad range of parameters, distributed according to the unknown posterior distributions. The non-linear exploration of both the seismic structure (velocity and thickness) and the source parameters relies on a fast forward problem using 1-D travel time computations. The a posteriori covariances between parameters (hypocentre depth, origin time and seismic structure among others) are computed and explicitly documented. This method manages to decrease the influence of the surrounding seismic network geometry (sparse and/or azimuthally inhomogeneous) and a too constrained velocity structure by inferring realistic distributions on hypocentral parameters. Our algorithm is successfully used to accurately locate events of the Armorican Massif (western France), which is characterized by moderate and apparently diffuse local seismicity.

Global-scale analysis of vegetation indices for moderate resolution monitoring of terrestrial vegetation

NASA Astrophysics Data System (ADS)

Huete, Alfredo R.; Didan, Kamel; van Leeuwen, Willem J. D.; Vermote, Eric F.

1999-12-01

Vegetation indices have emerged as important tools in the seasonal and inter-annual monitoring of the Earth's vegetation. They are radiometric measures of the amount and condition of vegetation. In this study, the Sea-viewing Wide Field-of-View sensor (SeaWiFS) is used to investigate coarse resolution monitoring of vegetation with multiple indices. A 30-day series of SeaWiFS data, corrected for molecular scattering and absorption, was composited to cloud-free, single channel reflectance images. The normalized difference vegetation index (NDVI) and an optimized index, the enhanced vegetation index (EVI), were computed over various 'continental' regions. The EVI had a normal distribution of values over the continental set of biomes while the NDVI was skewed toward higher values and saturated over forested regions. The NDVI resembled the skewed distributions found in the red band while the EVI resembled the normal distributions found in the NIR band. The EVI minimized smoke contamination over extensive portions of the tropics. As a result, major biome types with continental regions were discriminable in both the EVI imagery and histograms, whereas smoke and saturation considerably degraded the NDVI histogram structure preventing reliable discrimination of biome types.

A Hybrid Method for Accelerated Simulation of Coulomb Collisions in a Plasma

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

Caflisch, R; Wang, C; Dimarco, G

2007-10-09

If the collisional time scale for Coulomb collisions is comparable to the characteristic time scales for a plasma, then simulation of Coulomb collisions may be important for computation of kinetic plasma dynamics. This can be a computational bottleneck because of the large number of simulated particles and collisions (or phase-space resolution requirements in continuum algorithms), as well as the wide range of collision rates over the velocity distribution function. This paper considers Monte Carlo simulation of Coulomb collisions using the binary collision models of Takizuka & Abe and Nanbu. It presents a hybrid method for accelerating the computation of Coulombmore » collisions. The hybrid method represents the velocity distribution function as a combination of a thermal component (a Maxwellian distribution) and a kinetic component (a set of discrete particles). Collisions between particles from the thermal component preserve the Maxwellian; collisions between particles from the kinetic component are performed using the method of or Nanbu. Collisions between the kinetic and thermal components are performed by sampling a particle from the thermal component and selecting a particle from the kinetic component. Particles are also transferred between the two components according to thermalization and dethermalization probabilities, which are functions of phase space.« less

Highly dynamic animal contact network and implications on disease transmission

PubMed Central

Chen, Shi; White, Brad J.; Sanderson, Michael W.; Amrine, David E.; Ilany, Amiyaal; Lanzas, Cristina

2014-01-01

Contact patterns among hosts are considered as one of the most critical factors contributing to unequal pathogen transmission. Consequently, networks have been widely applied in infectious disease modeling. However most studies assume static network structure due to lack of accurate observation and appropriate analytic tools. In this study we used high temporal and spatial resolution animal position data to construct a high-resolution contact network relevant to infectious disease transmission. The animal contact network aggregated at hourly level was highly variable and dynamic within and between days, for both network structure (network degree distribution) and individual rank of degree distribution in the network (degree order). We integrated network degree distribution and degree order heterogeneities with a commonly used contact-based, directly transmitted disease model to quantify the effect of these two sources of heterogeneity on the infectious disease dynamics. Four conditions were simulated based on the combination of these two heterogeneities. Simulation results indicated that disease dynamics and individual contribution to new infections varied substantially among these four conditions under both parameter settings. Changes in the contact network had a greater effect on disease dynamics for pathogens with smaller basic reproduction number (i.e. R0 < 2). PMID:24667241

An Ultra-High Fluorescence Enhancement and High Throughput Assay for Revealing Expression and Internalization of Chemokine Receptor CXCR4.

PubMed

He, Hua; Wang, Xiaojuan; Cheng, Tiantian; Xia, Yongqing; Lao, Jun; Ge, Baosheng; Ren, Hao; Khan, Naseer Ullah; Huang, Fang

2016-04-18

Revealing chemokine receptor CXCR4 expression, distribution, and internalization levels in different cancers helps to evaluate cancer progression or prognosis and to set personalized treatment strategy. We here describe a sensitive and high-throughput immunoassay for determining CXCR4 expression and distribution in cancer cells. The assay is accessible to a wide range of users in an ordinary lab only by dip-coating poly(styrene-co-N-isopropylacrylamide) spheres on the glass substrate. The self- assembled spheres form three-dimensional photonic colloidal crystals which enhance the fluorescence of CF647 and Alexa Fluor 647 by a factor of up to 1000. CXCR4 in cells is detected by using the sandwich immunoassay, where the primary antibody recognizes CXCR4 and the secondary antibody is labeled with CF647. With the newly established assay, we quantified the total expression of CXCR4, its distribution on the cell membrane and cytoplasm, and revealed their internalization level upon SDF-1α activation in various cancer cells, even for those with extremely low expression level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of water depth on the distribution of iGDGTs in the surface sediments from the northern South China Sea: applicability of TEX86 in marginal seas

NASA Astrophysics Data System (ADS)

Chen, Jiali; Hu, Pengju; Li, Xing; Yang, Yang; Song, Jinming; Li, Xuegang; Yuan, Huamao; Li, Ning; Lü, Xiaoxia

2018-03-01

The TEX 86 H paleothermometer on the base of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) has been widely applied to various marine settings to reconstruct past sea surface temperatures (SSTs). However, it remains uncertain how well this proxy reconstructs SSTs in marginal seas. In this study, we analyze the environmental factors governing distribution of iGDGTs in surface sediments to assess the applicability of TEX 86 H paleothermometer in the South China Sea (SCS). Individual iGDGT concentrations increase gradually eastwards. Redundancy analysis based on the relative abundance of an individual iGDGT compound and environmental parameters suggests that water depth is the most influential factor to the distribution of iGDGTs, because thaumarchaeota communities are water-depth dependent. Interestingly, the SST difference (Δ T) between TEX 86 H derived temperature and remote-sensing SST is less than 1°C in sediments with water depth>200 m, indicating that TEX 86 H was the robust proxy to trace the paleo-SST in the region if water depth is greater than 200 m.

Optimal heavy tail estimation - Part 1: Order selection

NASA Astrophysics Data System (ADS)

Mudelsee, Manfred; Bermejo, Miguel A.

2017-12-01

The tail probability, P, of the distribution of a variable is important for risk analysis of extremes. Many variables in complex geophysical systems show heavy tails, where P decreases with the value, x, of a variable as a power law with a characteristic exponent, α. Accurate estimation of α on the basis of data is currently hindered by the problem of the selection of the order, that is, the number of largest x values to utilize for the estimation. This paper presents a new, widely applicable, data-adaptive order selector, which is based on computer simulations and brute force search. It is the first in a set of papers on optimal heavy tail estimation. The new selector outperforms competitors in a Monte Carlo experiment, where simulated data are generated from stable distributions and AR(1) serial dependence. We calculate error bars for the estimated α by means of simulations. We illustrate the method on an artificial time series. We apply it to an observed, hydrological time series from the River Elbe and find an estimated characteristic exponent of 1.48 ± 0.13. This result indicates finite mean but infinite variance of the statistical distribution of river runoff.

A wide-band fiber optic frequency distribution system employing thermally controlled phase compensation

NASA Technical Reports Server (NTRS)

Johnson, Dean; Calhoun, Malcolm; Sydnor, Richard; Lutes, George

1993-01-01

An active wide-band fiber optic frequency distribution system employing a thermally controlled phase compensator to stabilize phase variations induced by environmental temperature changes is described. The distribution system utilizes bidirectional dual wavelength transmission to provide optical feedback of induced phase variations of 100 MHz signals propagating along the distribution cable. The phase compensation considered differs from earlier narrow-band phase compensation designs in that it uses a thermally controlled fiber delay coil rather than a VCO or phase modulation to compensate for induced phase variations. Two advantages of the wide-band system over earlier designs are (1) that it provides phase compensation for all transmitted frequencies, and (2) the compensation is applied after the optical interface rather than electronically ahead of it as in earlier schemes. Experimental results on the first prototype shows that the thermal stabilizer reduces phase variations and Allan deviation by a factor of forty over an equivalent uncompensated fiber optic distribution system.

Rainfall estimation using microwave links. Results from an experimental setup in Luxembourg

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Matgen, Patrick; Pfister, Laurent

2010-05-01

Microwave links represent a valid alternative to traditional rainfall estimation methods. They are commonly used in mobile phone communication, and they constitute built-in widely distributed networks. Due to their ability of providing high temporal and spatial resolution measurements, their use is particularly suitable in urban settings. We here show results from an experimental setup in Luxembourg City, where two dual frequency links have been installed. The links cover a distance of about 4km, and measure power attenuation at 1 min. timestep. The links have been equipped with several recording raingauges, which measure rainfall in real-time communicating through a wireless connection. This set-up has been used to analyze in detail the mapping between attenuation and rainfall intensity, and gain insights into the potential accuracy of these instruments. In addition, we investigated the relation between rainfall and discharge response of the urban area of Luxembourg, which shows the potential utility of high frequency rainfall measurements for urban environments.

A Metric-Based Validation Process to Assess the Realism of Synthetic Power Grids

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

Birchfield, Adam; Schweitzer, Eran; Athari, Mir

Public power system test cases that are of high quality benefit the power systems research community with expanded resources for testing, demonstrating, and cross-validating new innovations. Building synthetic grid models for this purpose is a relatively new problem, for which a challenge is to show that created cases are sufficiently realistic. This paper puts forth a validation process based on a set of metrics observed from actual power system cases. These metrics follow the structure, proportions, and parameters of key power system elements, which can be used in assessing and validating the quality of synthetic power grids. Though wide diversitymore » exists in the characteristics of power systems, the paper focuses on an initial set of common quantitative metrics to capture the distribution of typical values from real power systems. The process is applied to two new public test cases, which are shown to meet the criteria specified in the metrics of this paper.« less

An Optimal CDS Construction Algorithm with Activity Scheduling in Ad Hoc Networks

PubMed Central

Penumalli, Chakradhar; Palanichamy, Yogesh

2015-01-01

A new energy efficient optimal Connected Dominating Set (CDS) algorithm with activity scheduling for mobile ad hoc networks (MANETs) is proposed. This algorithm achieves energy efficiency by minimizing the Broadcast Storm Problem [BSP] and at the same time considering the node's remaining energy. The Connected Dominating Set is widely used as a virtual backbone or spine in mobile ad hoc networks [MANETs] or Wireless Sensor Networks [WSN]. The CDS of a graph representing a network has a significant impact on an efficient design of routing protocol in wireless networks. Here the CDS is a distributed algorithm with activity scheduling based on unit disk graph [UDG]. The node's mobility and residual energy (RE) are considered as parameters in the construction of stable optimal energy efficient CDS. The performance is evaluated at various node densities, various transmission ranges, and mobility rates. The theoretical analysis and simulation results of this algorithm are also presented which yield better results. PMID:26221627

Comparison of $$\

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

Adams, C.; et al.

We measure a large set of observables in inclusive charged current muon neutrino scattering on argon with the MicroBooNE liquid argon time projection chamber operating at Fermilab. We evaluate three neutrino interaction models based on the widely used GENIE event generator using these observables. The measurement uses a data set consisting of neutrino interactions with a final state muon candidate fully contained within the MicroBooNE detector. These data were collected in 2016 with the Fermilab Booster Neutrino Beam, which has an average neutrino energy of 800 MeV, using an exposure corresponding to 5e19 protons-on-target. The analysis employs fully automatic eventmore » selection and charged particle track reconstruction and uses a data-driven technique to separate neutrino interactions from cosmic ray background events. We find that GENIE models consistently describe the shapes of a large number of kinematic distributions for fixed observed multiplicity, but we show an indication that the observed multiplicity fractions deviate from GENIE expectations.« less

Packet utilisation definitions for the ESA XMM mission

NASA Technical Reports Server (NTRS)

Nye, H. R.

