Boundary formulations for sensitivity analysis without matrix derivatives

NASA Technical Reports Server (NTRS)

Kane, J. H.; Guru Prasad, K.

1993-01-01

A new hybrid approach to continuum structural shape sensitivity analysis employing boundary element analysis (BEA) is presented. The approach uses iterative reanalysis to obviate the need to factor perturbed matrices in the determination of surface displacement and traction sensitivities via a univariate perturbation/finite difference (UPFD) step. The UPFD approach makes it possible to immediately reuse existing subroutines for computation of BEA matrix coefficients in the design sensitivity analysis process. The reanalysis technique computes economical response of univariately perturbed models without factoring perturbed matrices. The approach provides substantial computational economy without the burden of a large-scale reprogramming effort.

The Gulf Stream in Ocean Reanalyses: 1993-2010

NASA Astrophysics Data System (ADS)

Chi, L.; Wolfe, C.; Hameed, S.

2017-12-01

In recent years, significant progress has been made in the development of high-resolution ocean reanalysis products. However, errors are likely to remain because of inadequate coverage of observations, model resolutions, physical parameterizations, etc. We compare the representation of the Gulf Stream (GS) in several widely used global reanalysis products with resolutions ranging from 1° to 1/12°. This intercomparison focuses on the Florida Current transport, the separation of GS near Cape Hatteras, GS properties along the Oleander Line (from New Jersey to Bermuda), GS path and the GS north wall positions between 73°W and 55°W. A large spread exists across the reanalysis products. HYCOM and GLORYS2v4 stand out for their top performance in most metrics. Some common biases are found in all discussed products; for example, the velocity structure of the GS near the Oleander Line is too symmetric and the maximum velocity is weaker than in observations. In addition, the annual mean values of GS separation latitude near Cape Hatteras, the GS transport, and net transport across Oleander Line (which runs from New Jersey to Bermuda), less than half of the reanalysis products are correlated to the observations at 95% confidence level.

Diagnostic evaluation of the Community Earth System Model in simulating mineral dust emission with insight into large-scale dust storm mobilization in the Middle East and North Africa (MENA)

NASA Astrophysics Data System (ADS)

Parajuli, Sagar Prasad; Yang, Zong-Liang; Lawrence, David M.

2016-06-01

Large amounts of mineral dust are injected into the atmosphere during dust storms, which are common in the Middle East and North Africa (MENA) where most of the global dust hotspots are located. In this work, we present simulations of dust emission using the Community Earth System Model Version 1.2.2 (CESM 1.2.2) and evaluate how well it captures the spatio-temporal characteristics of dust emission in the MENA region with a focus on large-scale dust storm mobilization. We explicitly focus our analysis on the model's two major input parameters that affect the vertical mass flux of dust-surface winds and the soil erodibility factor. We analyze dust emissions in simulations with both prognostic CESM winds and with CESM winds that are nudged towards ERA-Interim reanalysis values. Simulations with three existing erodibility maps and a new observation-based erodibility map are also conducted. We compare the simulated results with MODIS satellite data, MACC reanalysis data, AERONET station data, and CALIPSO 3-d aerosol profile data. The dust emission simulated by CESM, when driven by nudged reanalysis winds, compares reasonably well with observations on daily to monthly time scales despite CESM being a global General Circulation Model. However, considerable bias exists around known high dust source locations in northwest/northeast Africa and over the Arabian Peninsula where recurring large-scale dust storms are common. The new observation-based erodibility map, which can represent anthropogenic dust sources that are not directly represented by existing erodibility maps, shows improved performance in terms of the simulated dust optical depth (DOD) and aerosol optical depth (AOD) compared to existing erodibility maps although the performance of different erodibility maps varies by region.

Assessment of upper tropospheric and stratospheric water vapor and ozone in reanalyses as part of S-RIP

NASA Astrophysics Data System (ADS)

Davis, Sean M.; Hegglin, Michaela I.; Fujiwara, Masatomo; Dragani, Rossana; Harada, Yayoi; Kobayashi, Chiaki; Long, Craig; Manney, Gloria L.; Nash, Eric R.; Potter, Gerald L.; Tegtmeier, Susann; Wang, Tao; Wargan, Krzysztof; Wright, Jonathon S.