1994-01-01

XMM, ESA's X-Ray Multi-Mirror satellite, due for launch at the end of 1999 will be the first ESA scientific spacecraft to implement the ESA packet telecommand and telemetry standards and will be the first ESOC-controlled science mission to take advantage of the new flight control system infrastructure development (based on object-oriented design and distributed-system architecture) due for deployment in 1995. The implementation of the packet standards is well defined at packet transport level. However, the standard relevant to the application level (the ESA Packet Utilization Standard) covers a wide range of on-board 'services' applicable in varying degrees to the needs of XMM. In defining which parts of the ESA PUS to implement, the XMM project first considered the mission objectives and the derived operations concept and went on to identify a minimum set of packet definitions compatible with these aspects. This paper sets the scene as above and then describes the services needed for XMM and the telecommand and telemetry packet types necessary to support each service.

Tests of neutrino interaction models with the MicroBooNE detector

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

Rafique, Aleena

2018-01-01

I measure a large set of observables in inclusive charged current muon neutrino scattering on argon with the MicroBooNE liquid argon time projection chamber operating at Fermilab. I evaluate three neutrino interaction models based on the widely used GENIE event generator using these observables. The measurement uses a data set consisting of neutrino interactions with a final state muon candidate fully contained within the MicroBooNE detector. These data were collected in 2016 with the Fermilab Booster Neutrino Beam, which has an average neutrino energy ofmore » $800$ MeV, using an exposure corresponding to $$5.0\\times10^{19}$$ protons-on-target. The analysis employs fully automatic event selection and charged particle track reconstruction and uses a data-driven technique to separate neutrino interactions from cosmic ray background events. I find that GENIE models consistently describe the shapes of a large number of kinematic distributions for fixed observed multiplicity, but I show an indication that the observed multiplicity fractions deviate from GENIE expectations.« less

A Metric-Based Validation Process to Assess the Realism of Synthetic Power Grids

DOE PAGES

Birchfield, Adam; Schweitzer, Eran; Athari, Mir; ...

2017-08-19

Public power system test cases that are of high quality benefit the power systems research community with expanded resources for testing, demonstrating, and cross-validating new innovations. Building synthetic grid models for this purpose is a relatively new problem, for which a challenge is to show that created cases are sufficiently realistic. This paper puts forth a validation process based on a set of metrics observed from actual power system cases. These metrics follow the structure, proportions, and parameters of key power system elements, which can be used in assessing and validating the quality of synthetic power grids. Though wide diversitymore » exists in the characteristics of power systems, the paper focuses on an initial set of common quantitative metrics to capture the distribution of typical values from real power systems. The process is applied to two new public test cases, which are shown to meet the criteria specified in the metrics of this paper.« less

What governs governance, and how does it evolve? The sociology of governance-in-action.

PubMed

Fox, Nick J; Ward, Katie J

2008-09-01

Governance addresses a wide range of issues including social, economic and political continuity, security and integrity, individual and collective safety and the liberty and rights to self-actualization of citizens. Questions to be answered include how governance can be achieved and sustained within a social context imbued with cultural values and in which power is distributed unevenly and dynamically, and how governance impacts on individuals and institutions. Drawing on Gramscian notions of hegemony and consent, and recent political science literatures on regulation and meta-regulation, this paper develops a sociological model of governance that emphasizes a dynamic and responsive governance in action. Empirical data from a study of pharmaceutical governance is used to show how multiple institutions and actors are involved in sustaining effective governance. The model addresses issues of how governance is sustained in the face of change, why governance of practices varies from setting to setting, and how governance is achieved without legislation.

Optimal Solutions of Multiproduct Batch Chemical Process Using Multiobjective Genetic Algorithm with Expert Decision System

PubMed Central

Mokeddem, Diab; Khellaf, Abdelhafid

2009-01-01

Optimal design problem are widely known by their multiple performance measures that are often competing with each other. In this paper, an optimal multiproduct batch chemical plant design is presented. The design is firstly formulated as a multiobjective optimization problem, to be solved using the well suited non dominating sorting genetic algorithm (NSGA-II). The NSGA-II have capability to achieve fine tuning of variables in determining a set of non dominating solutions distributed along the Pareto front in a single run of the algorithm. The NSGA-II ability to identify a set of optimal solutions provides the decision-maker DM with a complete picture of the optimal solution space to gain better and appropriate choices. Then an outranking with PROMETHEE II helps the decision-maker to finalize the selection of a best compromise. The effectiveness of NSGA-II method with multiojective optimization problem is illustrated through two carefully referenced examples. PMID:19543537

Wave-induced bedload transport - a study of the southern Baltic coastal zone

NASA Astrophysics Data System (ADS)

Dudkowska, Aleksandra; Gic-Grusza, Gabriela

2017-03-01

The wave-induced bedload transport and spatial distribution of its magnitude in the southern Baltic coastal zone of Poland are estimated. The vicinity of Lubiatowo was selected as a representative part of the Polish coast. It was assumed that transport is a function of shear stress; alternative approaches, based on force balances and discharge relationships, were not considered in the present study. Four models were studied and compared over a wide range of bottom shear stress and wind-wave conditions. The set of models comprises classic theories that assume a simplified influence of turbulence on sediment transport (e.g., advocated by authors such as Du Boys, Meyer-Peter and Müller, Ribberink, Engelund and Hansen). It is shown that these models allow to estimate transport comparable to measured values under similar environmental conditions. A united general model for bedload transport is proposed, and a set of maps of wave bedload transport for various wind conditions in the study area is presented.

GANGA: A tool for computational-task management and easy access to Grid resources

NASA Astrophysics Data System (ADS)

Mościcki, J. T.; Brochu, F.; Ebke, J.; Egede, U.; Elmsheuser, J.; Harrison, K.; Jones, R. W. L.; Lee, H. C.; Liko, D.; Maier, A.; Muraru, A.; Patrick, G. N.; Pajchel, K.; Reece, W.; Samset, B. H.; Slater, M. W.; Soroko, A.; Tan, C. L.; van der Ster, D. C.; Williams, M.

2009-11-01

In this paper, we present the computational task-management tool GANGA, which allows for the specification, submission, bookkeeping and post-processing of computational tasks on a wide set of distributed resources. GANGA has been developed to solve a problem increasingly common in scientific projects, which is that researchers must regularly switch between different processing systems, each with its own command set, to complete their computational tasks. GANGA provides a homogeneous environment for processing data on heterogeneous resources. We give examples from High Energy Physics, demonstrating how an analysis can be developed on a local system and then transparently moved to a Grid system for processing of all available data. GANGA has an API that can be used via an interactive interface, in scripts, or through a GUI. Specific knowledge about types of tasks or computational resources is provided at run-time through a plugin system, making new developments easy to integrate. We give an overview of the GANGA architecture, give examples of current use, and demonstrate how GANGA can be used in many different areas of science. Catalogue identifier: AEEN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL No. of lines in distributed program, including test data, etc.: 224 590 No. of bytes in distributed program, including test data, etc.: 14 365 315 Distribution format: tar.gz Programming language: Python Computer: personal computers, laptops Operating system: Linux/Unix RAM: 1 MB Classification: 6.2, 6.5 Nature of problem: Management of computational tasks for scientific applications on heterogenous distributed systems, including local, batch farms, opportunistic clusters and Grids. Solution method: High-level job management interface, including command line, scripting and GUI components. Restrictions: Access to the distributed resources depends on the installed, 3rd party software such as batch system client or Grid user interface.

FODEM: Developing Digital Learning Environments in Widely Dispersed Learning Communities

ERIC Educational Resources Information Center

Suhonen, Jarkko; Sutinen, Erkki

2006-01-01

FODEM (FOrmative DEvelopment Method) is a design method for developing digital learning environments for widely dispersed learning communities. These are communities in which the geographical distribution and density of learners is low when compared to the kind of learning communities in which there is a high distribution and density of learners…

Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure.

PubMed

Yang, Qingxiang; Tian, Tiantian; Niu, Tianqi; Wang, Panliang

2017-10-01

Diverse antibiotic-resistance genes (ARGs) are frequently reported to have high prevalence in veterinary manure samples due to extensive use of antibiotics in farm animals. However, the characteristics of the distribution and transmission of ARGs among bacteria, especially among different species of multiple antibiotic-resistant bacteria (MARB), have not been well explored. By applying high-throughput sequencing methods, our study uncovered a vast MARB reservoir in livestock manure. The genera Escherichia, Myroides, Acinetobacter, Proteus, Ignatzschineria, Alcaligenes, Providencia and Enterococcus were the predominant cultivable MARB, with compositions of 40.6%-85.7%. From chicken manure isolates, 33 MARB were selected for investigation of the molecular characteristics of antibiotic resistance. A total of 61 ARGs and 18 mobile genetic elements (MGEs) were investigated. We found that 47 ARGs were widely distributed among the 33 MARB isolates. Each isolate carried 27-36 genes responsible for resistance to eight classes of antibiotics frequently used in clinic or veterinary settings. ARGs to the six classes of antibiotics other than streptogramins and vancomycin were present in all 33 MARB isolates with a prevalence of 80%-100%. A total of 12 MGEs were widely distributed among the 33 MARB, with intI1, IS26, ISaba1, and ISEcp1 simultaneously present in 100% of isolates. In addition, 9 gene cassettes within integrons and ISCR1 were detected among MARB isolates encoding resistance to different antibiotic classes. This is the first report revealing the general co-presence of multiple ARGs, various MGEs and ARG cassettes in different species of individual MARB isolates in chicken manure. The results highlight a much higher risk of ARGs spreading through livestock manure to humans than we expected. Copyright © 2017 Elsevier Ltd. All rights reserved.

A new approach to process control using Instability Index

NASA Astrophysics Data System (ADS)

Weintraub, Jeffrey; Warrick, Scott

2016-03-01

The merits of a robust Statistical Process Control (SPC) methodology have long been established. In response to the numerous SPC rule combinations, processes, and the high cost of containment, the Instability Index (ISTAB) is presented as a tool for managing these complexities. ISTAB focuses limited resources on key issues and provides a window into the stability of manufacturing operations. ISTAB takes advantage of the statistical nature of processes by comparing the observed average run length (OARL) to the expected run length (ARL), resulting in a gap value called the ISTAB index. The ISTAB index has three characteristic behaviors that are indicative of defects in an SPC instance. Case 1: The observed average run length is excessively long relative to expectation. ISTAB > 0 is indicating the possibility that the limits are too wide. Case 2: The observed average run length is consistent with expectation. ISTAB near zero is indicating that the process is stable. Case 3: The observed average run length is inordinately short relative to expectation. ISTAB < 0 is indicating that the limits are too tight, the process is unstable or both. The probability distribution of run length is the basis for establishing an ARL. We demonstrate that the geometric distribution is a good approximation to run length across a wide variety of rule sets. Excessively long run lengths are associated with one kind of defect in an SPC instance; inordinately short run lengths are associated with another. A sampling distribution is introduced as a way to quantify excessively long and inordinately short observed run lengths. This paper provides detailed guidance for action limits on these run lengths. ISTAB as a statistical method of review facilitates automated instability detection. This paper proposes a management system based on ISTAB as an enhancement to more traditional SPC approaches.

ZENO: N-body and SPH Simulation Codes

NASA Astrophysics Data System (ADS)

Barnes, Joshua E.

2011-02-01

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere. Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include: Structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems.Snapshot generation routines create particle distributions with various properties. Systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium.Snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.Simulation codes include both pure N-body and combined N-body/SPH programs: Pure N-body codes are available in both uniprocessor and parallel versions.SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions.Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.).

PubMed

Sun, Lidan; Zhang, Qixiang; Xu, Zongda; Yang, Weiru; Guo, Yu; Lu, Jiuxing; Pan, Huitang; Cheng, Tangren; Cai, Ming

2013-10-06

Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume 'Fenban' and Prunus mume 'Kouzi Yudie' to identify high-quality polymorphic markers between the two cultivars on a large scale. A total of 1464.1 Mb and 1422.1 Mb of 'Fenban' and 'Kouzi Yudie' sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent's SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny. A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between 'Fenban' and 'Kouzi Yudie' using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.

A morphogram for silica-witherite biomorphs and its application to microfossil identification in the early earth rock record.

PubMed

Rouillard, J; García-Ruiz, J-M; Gong, J; van Zuilen, M A

2018-05-01

Archean hydrothermal environments formed a likely site for the origin and early evolution of life. These are also the settings, however, were complex abiologic structures can form. Low-temperature serpentinization of ultramafic crust can generate alkaline, silica-saturated fluids in which carbonate-silica crystalline aggregates with life-like morphologies can self-assemble. These "biomorphs" could have adsorbed hydrocarbons from Fischer-Tropsch type synthesis processes, leading to metamorphosed structures that resemble carbonaceous microfossils. Although this abiogenic process has been extensively cited in the literature and has generated important controversy, so far only one specific biomorph type with a filamentous shape has been discussed for the interpretation of Archean microfossils. It is therefore critical to precisely determine the full distribution in morphology and size of these biomorphs, and to study the range of plausible geochemical conditions under which these microstructures can form. Here, a set of witherite-silica biomorph synthesis experiments in silica-saturated solutions is presented, for a range of pH values (from 9 to 11.5) and barium ion concentrations (from 0.6 to 40 mmol/L BaCl 2 ). Under these varying conditions, a wide range of life-like structures is found, from fractal dendrites to complex shapes with continuous curvature. The size, spatial concentration, and morphology of the biomorphs are strongly controlled by environmental parameters, among which pH is the most important. This potentially limits the diversity of environments in which the growth of biomorphs could have occurred on Early Earth. Given the variety of the observed biomorph morphologies, our results show that the morphology of an individual microstructure is a poor criterion for biogenicity. However, biomorphs may be distinguished from actual populations of cellular microfossils by their wide, unimodal size distribution. Biomorphs grown by diffusion in silica gel can be differentiated by their continuous gradient in size, spatial density, and morphology along the direction of diffusion. © 2018 The Authors. Geobiology Published by John Wiley & Sons Ltd.

Testing Mechanisms and Scales of Equilibrium Using Textural and Compositional Analysis of Porphyroblasts in Rocks with Heterogeneous Garnet Distributions

NASA Astrophysics Data System (ADS)

Ruthven, R. C.; Ketcham, R. A.; Kelly, E. D.

2015-12-01

Three-dimensional textural analysis of garnet porphyroblasts and electron microprobe analyses can, in concert, be used to pose novel tests that challenge and ultimately increase our understanding of metamorphic crystallization mechanisms. Statistical analysis of high-resolution X-ray computed tomography (CT) data of garnet porphyroblasts tells us the degree of ordering or randomness of garnets, which can be used to distinguish the rate-limiting factors behind their nucleation and growth. Electron microprobe data for cores, rims, and core-to-rim traverses are used as proxies to ascertain porphyroblast nucleation and growth rates, and the evolution of sample composition during crystallization. MnO concentrations in garnet cores serve as a proxy for the relative timing of nucleation, and rim concentrations test the hypothesis that MnO is in equilibrium sample-wide during the final stages of crystallization, and that concentrations have not been greatly altered by intracrystalline diffusion. Crystal size distributions combined with compositional data can be used to quantify the evolution of nucleation rates and sample composition during crystallization. This study focuses on quartzite schists from the Picuris Mountains with heterogeneous garnet distributions consisting of dense and sparse layers. 3D data shows that the sparse layers have smaller, less euhedral garnets, and petrographic observations show that sparse layers have more quartz and less mica than dense layers. Previous studies on rocks with homogeneously distributed garnet have shown that crystallization rates are diffusion-controlled, meaning that they are limited by diffusion of nutrients to growth and nucleation sites. This research extends this analysis to heterogeneous rocks to determine nucleation and growth rates, and test the assumption of rock-wide equilibrium for some major elements, among a set of compositionally distinct domains evolving in mm- to cm-scale proximity under identical P-T conditions.

Evaluation and correction of uncertainty due to Gaussian approximation in radar - rain gauge merging using kriging with external drift

NASA Astrophysics Data System (ADS)

Cecinati, F.; Wani, O.; Rico-Ramirez, M. A.

2016-12-01

It is widely recognised that merging radar rainfall estimates (RRE) with rain gauge data can improve the RRE and provide areal and temporal coverage that rain gauges cannot offer. Many methods to merge radar and rain gauge data are based on kriging and require an assumption of Gaussianity on the variable of interest. In particular, this work looks at kriging with external drift (KED), because it is an efficient, widely used, and well performing merging method. Rainfall, especially at finer temporal scale, does not have a normal distribution and presents a bi-modal skewed distribution. In some applications a Gaussianity assumption is made, without any correction. In other cases, variables are transformed in order to obtain a distribution closer to Gaussian. This work has two objectives: 1) compare different transformation methods in merging applications; 2) evaluate the uncertainty arising when untransformed rainfall data is used in KED. The comparison of transformation methods is addressed under two points of view. On the one hand, the ability to reproduce the original probability distribution after back-transformation of merged products is evaluated with qq-plots, on the other hand the rainfall estimates are compared with an independent set of rain gauge measurements. The tested methods are 1) no transformation, 2) Box-Cox transformations with parameter equal to λ=0.5 (square root), 3) λ=0.25 (square root - square root), and 4) λ=0.1 (almost logarithmic), 5) normal quantile transformation, and 6) singularity analysis. The uncertainty associated with the use of non-transformed data in KED is evaluated in comparison with the best performing product. The methods are tested on a case study in Northern England, using hourly data from 211 tipping bucket rain gauges from the Environment Agency and radar rainfall data at 1 km/5-min resolutions from the UK Met Office. In addition, 25 independent rain gauges from the UK Met Office were used to assess the merged products.

Grid Technology as a Cyberinfrastructure for Delivering High-End Services to the Earth and Space Science Community

NASA Technical Reports Server (NTRS)

Hinke, Thomas H.

2004-01-01

Grid technology consists of middleware that permits distributed computations, data and sensors to be seamlessly integrated into a secure, single-sign-on processing environment. In &is environment, a user has to identify and authenticate himself once to the grid middleware, and then can utilize any of the distributed resources to which he has been,panted access. Grid technology allows resources that exist in enterprises that are under different administrative control to be securely integrated into a single processing environment The grid community has adopted commercial web services technology as a means for implementing persistent, re-usable grid services that sit on top of the basic distributed processing environment that grids provide. These grid services can then form building blocks for even more complex grid services. Each grid service is characterized using the Web Service Description Language, which provides a description of the interface and how other applications can access it. The emerging Semantic grid work seeks to associates sufficient semantic information with each grid service such that applications wii1 he able to automatically select, compose and if necessary substitute available equivalent services in order to assemble collections of services that are most appropriate for a particular application. Grid technology has been used to provide limited support to various Earth and space science applications. Looking to the future, this emerging grid service technology can provide a cyberinfrastructures for both the Earth and space science communities. Groups within these communities could transform those applications that have community-wide applicability into persistent grid services that are made widely available to their respective communities. In concert with grid-enabled data archives, users could easily create complex workflows that extract desired data from one or more archives and process it though an appropriate set of widely distributed grid services discovered using semantic grid technology. As required, high-end computational resources could be drawn from available grid resource pools. Using grid technology, this confluence of data, services and computational resources could easily be harnessed to transform data from many different sources into a desired product that is delivered to a user's workstation or to a web portal though which it could be accessed by its intended audience.

Models of multidimensional discrete distribution of probabilities of random variables in information systems

NASA Astrophysics Data System (ADS)

Gromov, Yu Yu; Minin, Yu V.; Ivanova, O. G.; Morozova, O. N.

2018-03-01

Multidimensional discrete distributions of probabilities of independent random values were received. Their one-dimensional distribution is widely used in probability theory. Producing functions of those multidimensional distributions were also received.

Set size manipulations reveal the boundary conditions of perceptual ensemble learning.

PubMed

Chetverikov, Andrey; Campana, Gianluca; Kristjánsson, Árni

2017-11-01

Recent evidence suggests that observers can grasp patterns of feature variations in the environment with surprising efficiency. During visual search tasks where all distractors are randomly drawn from a certain distribution rather than all being homogeneous, observers are capable of learning highly complex statistical properties of distractor sets. After only a few trials (learning phase), the statistical properties of distributions - mean, variance and crucially, shape - can be learned, and these representations affect search during a subsequent test phase (Chetverikov, Campana, & Kristjánsson, 2016). To assess the limits of such distribution learning, we varied the information available to observers about the underlying distractor distributions by manipulating set size during the learning phase in two experiments. We found that robust distribution learning only occurred for large set sizes. We also used set size to assess whether the learning of distribution properties makes search more efficient. The results reveal how a certain minimum of information is required for learning to occur, thereby delineating the boundary conditions of learning of statistical variation in the environment. However, the benefits of distribution learning for search efficiency remain unclear. Copyright © 2017 Elsevier Ltd. All rights reserved.

Goal setting practice in services delivering community-based stroke rehabilitation: a United Kingdom (UK) wide survey.

PubMed

Scobbie, Lesley; Duncan, Edward A; Brady, Marian C; Wyke, Sally

2015-01-01

We investigated the nature of services providing community-based stroke rehabilitation across the UK, and goal setting practice used within them, to inform evaluation of a goal setting and action planning (G-AP) framework. We designed, piloted and electronically distributed a survey to health professionals working in community-based stroke rehabilitation settings across the UK. We optimised recruitment using a multi-faceted strategy. Responses were analysed from 437 services. Services size, composition and input was highly variable; however, most were multi-disciplinary (82%; n = 335/407) and provided input to a mixed diagnostic group of patients (71%; n = 312/437). Ninety one percent of services (n = 358/395) reported setting goals with "all" or "most" stroke survivors. Seventeen percent (n = 65/380) reported that no methods were used to guide goal setting practice; 47% (n = 148/315) reported use of informal methods only. Goal setting practice varied, e.g. 98% of services (n = 362/369) reported routinely asking patients about goal priorities; 39% (n = 141/360) reported routinely providing patients with a copy of their goals. Goal setting is embedded within community-based stroke rehabilitation; however, practice varies and is potentially sub-optimal. Further evaluation of the G-AP framework is warranted to inform optimal practice. Evaluation design will take account of the diverse service models that exist. Implications for Rehabilitation Community-based stroke rehabilitation services across the UK are diverse and tend to see a mixed diagnostic group of patients. Goal setting is implemented routinely within community-based stroke rehabilitation services; however, practice is variable and potentially sub-optimal. Further evaluation of the G-AP framework is warranted to assess its effectiveness in practice.

Using machine learning to explore the long-term evolution of GRS 1915+105

NASA Astrophysics Data System (ADS)

Huppenkothen, Daniela; Heil, Lucy M.; Hogg, David W.; Mueller, Andreas

2017-04-01

Among the population of known Galactic black hole X-ray binaries, GRS 1915+105 stands out in multiple ways. It has been in continuous outburst since 1992, and has shown a wide range of different states that can be distinguished by their timing and spectral properties. These states, also observed in IGR J17091-3624, have in the past been linked to accretion dynamics. Here, we present the first comprehensive study into the long-term evolution of GRS 1915+105, using the entire data set observed with Rossi X-ray Timing Explorer over its 16-yr lifetime. We develop a set of descriptive features allowing for automatic separation of states, and show that supervised machine learning in the form of logistic regression and random forests can be used to efficiently classify the entire data set. For the first time, we explore the duty cycle and time evolution of states over the entire 16-yr time span, and find that the temporal distribution of states has likely changed over the span of the observations. We connect the machine classification with physical interpretations of the phenomenology in terms of chaotic and stochastic processes.

Toward a New Brewing Control Chart for the 21st Century.