2017-10-01

Reanalysis data sets are widely used to understand atmospheric processes and past variability, and are often used to stand in as "observations" for comparisons with climate model output. Because of the central role of water vapor (WV) and ozone (O3) in climate change, it is important to understand how accurately and consistently these species are represented in existing global reanalyses. In this paper, we present the results of WV and O3 intercomparisons that have been performed as part of the SPARC (Stratosphere-troposphere Processes and their Role in Climate) Reanalysis Intercomparison Project (S-RIP). The comparisons cover a range of timescales and evaluate both inter-reanalysis and observation-reanalysis differences. We also provide a systematic documentation of the treatment of WV and O3 in current reanalyses to aid future research and guide the interpretation of differences amongst reanalysis fields.The assimilation of total column ozone (TCO) observations in newer reanalyses results in realistic representations of TCO in reanalyses except when data coverage is lacking, such as during polar night. The vertical distribution of ozone is also relatively well represented in the stratosphere in reanalyses, particularly given the relatively weak constraints on ozone vertical structure provided by most assimilated observations and the simplistic representations of ozone photochemical processes in most of the reanalysis forecast models. However, significant biases in the vertical distribution of ozone are found in the upper troposphere and lower stratosphere in all reanalyses.In contrast to O3, reanalysis estimates of stratospheric WV are not directly constrained by assimilated data. Observations of atmospheric humidity are typically used only in the troposphere, below a specified vertical level at or near the tropopause. The fidelity of reanalysis stratospheric WV products is therefore mainly dependent on the reanalyses' representation of the physical drivers that influence stratospheric WV, such as temperatures in the tropical tropopause layer, methane oxidation, and the stratospheric overturning circulation. The lack of assimilated observations and known deficiencies in the representation of stratospheric transport in reanalyses result in much poorer agreement amongst observational and reanalysis estimates of stratospheric WV. Hence, stratospheric WV products from the current generation of reanalyses should generally not be used in scientific studies.

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm.

PubMed

Wu, Wei-Sheng; Jhou, Meng-Jhun

2017-01-13

Missing value imputation is important for microarray data analyses because microarray data with missing values would significantly degrade the performance of the downstream analyses. Although many microarray missing value imputation algorithms have been developed, an objective and comprehensive performance comparison framework is still lacking. To solve this problem, we previously proposed a framework which can perform a comprehensive performance comparison of different existing algorithms. Also the performance of a new algorithm can be evaluated by our performance comparison framework. However, constructing our framework is not an easy task for the interested researchers. To save researchers' time and efforts, here we present an easy-to-use web tool named MVIAeval (Missing Value Imputation Algorithm evaluator) which implements our performance comparison framework. MVIAeval provides a user-friendly interface allowing users to upload the R code of their new algorithm and select (i) the test datasets among 20 benchmark microarray (time series and non-time series) datasets, (ii) the compared algorithms among 12 existing algorithms, (iii) the performance indices from three existing ones, (iv) the comprehensive performance scores from two possible choices, and (v) the number of simulation runs. The comprehensive performance comparison results are then generated and shown as both figures and tables. MVIAeval is a useful tool for researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be represented as a matrix form (e.g. NGS data or proteomics data). Thus, MVIAeval will greatly expedite the progress in the research of missing value imputation algorithms.

The tropopause inversion layer in models and analyses

NASA Astrophysics Data System (ADS)

Birner, T.; Sankey, D.; Shepherd, T. G.

2006-07-01

Recent high-resolution radiosonde climatologies have revealed a tropopause inversion layer (TIL) in the extratropics: temperature strongly increases just above a sharp local cold point tropopause. Here, it is asked to what extent a TIL exists in current general circulation models (GCMs) and meteorological analyses. Only a weak hint of a TIL exists in NCEP/NCAR reanalysis data. In contrast, the Canadian Middle Atmosphere Model (CMAM), a comprehensive GCM, exhibits a TIL of realistic strength. However, in data assimilation mode CMAM exhibits a much weaker TIL, especially in the Southern Hemisphere where only coarse satellite data are available. The discrepancy between the analyses and the GCM is thus hypothesized to be mainly due to data assimilation acting to smooth the observed strong curvature in temperature around the tropopause. This is confirmed in the reanalysis where the stratification around the tropopause exhibits a strong discontinuity at the start of the satellite era.