PubMed

Melrose, John; Roman-Corrochano, Borja; Montoya-Guerra, Marcela; Bakalis, Serafim

2018-04-23

This paper describes new results from a base model of brewing from a bed of packed coffee grains. The model solves for the diffusion of soluble species out of a distribution of particles into the flow through the bed pore space. It requires a limited set of input parameters. It gives a simple picture of the basic physics of coffee brewing and sets out a set of reduced variables for this process. The importance of bed extraction efficiency is elucidated. A coffee brewing control chart has been widely used to describe the region of ideal coffee brewing for some 50 years. A new chart is needed, however, one that connects actual brewing conditions (weight, flow rate, brew time, grind, etc.) to the yield and strength of brews. The paper shows a new approach to brewing control charts, including brew time and bed extraction efficiency as control parameters. Using the base model, an example chart will be given for a particular grind ratio of coarse to fine particles, and an "espresso regime" will be picked out. From such a chart yield, volume and strength of a brew can be read off at will.

Geodesic denoising for optical coherence tomography images

NASA Astrophysics Data System (ADS)

Shahrian Varnousfaderani, Ehsan; Vogl, Wolf-Dieter; Wu, Jing; Gerendas, Bianca S.; Simader, Christian; Langs, Georg; Waldstein, Sebastian M.; Schmidt-Erfurth, Ursula

2016-03-01

Optical coherence tomography (OCT) is an optical signal acquisition method capturing micrometer resolution, cross-sectional three-dimensional images. OCT images are used widely in ophthalmology to diagnose and monitor retinal diseases such as age-related macular degeneration (AMD) and Glaucoma. While OCT allows the visualization of retinal structures such as vessels and retinal layers, image quality and contrast is reduced by speckle noise, obfuscating small, low intensity structures and structural boundaries. Existing denoising methods for OCT images may remove clinically significant image features such as texture and boundaries of anomalies. In this paper, we propose a novel patch based denoising method, Geodesic Denoising. The method reduces noise in OCT images while preserving clinically significant, although small, pathological structures, such as fluid-filled cysts in diseased retinas. Our method selects optimal image patch distribution representations based on geodesic patch similarity to noisy samples. Patch distributions are then randomly sampled to build a set of best matching candidates for every noisy sample, and the denoised value is computed based on a geodesic weighted average of the best candidate samples. Our method is evaluated qualitatively on real pathological OCT scans and quantitatively on a proposed set of ground truth, noise free synthetic OCT scans with artificially added noise and pathologies. Experimental results show that performance of our method is comparable with state of the art denoising methods while outperforming them in preserving the critical clinically relevant structures.

The clustering of baryonic matter. I: a halo-model approach

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

Fedeli, C., E-mail: cosimo.fedeli@oabo.inaf.it

2014-04-01

In this paper I generalize the halo model for the clustering of dark matter in order to produce the power spectra of the two main baryonic matter components in the Universe: stars and hot gas. As a natural extension, this can be also used to describe the clustering of all mass. According to the design of the halo model, the large-scale power spectra of the various matter components are physically connected with the distribution of each component within bound structures and thus, ultimately, with the complete set of physical processes that drive the formation of galaxies and galaxy clusters. Besidesmore » being practical for cosmological and parametric studies, the semi-analytic model presented here has also other advantages. Most importantly, it allows one to understand on physical ground what is the relative contribution of each matter component to the total clustering of mass as a function of scale, and thus it opens an interesting new window to infer the distribution of baryons through high precision cosmic shear measurements. This is particularly relevant for future wide-field photometric surveys such as Euclid. In this work the concept of the model and its uncertainties are illustrated in detail, while in a companion paper we use a set of numerical hydrodynamic simulations to show a practical application and to investigate where the model itself needs to be improved.« less

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

PubMed Central

2010-01-01

Background An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets. Methods This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model. Results A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center. Conclusion WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data. PMID:21210985

NREL Topic 1 Final Report: Cohesive Application of Standards-Based Connected Devices to Enable Clean Energy Technologies

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

Hudgins, Andrew P.; Sparn, Bethany F.; Jin, Xin

This document is the final report of a two-year development, test, and demonstration project entitled 'Cohesive Application of Standards-Based Connected Devices to Enable Clean Energy Technologies.' The project was part of the National Renewable Energy Laboratory's (NREL) Integrated Network Test-bed for Energy Grid Research and Technology (INTEGRATE) initiative. The Electric Power Research Institute (EPRI) and a team of partners were selected by NREL to carry out a project to develop and test how smart, connected consumer devices can act to enable the use of more clean energy technologies on the electric power grid. The project team includes a set ofmore » leading companies that produce key products in relation to achieving this vision: thermostats, water heaters, pool pumps, solar inverters, electric vehicle supply equipment, and battery storage systems. A key requirement of the project was open access at the device level - a feature seen as foundational to achieving a future of widespread distributed generation and storage. The internal intelligence, standard functionality and communication interfaces utilized in this project result in the ability to integrate devices at any level, to work collectively at the level of the home/business, microgrid, community, distribution circuit or other. Collectively, the set of products serve as a platform on which a wide range of control strategies may be developed and deployed.« less

Gaussian closure technique applied to the hysteretic Bouc model with non-zero mean white noise excitation

NASA Astrophysics Data System (ADS)

Waubke, Holger; Kasess, Christian H.

2016-11-01

Devices that emit structure-borne sound are commonly decoupled by elastic components to shield the environment from acoustical noise and vibrations. The elastic elements often have a hysteretic behavior that is typically neglected. In order to take hysteretic behavior into account, Bouc developed a differential equation for such materials, especially joints made of rubber or equipped with dampers. In this work, the Bouc model is solved by means of the Gaussian closure technique based on the Kolmogorov equation. Kolmogorov developed a method to derive probability density functions for arbitrary explicit first-order vector differential equations under white noise excitation using a partial differential equation of a multivariate conditional probability distribution. Up to now no analytical solution of the Kolmogorov equation in conjunction with the Bouc model exists. Therefore a wide range of approximate solutions, especially the statistical linearization, were developed. Using the Gaussian closure technique that is an approximation to the Kolmogorov equation assuming a multivariate Gaussian distribution an analytic solution is derived in this paper for the Bouc model. For the stationary case the two methods yield equivalent results, however, in contrast to statistical linearization the presented solution allows to calculate the transient behavior explicitly. Further, stationary case leads to an implicit set of equations that can be solved iteratively with a small number of iterations and without instabilities for specific parameter sets.

Environmental determinants of radiolarian assemblages in the western Pacific since the last deglaciation

NASA Astrophysics Data System (ADS)

Hernández-Almeida, I.; Cortese, G.; Yu, P.-S.; Chen, M.-T.; Kucera, M.

2017-08-01

Radiolarians are a very diverse microzooplanktonic group, often distributed in regionally restricted assemblages and responding to specific environmental factors. These properties of radiolarian assemblages make the group more conducive for the development and application of basin-wide ecological models. Here we use a new surface sediment data set from the western Pacific to demonstrate that ecological patterns derived from basin-wide open-ocean data sets cannot be transferred on semirestricted marginal seas. The data set consists of 160 surface sediment samples from three tropical-subtropical regions (East China Sea, South China Sea, and western Pacific), combining 54 new assemblage counts with taxonomically harmonized data from previous studies. Multivariate statistical analyses indicate that winter sea surface temperature at 10 m depth (SSTw) was the most significant environmental variable affecting the composition of radiolarian assemblages, allowing the development of an optimal calibration model (Locally Weighted-Weighted Averaging regression inverse deshrinking, R2cv = 0.88, root-mean-square error of prediction = 1.6°C). The dominant effect of SSTw on radiolarian assemblage composition in the western Pacific is attributed to the East Asian Winter Monsoon (EAWM), which is particularly strong in the marginal seas. To test the applicability of the calibration model on fossil radiolarian assemblages from the marginal seas, the calibration model was applied to two downcore records from the Okinawa Trough, covering the last 18 ka. We observe that these assemblages find most appropriate analogs among modern samples from the marginal basins (East China Sea and South China Sea). Downcore temperature reconstructions at both sites show similarities to known regional SST reconstructions, providing proof of concept for the new radiolarian-based SSTw calibration model.

Generalized index for spatial data sets as a measure of complete spatial randomness

NASA Astrophysics Data System (ADS)

Hackett-Jones, Emily J.; Davies, Kale J.; Binder, Benjamin J.; Landman, Kerry A.

2012-06-01

Spatial data sets, generated from a wide range of physical systems can be analyzed by counting the number of objects in a set of bins. Previous work has been limited to equal-sized bins, which are inappropriate for some domains (e.g., circular). We consider a nonequal size bin configuration whereby overlapping or nonoverlapping bins cover the domain. A generalized index, defined in terms of a variance between bin counts, is developed to indicate whether or not a spatial data set, generated from exclusion or nonexclusion processes, is at the complete spatial randomness (CSR) state. Limiting values of the index are determined. Using examples, we investigate trends in the generalized index as a function of density and compare the results with those using equal size bins. The smallest bin size must be much larger than the mean size of the objects. We can determine whether a spatial data set is at the CSR state or not by comparing the values of a generalized index for different bin configurations—the values will be approximately the same if the data is at the CSR state, while the values will differ if the data set is not at the CSR state. In general, the generalized index is lower than the limiting value of the index, since objects do not have access to the entire region due to blocking by other objects. These methods are applied to two applications: (i) spatial data sets generated from a cellular automata model of cell aggregation in the enteric nervous system and (ii) a known plant data distribution.

Dynamical downscaling of wind fields for wind power applications

NASA Astrophysics Data System (ADS)

Mengelkamp, H.-T.; Huneke, S.; Geyer, J.

2010-09-01

Dynamical downscaling of wind fields for wind power applications H.-T. Mengelkamp*,**, S. Huneke**, J, Geyer** *GKSS Research Center Geesthacht GmbH **anemos Gesellschaft für Umweltmeteorologie mbH Investments in wind power require information on the long-term mean wind potential and its temporal variations on daily to annual and decadal time scales. This information is rarely available at specific wind farm sites. Short-term on-site measurements usually are only performed over a 12 months period. These data have to be set into the long-term perspective through correlation to long-term consistent wind data sets. Preliminary wind information is often asked for to select favourable wind sites over regional and country wide scales. Lack of high-quality wind measurements at weather stations was the motivation to start high resolution wind field simulations The simulations are basically a refinement of global scale reanalysis data by means of high resolution simulations with an atmospheric mesoscale model using high-resolution terrain and land-use data. The 3-dimensional representation of the atmospheric state available every six hours at 2.5 degree resolution over the globe, known as NCAR/NCEP reanalysis data, forms the boundary conditions for continuous simulations with the non-hydrostatic atmospheric mesoscale model MM5. MM5 is nested in itself down to a horizontal resolution of 5 x 5 km². The simulation is performed for different European countries and covers the period 2000 to present and is continuously updated. Model variables are stored every 10 minutes for various heights. We have analysed the wind field primarily. The wind data set is consistent in space and time and provides information on the regional distribution of the long-term mean wind potential, the temporal variability of the wind potential, the vertical variation of the wind potential, and the temperature, and pressure distribution (air density). In the context of wind power these data are used • as an initial estimate of wind and energy potential • for the long-term correlation of wind measurements and turbine production data • to provide wind potential maps on a regional to country wide scale • to provide input data sets for simulation models • to determine the spatial correlation of the wind field in portfolio calculations • to calculate the wind turbine energy loss during prescribed downtimes • to provide information on the temporal variations of the wind and wind turbine energy production The time series of wind speed and wind direction are compared to measurements at offshore and onshore locations.

Alu distribution and mutation types of cancer genes

PubMed Central

2011-01-01

Background Alu elements are the most abundant retrotransposable elements comprising ~11% of the human genome. Many studies have highlighted the role that Alu elements have in genetic instability and how their contribution to the assortment of mutagenic events can lead to cancer. As of yet, little has been done to quantitatively assess the association between Alu distribution and genes that are causally implicated in oncogenesis. Results We have investigated the effect of various Alu densities on the mutation type based classifications of cancer genes. In order to establish the direct relationship between Alus and the cancer genes of interest, genome wide Alu-related densities were measured using genes rather than the sliding windows of fixed length as the units. Several novel genomic features, such as the density of the adjacent Alu pairs and the number of Alu-Exon-Alu triplets, were developed in order to extend the investigation via the multivariate statistical analysis toward more advanced biological insight. In addition, we characterized the genome-wide intron Alu distribution with a mixture model that distinguished genes containing Alu elements from those with no Alus, and evaluated the gene-level effect of the 5'-TTAAAA motif associated with Alu insertion sites using a two-step regression analysis method. Conclusions The study resulted in several novel findings worthy of further investigation. They include: (1) Recessive cancer genes (tumor suppressor genes) are enriched with Alu elements (p < 0.01) compared to dominant cancer genes (oncogenes) and the entire set of genes in the human genome; (2) Alu-related genomic features can be used to cluster cancer genes into biological meaningful groups; (3) The retention of exon Alus has been restricted in the human genome development, and an upper limit to the chromosome-level exon Alu densities is suggested by the distribution profile; (4) For the genes with at least one intron Alu repeat in individual chromosomes, the intron Alu densities can be well fitted by a Gamma distribution; (5) The effect of the 5'-TTAAAA motif on Alu densities varies across different chromosomes. PMID:21429208

Conformal flight path symbology for head-up displays: Defining the distribution of visual attention in three-dimensional space

NASA Astrophysics Data System (ADS)

Ververs, Patricia May

An extensive investigation of the format for head-up display (HUD) instrumentation was conducted in a two-part experiment. First, a pilot's information requirements for the tasks of approach, landing, and taxi were determined through a survey administered to professional commercial pilots via the world wide web. The results of the survey were applied in the development of two symbology sets, one set for flight navigation and the second for ground navigation. Second, twenty pilots from the University of Illinois at Urbana-Champaign were recruited to participate in a 3-day experiment. The study was designed to investigate the format for symbology on HUDs and the performance effects of using conformal and partially conformal symbology to support the pilots' tasks. In addition, two different methods were investigated for supporting the pilots' transition between the task of flying and the task of landing. A seamless transition used visual momentum techniques to smoothly guide the pilots' cognitive transition between the serial displays and the associated tasks. A seamed approach employed an abrupt change between the displays to alert the pilots of the task switch. The results indicate that incorporating a virtually conformal, tunnel-in-the-sky symbology into a complete HUD instrumentation set offers promising pilot performance effects. Pilots easily navigated the complex curved approaches with little to no deviation from the flight path (approximately 10 feet), while performing the secondary tasks of the scanning their instruments and the environment. The seamless transition between the flight and ground symbology offered the pilots a preview of the upcoming landing task, thereby preparing them for the task switch. On the ground, the perspective (scene-linked) symbology set supported landing and taxi navigation tasks with the equal efficiency to the plan view display but with much greater precision. Theories of allocation of attention were used to interpret the experimental findings. Attention was found to be more widely distributed in X-Y space when the pilots were flying with the conformal, tunnel-in-the-sky as compared to the partially conformal ILS (instrument landing system) symbology set. There was little evidence that the air-based navigation displays were supporting divided attention in three-dimensional space. The ground-based scene-linked (truly conformal) display indicated promising effects of dividing attention in depth without negative consequences to processing the near domain symbology. Event expectancy was found to modulate pilot performance in the detection of events both on the symbology and in the environment. The phenomenon known as cognitive tunneling is discussed as a possible cause of the inadequate response times in resolving the anomalous events.

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.

PubMed

Schaid, Daniel J; Sinnwell, Jason P; Jenkins, Gregory D; McDonnell, Shannon K; Ingle, James N; Kubo, Michiaki; Goss, Paul E; Costantino, Joseph P; Wickerham, D Lawrence; Weinshilboum, Richard M

2012-01-01

Gene-set analyses have been widely used in gene expression studies, and some of the developed methods have been extended to genome wide association studies (GWAS). Yet, complications due to linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs), and variable numbers of SNPs per gene and genes per gene-set, have plagued current approaches, often leading to ad hoc "fixes." To overcome some of the current limitations, we developed a general approach to scan GWAS SNP data for both gene-level and gene-set analyses, building on score statistics for generalized linear models, and taking advantage of the directed acyclic graph structure of the gene ontology when creating gene-sets. However, other types of gene-set structures can be used, such as the popular Kyoto Encyclopedia of Genes and Genomes (KEGG). Our approach combines SNPs into genes, and genes into gene-sets, but assures that positive and negative effects of genes on a trait do not cancel. To control for multiple testing of many gene-sets, we use an efficient computational strategy that accounts for LD and provides accurate step-down adjusted P-values for each gene-set. Application of our methods to two different GWAS provide guidance on the potential strengths and weaknesses of our proposed gene-set analyses. © 2011 Wiley Periodicals, Inc.

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)

PubMed Central

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus. PMID:27336696

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).

PubMed

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

Methods and apparatuses for information analysis on shared and distributed computing systems

DOEpatents

Bohn, Shawn J [Richland, WA; Krishnan, Manoj Kumar [Richland, WA; Cowley, Wendy E [Richland, WA; Nieplocha, Jarek [Richland, WA

2011-02-22

Apparatuses and computer-implemented methods for analyzing, on shared and distributed computing systems, information comprising one or more documents are disclosed according to some aspects. In one embodiment, information analysis can comprise distributing one or more distinct sets of documents among each of a plurality of processes, wherein each process performs operations on a distinct set of documents substantially in parallel with other processes. Operations by each process can further comprise computing term statistics for terms contained in each distinct set of documents, thereby generating a local set of term statistics for each distinct set of documents. Still further, operations by each process can comprise contributing the local sets of term statistics to a global set of term statistics, and participating in generating a major term set from an assigned portion of a global vocabulary.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

PubMed Central

Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; M. Wade, Claire; McCue, Molly E.

2013-01-01

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. PMID:23383025

Genome-wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection.

PubMed

Bandillo, Nonoy B; Lorenz, Aaron J; Graef, George L; Jarquin, Diego; Hyten, David L; Nelson, Randall L; Specht, James E

2017-07-01

Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ∼13,000 soybean [ (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 24 classical genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of these genes had been cloned, we were able to show that the narrow GWA mapping SNP signal regions that we detected for the phenotypic variants had chromosomal bp spans that, with just one exception, overlapped the bp region of the cloned genes, despite local variation in SNP number and nonuniform SNP distribution in the chip set. Copyright © 2017 Crop Science Society of America.

High quality Gaussian basis sets for fourth-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Faegri, Knut, Jr.

1992-01-01

Energy optimized Gaussian basis sets of triple-zeta quality for the atoms Rb-Xe have been derived. Two series of basis sets are developed: (24s 16p 10d) and (26s 16p 10d) sets which were expanded to 13d and 19p functions as the 4d and 5p shells become occupied. For the atoms lighter than Cd, the (24s 16p 10d) sets with triple-zeta valence distributions are higher in energy than the corresponding double-zeta distribution. To ensure a triple-zeta distribution and a global energy minimum, the (26s 16p 10d) sets were derived. Total atomic energies from the largest basis sets are between 198 and 284 (mu)E(sub H) above the numerical Hartree-Fock energies.

NASA Access Mechanism - Graphical user interface information retrieval system

NASA Technical Reports Server (NTRS)

Hunter, Judy F.; Generous, Curtis; Duncan, Denise

1993-01-01

Access to online information sources of aerospace, scientific, and engineering data, a mission focus for NASA's Scientific and Technical Information Program, has always been limited by factors such as telecommunications, query language syntax, lack of standardization in the information, and the lack of adequate tools to assist in searching. Today, the NASA STI Program's NASA Access Mechanism (NAM) prototype offers a solution to these problems by providing the user with a set of tools that provide a graphical interface to remote, heterogeneous, and distributed information in a manner adaptable to both casual and expert users. Additionally, the NAM provides access to many Internet-based services such as Electronic Mail, the Wide Area Information Servers system, Peer Locating tools, and electronic bulletin boards.

NASA access mechanism: Graphical user interface information retrieval system

NASA Technical Reports Server (NTRS)

Hunter, Judy; Generous, Curtis; Duncan, Denise

1993-01-01

Access to online information sources of aerospace, scientific, and engineering data, a mission focus for NASA's Scientific and Technical Information Program, has always been limited to factors such as telecommunications, query language syntax, lack of standardization in the information, and the lack of adequate tools to assist in searching. Today, the NASA STI Program's NASA Access Mechanism (NAM) prototype offers a solution to these problems by providing the user with a set of tools that provide a graphical interface to remote, heterogeneous, and distributed information in a manner adaptable to both casual and expert users. Additionally, the NAM provides access to many Internet-based services such as Electronic Mail, the Wide Area Information Servers system, Peer Locating tools, and electronic bulletin boards.

Recruitment of local inhibitory networks by horizontal connections in layer 2/3 of ferret visual cortex.

PubMed

Tucker, Thomas R; Katz, Lawrence C

2003-01-01

To investigate how neurons in cortical layer 2/3 integrate horizontal inputs arising from widely distributed sites, we combined intracellular recording and voltage-sensitive dye imaging to visualize the spatiotemporal dynamics of neuronal activity evoked by electrical stimulation of multiple sites in visual cortex. Individual stimuli evoked characteristic patterns of optical activity, while delivering stimuli at multiple sites generated interacting patterns in the regions of overlap. We observed that neurons in overlapping regions received convergent horizontal activation that generated nonlinear responses due to the emergence of large inhibitory potentials. The results indicate that co-activation of multiple sets of horizontal connections recruit strong inhibition from local inhibitory networks, causing marked deviations from simple linear integration.

Combined Parameter and State Estimation Problem in a Complex Domain: RF Hyperthermia Treatment Using Nanoparticles

NASA Astrophysics Data System (ADS)

Bermeo Varon, L. A.; Orlande, H. R. B.; Eliçabe, G. E.

2016-09-01

The particle filter methods have been widely used to solve inverse problems with sequential Bayesian inference in dynamic models, simultaneously estimating sequential state variables and fixed model parameters. This methods are an approximation of sequences of probability distributions of interest, that using a large set of random samples, with presence uncertainties in the model, measurements and parameters. In this paper the main focus is the solution combined parameters and state estimation in the radiofrequency hyperthermia with nanoparticles in a complex domain. This domain contains different tissues like muscle, pancreas, lungs, small intestine and a tumor which is loaded iron oxide nanoparticles. The results indicated that excellent agreements between estimated and exact value are obtained.

Resolvent-Techniques for Multiple Exercise Problems

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

Christensen, Sören, E-mail: christensen@math.uni-kiel.de; Lempa, Jukka, E-mail: jukka.lempa@hioa.no

2015-02-15

We study optimal multiple stopping of strong Markov processes with random refraction periods. The refraction periods are assumed to be exponentially distributed with a common rate and independent of the underlying dynamics. Our main tool is using the resolvent operator. In the first part, we reduce infinite stopping problems to ordinary ones in a general strong Markov setting. This leads to explicit solutions for wide classes of such problems. Starting from this result, we analyze problems with finitely many exercise rights and explain solution methods for some classes of problems with underlying Lévy and diffusion processes, where the optimal characteristicsmore » of the problems can be identified more explicitly. We illustrate the main results with explicit examples.« less

Wind shear and turbulence around airports

NASA Technical Reports Server (NTRS)

Lewellen, W. S.; Williamson, G. G.

1976-01-01

A two part study was conducted to determine the feasibility of predicting the conditions under which wind/turbulence environments hazardous to aviation operations exist. The computer model used to solve the velocity temperature, and turbulence distributions in the atmospheric boundary layer is described, and the results of a parameteric analysis to determine the expected range of wind shear and turbulence to be encountered in the vicinity of airports are given. The second part describes the delineation of an ensemble of aircraft accidents in which low level wind shear and/or turbulence appeared to be causative factors. This set of accidents, encompassing a wide range of meteorological conditions, should prove useful in developing techniques for reconstructing hazardous wind environments for aircraft safety investigation purposes.

A new method to generate dust with astrophysical properties

NASA Astrophysics Data System (ADS)

Hansen, J. F.; van Breugel, W.; Bringa, E. M.; Eberly, B.; Graham, G. A.; Remington, B. A.; Taylor, E. A.; Tielens, A. G. G. M.

2011-05-01

To model the size distribution and composition of interstellar and interplanetary dust grains, and their effect on a wide range of phenomena, it is vital to understand the mechanism of dust-shock interaction. We demonstrate a new laser experiment that subjects dust grains to pressure spikes similar to those of colliding astrophysical dust, and that accelerates the grains to astrophysical velocities. This new method generates much larger data sets than earlier methods; we show how large quantities (thousands) of grains are accelerated at once, rather than accelerating individual grains, as is the case of earlier methods using electric fields. We also measure the in-flight velocity ( ~ 4.5km/s) of hundreds of grains simultaneously by use of a particle image velocimetry (PIV) technique.

Governance and assessment in a widely distributed medical education program in Australia.

PubMed

Solarsh, Geoff; Lindley, Jennifer; Whyte, Gordon; Fahey, Michael; Walker, Amanda

2012-06-01

The learning objectives, curriculum content, and assessment standards for distributed medical education programs must be aligned across the health care systems and community contexts in which their students train. In this article, the authors describe their experiences at Monash University implementing a distributed medical education program at metropolitan, regional, and rural Australian sites and an offshore Malaysian site, using four different implementation models. Standardizing learning objectives, curriculum content, and assessment standards across all sites while allowing for site-specific implementation models created challenges for educational alignment. At the same time, this diversity created opportunities to customize the curriculum to fit a variety of settings and for innovations that have enriched the educational system as a whole.Developing these distributed medical education programs required a detailed review of Monash's learning objectives and curriculum content and their relevance to the four different sites. It also required a review of assessment methods to ensure an identical and equitable system of assessment for students at all sites. It additionally demanded changes to the systems of governance and the management of the educational program away from a centrally constructed and mandated curriculum to more collaborative approaches to curriculum design and implementation involving discipline leaders at multiple sites.Distributed medical education programs, like that at Monash, in which cohorts of students undertake the same curriculum in different contexts, provide potentially powerful research platforms to compare different pedagogical approaches to medical education and the impact of context on learning outcomes.

Multisample adjusted U-statistics that account for confounding covariates.

PubMed

Satten, Glen A; Kong, Maiying; Datta, Somnath

2018-06-19

Multisample U-statistics encompass a wide class of test statistics that allow the comparison of 2 or more distributions. U-statistics are especially powerful because they can be applied to both numeric and nonnumeric data, eg, ordinal and categorical data where a pairwise similarity or distance-like measure between categories is available. However, when comparing the distribution of a variable across 2 or more groups, observed differences may be due to confounding covariates. For example, in a case-control study, the distribution of exposure in cases may differ from that in controls entirely because of variables that are related to both exposure and case status and are distributed differently among case and control participants. We propose to use individually reweighted data (ie, using the stratification score for retrospective data or the propensity score for prospective data) to construct adjusted U-statistics that can test the equality of distributions across 2 (or more) groups in the presence of confounding covariates. Asymptotic normality of our adjusted U-statistics is established and a closed form expression of their asymptotic variance is presented. The utility of our approach is demonstrated through simulation studies, as well as in an analysis of data from a case-control study conducted among African-Americans, comparing whether the similarity in haplotypes (ie, sets of adjacent genetic loci inherited from the same parent) occurring in a case and a control participant differs from the similarity in haplotypes occurring in 2 control participants. Copyright © 2018 John Wiley & Sons, Ltd.

Differential distribution of the sodium‐activated potassium channels slick and slack in mouse brain

PubMed Central

Knaus, Hans‐Günther; Schwarzer, Christoph

2015-01-01

ABSTRACT The sodium‐activated potassium channels Slick (Slo2.1, KCNT2) and Slack (Slo2.2, KCNT1) are high‐conductance potassium channels of the Slo family. In neurons, Slick and Slack channels are involved in the generation of slow afterhyperpolarization, in the regulation of firing patterns, and in setting and stabilizing the resting membrane potential. The distribution and subcellular localization of Slick and Slack channels in the mouse brain have not yet been established in detail. The present study addresses this issue through in situ hybridization and immunohistochemistry. Both channels were widely distributed and exhibited distinct distribution patterns. However, in some brain regions, their expression overlapped. Intense Slick channel immunoreactivity was observed in processes, varicosities, and neuronal cell bodies of the olfactory bulb, granular zones of cortical regions, hippocampus, amygdala, lateral septal nuclei, certain hypothalamic and midbrain nuclei, and several regions of the brainstem. The Slack channel showed primarily a diffuse immunostaining pattern, and labeling of cell somata and processes was observed only occasionally. The highest Slack channel expression was detected in the olfactory bulb, lateral septal nuclei, basal ganglia, and distinct areas of the midbrain, brainstem, and cerebellar cortex. In addition, comparing our data obtained from mouse brain with a previously published study on rat brain revealed some differences in the expression and distribution of Slick and Slack channels in these species. J. Comp. Neurol. 524:2093–2116, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:26587966

Semantic Data Access Services at NASA's Atmospheric Science Data Center

NASA Astrophysics Data System (ADS)

Huffer, E.; Hertz, J.; Kusterer, J.

2012-12-01

The corpus of Earth Science data products at the Atmospheric Science Data Center at NASA's Langley Research Center comprises a widely heterogeneous set of products, even among those whose subject matter is very similar. Two distinct data products may both contain data on the same parameter, for instance, solar irradiance; but the instruments used, and the circumstances under which the data were collected and processed, may differ significantly. Understanding the differences is critical to using the data effectively. Data distribution services must be able to provide prospective users with enough information to allow them to meaningfully compare and evaluate the data products offered. Semantic technologies - ontologies, triple stores, reasoners, linked data - offer functionality for addressing this issue. Ontologies can provide robust, high-fidelity domain models that serve as common schema for discovering, evaluating, comparing and integrating data from disparate products. Reasoning engines and triple stores can leverage ontologies to support intelligent search applications that allow users to discover, query, retrieve, and easily reformat data from a broad spectrum of sources. We argue that because of the extremely complex nature of scientific data, data distribution systems should wholeheartedly embrace semantic technologies in order to make their data accessible to a broad array of prospective end users, and to ensure that the data they provide will be clearly understood and used appropriately by consumers. Toward this end, we propose a distribution system in which formal ontological models that accurately and comprehensively represent the ASDC's data domain, and fully leverage the expressivity and inferential capabilities of first order logic, are used to generate graph-based representations of the relevant relationships among data sets, observational systems, metadata files, and geospatial, temporal and scientific parameters to help prospective data consumers navigate directly to relevant data sets and query, subset, retrieve and compare the measurement and calculation data they contain. A critical part of developing semantically-enabled data distribution capabilities is developing an ontology that adequately describes 1) the data products - their structure, their content, and any supporting documentation; 2) the data domain - the objects and processes that the products denote; and 3) the relationship between the data and the domain. The ontology, in addition, should be machine readable and capable of integrating with the larger data distribution system to provide an interactive user experience. We will demonstrate how a formal, high-fidelity, queriable ontology representing the atmospheric science domain objects and data products, together with a robust set of inference rules for generating interactive graphs, allows researchers to navigate quickly and painlessly through the large volume of data at the ASDC. Scientists will be able to discover data products that exactly meet their particular criteria, link to information about the instruments and processing methods that generated the data; and compare and contrast related products.

CDF-XL: computing cumulative distribution functions of reaction time data in Excel.

PubMed

Houghton, George; Grange, James A

2011-12-01

In experimental psychology, central tendencies of reaction time (RT) distributions are used to compare different experimental conditions. This emphasis on the central tendency ignores additional information that may be derived from the RT distribution itself. One method for analysing RT distributions is to construct cumulative distribution frequency plots (CDFs; Ratcliff, Psychological Bulletin 86:446-461, 1979). However, this method is difficult to implement in widely available software, severely restricting its use. In this report, we present an Excel-based program, CDF-XL, for constructing and analysing CDFs, with the aim of making such techniques more readily accessible to researchers, including students (CDF-XL can be downloaded free of charge from the Psychonomic Society's online archive). CDF-XL functions as an Excel workbook and starts from the raw experimental data, organised into three columns (Subject, Condition, and RT) on an Input Data worksheet (a point-and-click utility is provided for achieving this format from a broader data set). No further preprocessing or sorting of the data is required. With one click of a button, CDF-XL will generate two forms of cumulative analysis: (1) "standard" CDFs, based on percentiles of participant RT distributions (by condition), and (2) a related analysis employing the participant means of rank-ordered RT bins. Both analyses involve partitioning the data in similar ways, but the first uses a "median"-type measure at the participant level, while the latter uses the mean. The results are presented in three formats: (i) by participants, suitable for entry into further statistical analysis; (ii) grand means by condition; and (iii) completed CDF plots in Excel charts.

Goodness-of-Fit Tests for Generalized Normal Distribution for Use in Hydrological Frequency Analysis

NASA Astrophysics Data System (ADS)

Das, Samiran

2018-04-01

The use of three-parameter generalized normal (GNO) as a hydrological frequency distribution is well recognized, but its application is limited due to unavailability of popular goodness-of-fit (GOF) test statistics. This study develops popular empirical distribution function (EDF)-based test statistics to investigate the goodness-of-fit of the GNO distribution. The focus is on the case most relevant to the hydrologist, namely, that in which the parameter values are unidentified and estimated from a sample using the method of L-moments. The widely used EDF tests such as Kolmogorov-Smirnov, Cramer von Mises, and Anderson-Darling (AD) are considered in this study. A modified version of AD, namely, the Modified Anderson-Darling (MAD) test, is also considered and its performance is assessed against other EDF tests using a power study that incorporates six specific Wakeby distributions (WA-1, WA-2, WA-3, WA-4, WA-5, and WA-6) as the alternative distributions. The critical values of the proposed test statistics are approximated using Monte Carlo techniques and are summarized in chart and regression equation form to show the dependence of shape parameter and sample size. The performance results obtained from the power study suggest that the AD and a variant of the MAD (MAD-L) are the most powerful tests. Finally, the study performs case studies involving annual maximum flow data of selected gauged sites from Irish and US catchments to show the application of the derived critical values and recommends further assessments to be carried out on flow data sets of rivers with various hydrological regimes.

Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight

PubMed Central

Hufford, Matthew B.; Martínez-Meyer, Enrique; Gaut, Brandon S.; Eguiarte, Luis E.; Tenaillon, Maud I.

2012-01-01

Background The species Zea mays includes both domesticated maize (ssp. mays) and its closest wild relatives known as the teosintes. While genetic and archaeological studies have provided a well-established history of Z. mays evolution, there is currently minimal description of its current and past distribution. Here, we implemented species distribution modeling using paleoclimatic models of the last interglacial (LI; ∼135,000 BP) and the last glacial maximum (LGM; ∼21,000 BP) to hindcast the distribution of Zea mays subspecies over time and to revisit current knowledge of its phylogeography and evolutionary history. Methodology/Principal Findings Using a large occurrence data set and the distribution modeling MaxEnt algorithm, we obtained robust present and past species distributions of the two widely distributed teosinte subspecies (ssps. parviglumis and mexicana) revealing almost perfect complementarity, stable through time, of their occupied distributions. We also investigated the present distributions of primitive maize landraces, which overlapped but were broader than those of the teosintes. Our data reinforced the idea that little historical gene flow has occurred between teosinte subspecies, but maize has served as a genetic bridge between them. We observed an expansion of teosinte habitat from the LI, consistent with population genetic data. Finally, we identified locations potentially serving as refugia for the teosintes throughout epochs of climate change and sites that should be targeted in future collections. Conclusion/Significance The restricted and highly contrasting ecological niches of the wild teosintes differ substantially from domesticated maize. Variables determining the distributions of these taxa can inform future considerations of local adaptation and the impacts of climate change. Our assessment of the changing distributions of Zea mays taxa over time offers a unique glimpse into the history of maize, highlighting a strategy for the study of domestication that may prove useful for other species. PMID:23155371

75 FR 44224 - Grant of Authority for Subzone Status; Yankee Candle Corporation (Candles and Gift Sets); Whately...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-28

... Status; Yankee Candle Corporation (Candles and Gift Sets); Whately and South Deerfield, MA Pursuant to... special-purpose subzone at the candle and gift set manufacturing and distribution facilities of Yankee... activity related to the manufacturing and distribution of candles and gift sets at the facilities of Yankee...

Distribution, microfabric, and geochemical characteristics of siliceous rocks in central orogenic belt, China: implications for a hydrothermal sedimentation model.

PubMed

Li, Hongzhong; Zhai, Mingguo; Zhang, Lianchang; Gao, Le; Yang, Zhijun; Zhou, Yongzhang; He, Junguo; Liang, Jin; Zhou, Liuyu; Voudouris, Panagiotis Ch

2014-01-01

Marine siliceous rocks are widely distributed in the central orogenic belt (COB) of China and have a close connection to the geological evolution and metallogenesis. They display periodic distributions from Mesoproterozoic to Jurassic with positive peaks in the Mesoproterozoic, Cambrian--Ordovician, and Carboniferous--Permian and their deposition is enhanced by the tensional geological settings. The compressional regimes during the Jinning, Caledonian, Hercynian, Indosinian, and Yanshanian orogenies resulted in sudden descent in their distribution. The siliceous rocks of the Bafangshan-Erlihe ore deposit include authigenic quartz, syn-depositional metal sulphides, and scattered carbonate minerals. Their SiO2 content (71.08-95.30%), Ba (42.45-503.0 ppm), and ΣREE (3.28-19.75 ppm) suggest a hydrothermal sedimentation origin. As evidenced by the Al/(Al + Fe + Mn), Sc/Th, (La/Yb) N, and (La/Ce) N ratios and δCe values, the studied siliceous rocks were deposited in a marginal sea basin of a limited ocean. We suggest that the Bafangshan-Erlihe area experienced high- and low-temperature stages of hydrothermal activities. The hydrothermal sediments of the former stage include metal sulphides and silica, while the latter was mainly composed of silica. Despite the hydrothermal sedimentation of the siliceous rocks, minor terrigenous input, magmatism, and biological activity partly contributed to geochemical features deviating from the typical hydrothermal characteristics.

Distribution, Microfabric, and Geochemical Characteristics of Siliceous Rocks in Central Orogenic Belt, China: Implications for a Hydrothermal Sedimentation Model

PubMed Central

Li, Hongzhong; Zhai, Mingguo; Zhang, Lianchang; Gao, Le; Yang, Zhijun; Zhou, Yongzhang; He, Junguo; Liang, Jin; Zhou, Liuyu; Voudouris, Panagiotis Ch.

2014-01-01

Marine siliceous rocks are widely distributed in the central orogenic belt (COB) of China and have a close connection to the geological evolution and metallogenesis. They display periodic distributions from Mesoproterozoic to Jurassic with positive peaks in the Mesoproterozoic, Cambrian—Ordovician, and Carboniferous—Permian and their deposition is enhanced by the tensional geological settings. The compressional regimes during the Jinning, Caledonian, Hercynian, Indosinian, and Yanshanian orogenies resulted in sudden descent in their distribution. The siliceous rocks of the Bafangshan-Erlihe ore deposit include authigenic quartz, syn-depositional metal sulphides, and scattered carbonate minerals. Their SiO2 content (71.08–95.30%), Ba (42.45–503.0 ppm), and ΣREE (3.28–19.75 ppm) suggest a hydrothermal sedimentation origin. As evidenced by the Al/(Al + Fe + Mn), Sc/Th, (La/Yb)N, and (La/Ce)N ratios and δCe values, the studied siliceous rocks were deposited in a marginal sea basin of a limited ocean. We suggest that the Bafangshan-Erlihe area experienced high- and low-temperature stages of hydrothermal activities. The hydrothermal sediments of the former stage include metal sulphides and silica, while the latter was mainly composed of silica. Despite the hydrothermal sedimentation of the siliceous rocks, minor terrigenous input, magmatism, and biological activity partly contributed to geochemical features deviating from the typical hydrothermal characteristics. PMID:25140349

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

PubMed

Neuwald, Andrew F; Altschul, Stephen F

2016-12-01

Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

Optimization of active distribution networks: Design and analysis of significative case studies for enabling control actions of real infrastructure

NASA Astrophysics Data System (ADS)

Moneta, Diana; Mora, Paolo; Viganò, Giacomo; Alimonti, Gianluca

2014-12-01

The diffusion of Distributed Generation (DG) based on Renewable Energy Sources (RES) requires new strategies to ensure reliable and economic operation of the distribution networks and to support the diffusion of DG itself. An advanced algorithm (DISCoVER - DIStribution Company VoltagE Regulator) is being developed to optimize the operation of active network by means of an advanced voltage control based on several regulations. Starting from forecasted load and generation, real on-field measurements, technical constraints and costs for each resource, the algorithm generates for each time period a set of commands for controllable resources that guarantees achievement of technical goals minimizing the overall cost. Before integrating the controller into the telecontrol system of the real networks, and in order to validate the proper behaviour of the algorithm and to identify possible critical conditions, a complete simulation phase has started. The first step is concerning the definition of a wide range of "case studies", that are the combination of network topology, technical constraints and targets, load and generation profiles and "costs" of resources that define a valid context to test the algorithm, with particular focus on battery and RES management. First results achieved from simulation activity on test networks (based on real MV grids) and actual battery characteristics are given, together with prospective performance on real case applications.

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

PubMed Central

Ma, Yue; Tuskan, Gerald A.

2018-01-01

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln(L) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level. PMID:29686995

Slope mass movements on rocky sea-cliffs: A power-law distributed natural hazard on the Barlavento Coast, Algarve, Portugal

NASA Astrophysics Data System (ADS)

Teixeira, Sebastião Braz

2006-06-01

The coast of the Central Algarve, Portugal, is dominated by sea-cliffs, cut on Miocene calcarenites; here, the main coastal geologic hazards result from the conflict between human occupation and sea-cliff recession. The evolution of this rocky coast occurs through an intermittent and discontinuous series of slope mass movements, along a 46 km cliff front. For the last 30 years, the increase of tourism occupation has amplified the risks to both people and buildings. In the last decade we have seen several accidents caused by cliff failure, which killed or wounded people and destroyed several buildings. The definition of buffer zones limited by hazard lines parallel to the cliff edge, where land use is restricted, is a widely used and effective preventive measure for mitigating risk. Rocky coasts typically show a slow cliff evolution. The process of gathering statistically significant field inventories of mass movements is, thus, very long. Although mass movement catalogues provide fundamental information on sea cliff evolution patterns and are an outstanding tool in hazard assessment, published data sets are still rare. In this work, we use two inventories of mass movement width, recorded on sea cliffs cut on Miocene calcarenites: a nine year long continuous field inventory (1995-2004) with 140 recorded events, and a 44 year long catalogue based on comparative analysis of aerial photographs (1947-1991), that includes 177 events. The cumulative frequency-width distributions of both data sets fit, above a critical width value corresponding to the threshold of full completeness of the inventories, to power-law distributions. The knowledge of the limits of the catalogues enabled the construction of a 53 year long record inventory over the range of mean width ⩾3 m ( n=167 events) and maximum width ⩾4 m ( n=155 events). The data assembled corresponds to a partial series and was converted to a return period-size distribution. Both return period-width distributions (mean width and maximum width) are also power-law distributions. Equations of return period-width distributions give the width of hazard lines corresponding to the width of mass movement, in which return period equals the period that hazard line is referred to.

Double stars with wide separations in the AGK3 - II. The wide binaries and the multiple systems*

NASA Astrophysics Data System (ADS)

Halbwachs, J.-L.; Mayor, M.; Udry, S.

2017-02-01

A large observation programme was carried out to measure the radial velocities of the components of a selection of common proper motion (CPM) stars to select the physical binaries. 80 wide binaries (WBs) were detected, and 39 optical pairs were identified. By adding CPM stars with separations close enough to be almost certain that they are physical, a bias-controlled sample of 116 WBs was obtained, and used to derive the distribution of separations from 100 to 30 000 au. The distribution obtained does not match the log-constant distribution, but agrees with the log-normal distribution. The spectroscopic binaries detected among the WB components were used to derive statistical information about the multiple systems. The close binaries in WBs seem to be like those detected in other field stars. As for the WBs, they seem to obey the log-normal distribution of periods. The number of quadruple systems agrees with the no correlation hypothesis; this indicates that an environment conducive to the formation of WBs does not favour the formation of subsystems with periods shorter than 10 yr.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

An Old-Growth Definition for Dry and Dry-Mesic Oak-Pine Forests.

Treesearch

David L. White; F. Thomas Lloyd

1998-01-01

Dry and dry-mesic oak-pine forests are widely distributed from New Jersey to Texas, but representative old-growth stands are rare. Historical accounts of composition, along with information from existing old-growth stands, were used to characterize this type. Shortleaf pine and white oak were the most widely distributed trees across all old-growth stands. Shortleaf was...

End-of-winter snow depth variability on glaciers in Alaska

NASA Astrophysics Data System (ADS)

McGrath, Daniel; Sass, Louis; O'Neel, Shad; Arendt, Anthony; Wolken, Gabriel; Gusmeroli, Alessio; Kienholz, Christian; McNeil, Christopher

2015-08-01

A quantitative understanding of snow thickness and snow water equivalent (SWE) on glaciers is essential to a wide range of scientific and resource management topics. However, robust SWE estimates are observationally challenging, in part because SWE can vary abruptly over short distances in complex terrain due to interactions between topography and meteorological processes. In spring 2013, we measured snow accumulation on several glaciers around the Gulf of Alaska using both ground- and helicopter-based ground-penetrating radar surveys, complemented by extensive ground truth observations. We found that SWE can be highly variable (40% difference) over short spatial scales (tens to hundreds of meters), especially in the ablation zone where the underlying ice surfaces are typically rough. Elevation provides the dominant basin-scale influence on SWE, with gradients ranging from 115 to 400 mm/100 m. Regionally, total accumulation and the accumulation gradient are strongly controlled by a glacier's distance from the coastal moisture source. Multiple linear regressions, used to calculate distributed SWE fields, show that robust results require adequate sampling of the true distribution of multiple terrain parameters. Final SWE estimates (comparable to winter balances) show reasonable agreement with both the Parameter-elevation Relationships on Independent Slopes Model climate data set (9-36% difference) and the U.S. Geological Survey Alaska Benchmark Glaciers (6-36% difference). All the glaciers in our study exhibit substantial sensitivity to changing snow-rain fractions, regardless of their location in a coastal or continental climate. While process-based SWE projections remain elusive, the collection of ground-penetrating radar (GPR)-derived data sets provides a greatly enhanced perspective on the spatial distribution of SWE and will pave the way for future work that may eventually allow such projections.

Advancing cloud lifecycle representation in numerical models using innovative analysis methods that bridge arm observations over a breadth of scales

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

Tselioudis, George

2016-03-04

From its location on the subtropics-midlatitude boundary, the Azores is influenced by both the subtropical high pressure and the midlatitude baroclinic storm regimes, and therefore experiences a wide range of cloud structures, from fair-weather scenes to stratocumulus sheets to deep convective systems. This project combined three types of data sets to study cloud variability in the Azores: a satellite analysis of cloud regimes, a reanalysis characterization of storminess, and a 19-month field campaign that occurred on Graciosa Island. Combined analysis of the three data sets provides a detailed picture of cloud variability and the respective dynamic influences, with emphasis onmore » low clouds that constitute a major uncertainty source in climate model simulations. The satellite cloud regime analysis shows that the Azores cloud distribution is similar to the mean global distribution and can therefore be used to evaluate cloud simulation in global models. Regime analysis of low clouds shows that stratocumulus decks occur under the influence of the Azores high-pressure system, while shallow cumulus clouds are sustained by cold-air outbreaks, as revealed by their preference for post-frontal environments and northwesterly flows. An evaluation of CMIP5 climate model cloud regimes over the Azores shows that all models severely underpredict shallow cumulus clouds, while most models also underpredict the occurrence of stratocumulus cloud decks. It is demonstrated that carefully selected case studies can be related through regime analysis to climatological cloud distributions, and a methodology is suggested utilizing process-resolving model simulations of individual cases to better understand cloud-dynamics interactions and attempt to explain and correct climate model cloud deficiencies.« less

Cytotype stability, facultative apomixis and geographical parthenogenesis in Ranunculus kuepferi (Ranunculaceae).

PubMed

Cosendai, Anne-Caroline; Hörandl, Elvira

2010-03-01

Asexual organisms are more widespread in previously glaciated areas than their sexual relatives ('geographical parthenogenesis'). In plants, this pattern is probably dependent on reproductive isolation and stability of cytotypes within their respective distribution areas. Both partial apomixis and introgressive hybridization potentially destabilize the spatial separation of sexual and apomictic populations. The wide distribution of apomicts may be further enhanced by uniparental reproduction which is advantageous for colonization. These factors are studied in the alpine species Ranunculus kuepferi. Geographical distribution, diversity and mode of reproduction of cytotypes were assessed using flow cytometry and flow cytometric seed screening on samples from 59 natural populations of Ranunculus kuepferi. Seed set of cytotypes was compared in the wild. Diploid sexuals are confined to the south-western parts of the Alps, while tetraploid apomicts dominate in previously glaciated and in geographically isolated areas despite a significantly lower fertility. Other cytotypes (3x, 5x and 6x) occur mainly in the sympatric zone, but without establishing populations. The tetraploids are predominantly apomictic, but also show a partial apomixis via an uncoupling of apomeiosis and parthenogenesis in the seed material. Both pseudogamy and autonomous endosperm formation are observed which may enhance uniparental reproduction. Diploids occupy a glacial relic area and resist introgression of apomixis, probably because of a significantly higher seed set. Among the polyploids, only apomictic tetraploids form stable populations; the other cytotypes arising from partial apomixis fail to establish, probably because of minority cytotype disadvantages. Tetraploid apomicts colonize previously devastated and also distant areas via long-distance dispersal, confirming Baker's law of an advantage of uniparental reproduction. It is concluded that stability of cytotypes and of modes of reproduction are important factors for establishing a pattern of geographical parthenogenesis.

Cytotype stability, facultative apomixis and geographical parthenogenesis in Ranunculus kuepferi (Ranunculaceae)

PubMed Central

Cosendai, Anne-Caroline; Hörandl, Elvira

2010-01-01

Background and Aims Asexual organisms are more widespread in previously glaciated areas than their sexual relatives (‘geographical parthenogenesis’). In plants, this pattern is probably dependent on reproductive isolation and stability of cytotypes within their respective distribution areas. Both partial apomixis and introgressive hybridization potentially destabilize the spatial separation of sexual and apomictic populations. The wide distribution of apomicts may be further enhanced by uniparental reproduction which is advantageous for colonization. These factors are studied in the alpine species Ranunculus kuepferi. Methods Geographical distribution, diversity and mode of reproduction of cytotypes were assessed using flow cytometry and flow cytometric seed screening on samples from 59 natural populations of Ranunculus kuepferi. Seed set of cytotypes was compared in the wild. Key Results Diploid sexuals are confined to the south-western parts of the Alps, while tetraploid apomicts dominate in previously glaciated and in geographically isolated areas despite a significantly lower fertility. Other cytotypes (3x, 5x and 6x) occur mainly in the sympatric zone, but without establishing populations. The tetraploids are predominantly apomictic, but also show a partial apomixis via an uncoupling of apomeiosis and parthenogenesis in the seed material. Both pseudogamy and autonomous endosperm formation are observed which may enhance uniparental reproduction. Conclusions Diploids occupy a glacial relic area and resist introgression of apomixis, probably because of a significantly higher seed set. Among the polyploids, only apomictic tetraploids form stable populations; the other cytotypes arising from partial apomixis fail to establish, probably because of minority cytotype disadvantages. Tetraploid apomicts colonize previously devastated and also distant areas via long-distance dispersal, confirming Baker's law of an advantage of uniparental reproduction. It is concluded that stability of cytotypes and of modes of reproduction are important factors for establishing a pattern of geographical parthenogenesis. PMID:20100695

Offshore sand resources for coastal erosion control in Louisiana

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

Ramsey, K.E.; Penland, S.; McBride, R.A.

1990-09-01

An inventory of existing geophysical data supplemented by more than 15,000 km of high-resolution seismic profiles and 400 vibracores collected cooperatively by the Louisiana Geological Survey and US Geological Survey since 1981 indicates that a wide range of aggregate minerals occurs on the continental shelf in a variety of depositional settings. The distribution of these deposits is controlled by the geometry of the preexisting fluvial and deltaic channel systems and the stratigraphic signature of the Holocene Transgression across these features. The geology of coastal and offshore Louisiana is tied to the depositional history of the Mississippi River. Offshore of themore » delta plain, five types of aggregate sources can be identified: inner shelf shoals, submerged barrier islands, tidal inlets, distributary channels, and barrier platforms. This paper describes the geology of offshore Louisiana, the available geophysical data sets, and the distribution of aggregate mineral resources. On the continental shelf of the Mississippi River delta plain, two extensive seismic survey grids have been developed by the Louisiana Geological Survey and US Geological Survey. The most prospective resources found are the huge sand bodies of Ship Shoal and associated distributaries, Cat Island Pass tidal channels and associated tidal deltas, and Barataria Pass/Grand Terre tidal channels and associated tidal deltas. East of the mouth of the Mississippi River are the Chandeleur Islands, where LGS identified seven major sand resource targets, truncated barrier-spit and tidal inlet deposits, submerged beach ridges, and distributaries associated with abandoned St. Bernard delta complexes. Abundant sand resources can be found in offshore Louisiana. Many of the sand bodies contain heavy minerals, but their concentration and distribution is unknown. Other potential sand resources not yet adequately explored include Sabine Bank, the Outer Shoal, and the St. Bernard shoal.« less

Fractal analysis of urban catchments and their representation in semi-distributed models: imperviousness and sewer system

NASA Astrophysics Data System (ADS)

Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel; Ochoa-Rodriguez, Susana; Willems, Patrick; Ichiba, Abdellah; Wang, Lipen; Pina, Rui; Van Assel, Johan; Bruni, Guendalina; Murla Tuyls, Damian; ten Veldhuis, Marie-Claire

2017-04-01

Land use distribution and sewer system geometry exhibit complex scale dependent patterns in urban environment. This scale dependency is even more visible in a rasterized representation where only a unique class is affected to each pixel. Such features are well grasped with fractal tools, which are based scale invariance and intrinsically designed to characterise and quantify the space filled by a geometrical set exhibiting complex and tortuous patterns. Fractal tools have been widely used in hydrology but seldom in the specific context of urban hydrology. In this paper, they are used to analyse surface and sewer data from 10 urban or peri-urban catchments located in 5 European countries in the framework of the NWE Interreg RainGain project (www.raingain.eu). The aim was to characterise urban catchment properties accounting for the complexity and inhomogeneity typical of urban water systems. Sewer system density and imperviousness (roads or buildings), represented in rasterized maps of 2 m x 2 m pixels, were analysed to quantify their fractal dimension, characteristic of scaling invariance. It appears that both sewer density and imperviousness exhibit scale invariant features that can be characterized with the help of fractal dimensions ranging from 1.6 to 2, depending on the catchment. In a given area, consistent results were found for the two geometrical features, yielding a robust and innovative way of quantifying the level of urbanization. The representation of imperviousness in operational semi-distributed hydrological models for these catchments was also investigated by computing fractal dimensions of the geometrical sets made up of the sub-catchments with coefficients of imperviousness greater than a range of thresholds. It enables to quantify how well spatial structures of imperviousness are represented in the urban hydrological models.

Patterns of Limnohabitans Microdiversity across a Large Set of Freshwater Habitats as Revealed by Reverse Line Blot Hybridization

PubMed Central

Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, Martin W.

2013-01-01

Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria. Instead, our observations suggest that the genus Limnohabitans, as well as its R-BT subgroup, represent ecologically heterogeneous taxa, which underwent pronounced ecological diversification. PMID:23554898

Estimating distribution and connectivity of recolonizing American marten in the northeastern United States using expert elicitation techniques

USGS Publications Warehouse

Aylward, C.M.; Murdoch, J.D.; Donovan, Therese M.; Kilpatrick, C.W.; Bernier, C.; Katz, J.

2018-01-01

The American marten Martes americana is a species of conservation concern in the northeastern United States due to widespread declines from over‐harvesting and habitat loss. Little information exists on current marten distribution and how landscape characteristics shape patterns of occupancy across the region, which could help develop effective recovery strategies. The rarity of marten and lack of historical distribution records are also problematic for region‐wide conservation planning. Expert opinion can provide a source of information for estimating species–landscape relationships and is especially useful when empirical data are sparse. We created a survey to elicit expert opinion and build a model that describes marten occupancy in the northeastern United States as a function of landscape conditions. We elicited opinions from 18 marten experts that included wildlife managers, trappers and researchers. Each expert estimated occupancy probability at 30 sites in their geographic region of expertise. We, then, fit the response data with a set of 58 models that incorporated the effects of covariates related to forest characteristics, climate, anthropogenic impacts and competition at two spatial scales (1.5 and 5 km radii), and used model selection techniques to determine the best model in the set. Three top models had strong empirical support, which we model averaged based on AIC weights. The final model included effects of five covariates at the 5‐km scale: percent canopy cover (positive), percent spruce‐fir land cover (positive), winter temperature (negative), elevation (positive) and road density (negative). A receiver operating characteristic curve indicated that the model performed well based on recent occurrence records. We mapped distribution across the region and used circuit theory to estimate movement corridors between isolated core populations. The results demonstrate the effectiveness of expert‐opinion data at modeling occupancy for rare species and provide tools for planning marten recovery in the northeastern United States.

Unidata Internet Data Distribution (IDD) and THematic Real-time Environmental Distributed Data Services (THREDDS)

NASA Astrophysics Data System (ADS)

Domenico, B.

2001-12-01

Universities across the nation are transforming their teaching and research efforts through increased use of a rapidly expanding menu of environmental data. With funding from the Division of Atmospheric Sciences (ATM ) of the National Science Foundation (NSF), the Unidata Program is playing a central role in this transformation by enabling universities to employ innovative computing and networking technologies to acquire such data sets in real-time and use them routinely in their classrooms and research labs. Working with the Unidata Program Center (UPC), the Unidata community, comprising over 140 departments, has built a national Internet Data Distribution (IDD ) system. The IDD allows users to "subscribe" to certain sets of data products; IDD servers then deliver the requested data to their local servers as soon as they are available from the source. With the initial national implementation in 1994, the IDD may have been the original example of Internet "push" technology. It now provides the reliability, flexibility, and efficiency required by participating institutions. As the underlying Internet technology evolves, we anticipate dramatic increases in the volume of data delivered. We plan to augment the system to better serve disciplines outside the atmospheric sciences and to incorporate anticipated new networking technologies to minimize the impact of the IDD on the underlying network. Unidata has recently undertaken a new initiative called THREDDS (THematic Real-time Environmental Distributed Data Services) under a grant from the NSF Division of Undergraduate Education NSDL (National Science, Math, Engineering, Technology Education Digital Library). The goal of THREDDs is to make it possible for students, educators and researchers to publish, contribute, find, and interact with data relating to the Earth system in a convenient, effective, and integrated fashion. Just as the World Wide Web and digital-library technologies have simplified the process of publishing and accessing multimedia documents, THREDDS will provide needed infrastructure for publishing and accessing scientific data in a similarly convenient fashion.

When Theory Meets Data: Comparing Model Predictions Of Hillslope Sediment Size With Field Measurements.

NASA Astrophysics Data System (ADS)

Mahmoudi, M.; Sklar, L. S.; Leclere, S.; Davis, J. D.; Stine, A.

2017-12-01

The size distributions of sediment produced on hillslopes and supplied to river channels influence a wide range of fluvial processes, from bedrock river incision to the creation of aquatic habitats. However, the factors that control hillslope sediment size are poorly understood, limiting our ability to predict sediment size and model the evolution of sediment size distributions across landscapes. Recently separate field and theoretical investigations have begun to address this knowledge gap. Here we compare the predictions of several emerging modeling approaches to landscapes where high quality field data are available. Our goals are to explore the sensitivity and applicability of the theoretical models in each field context, and ultimately to provide a foundation for incorporating hillslope sediment size into models of landscape evolution. The field data include published measurements of hillslope sediment size from the Kohala peninsula on the island of Hawaii and tributaries to the Feather River in the northern Sierra Nevada mountains of California, and an unpublished data set from the Inyo Creek catchment of the southern Sierra Nevada. These data are compared to predictions adapted from recently published modeling approaches that include elements of topography, geology, structure, climate and erosion rate. Predictive models for each site are built in ArcGIS using field condition datasets: DEM topography (slope, aspect, curvature), bedrock geology (lithology, mineralogy), structure (fault location, fracture density), climate data (mean annual precipitation and temperature), and estimates of erosion rates. Preliminary analysis suggests that models may be finely tuned to the calibration sites, particularly when field conditions most closely satisfy model assumptions, leading to unrealistic predictions from extrapolation. We suggest a path forward for developing a computationally tractable method for incorporating spatial variation in production of hillslope sediment size distributions in landscape evolution models. Overall, this work highlights the need for additional field data sets as well as improved theoretical models, but also demonstrates progress in predicting the size distribution of sediments produced on hillslopes and supplied to channels.