GeneXplorer: an interactive web application for microarray data visualization and analysis.

PubMed

Rees, Christian A; Demeter, Janos; Matese, John C; Botstein, David; Sherlock, Gavin

2004-10-01

When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

CEM-designer: design of custom expression microarrays in the post-ENCODE Era.

PubMed

Arnold, Christian; Externbrink, Fabian; Hackermüller, Jörg; Reiche, Kristin

2014-11-10

Microarrays are widely used in gene expression studies, and custom expression microarrays are popular to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes uncovered recently make custom expression microarray design a non-trivial task. Pervasive transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that requires well-considered probe design strategies and is largely neglected in existing approaches. We developed the web server CEM-Designer that facilitates microarray platform independent design of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection and generation of a set of unique target sequences from different sources and (ii) the selection of a set of sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to third party software to ensure that probes meet provider-specific constraints. CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de. Copyright © 2014 Elsevier B.V. All rights reserved.

A Reanalysis of the Effects of Teacher Replacement Using Value-Added Modeling

ERIC Educational Resources Information Center

Yeh, Stuart S.

2013-01-01

Background: In principle, value-added modeling (VAM) might be justified if it can be shown to be a more reliable indicator of teacher quality than existing indicators for existing low-stakes decisions that are already being made, such as the award of small merit bonuses. However, a growing number of researchers now advocate the use of VAM to…

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

PubMed

Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

Chondrocyte channel transcriptomics

PubMed Central

Lewis, Rebecca; May, Hannah; Mobasheri, Ali; Barrett-Jolley, Richard

2013-01-01

To date, a range of ion channels have been identified in chondrocytes using a number of different techniques, predominantly electrophysiological and/or biomolecular; each of these has its advantages and disadvantages. Here we aim to compare and contrast the data available from biophysical and microarray experiments. This letter analyses recent transcriptomics datasets from chondrocytes, accessible from the European Bioinformatics Institute (EBI). We discuss whether such bioinformatic analysis of microarray datasets can potentially accelerate identification and discovery of ion channels in chondrocytes. The ion channels which appear most frequently across these microarray datasets are discussed, along with their possible functions. We discuss whether functional or protein data exist which support the microarray data. A microarray experiment comparing gene expression in osteoarthritis and healthy cartilage is also discussed and we verify the differential expression of 2 of these genes, namely the genes encoding large calcium-activated potassium (BK) and aquaporin channels. PMID:23995703

Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.

PubMed

Motakis, E S; Nason, G P; Fryzlewicz, P; Rutter, G A

2006-10-15

Many standard statistical techniques are effective on data that are normally distributed with constant variance. Microarray data typically violate these assumptions since they come from non-Gaussian distributions with a non-trivial mean-variance relationship. Several methods have been proposed that transform microarray data to stabilize variance and draw its distribution towards the Gaussian. Some methods, such as log or generalized log, rely on an underlying model for the data. Others, such as the spread-versus-level plot, do not. We propose an alternative data-driven multiscale approach, called the Data-Driven Haar-Fisz for microarrays (DDHFm) with replicates. DDHFm has the advantage of being 'distribution-free' in the sense that no parametric model for the underlying microarray data is required to be specified or estimated; hence, DDHFm can be applied very generally, not just to microarray data. DDHFm achieves very good variance stabilization of microarray data with replicates and produces transformed intensities that are approximately normally distributed. Simulation studies show that it performs better than other existing methods. Application of DDHFm to real one-color cDNA data validates these results. The R package of the Data-Driven Haar-Fisz transform (DDHFm) for microarrays is available in Bioconductor and CRAN.

Development of a DNA microarray for species identification of quarantine aphids.

PubMed

Lee, Won Sun; Choi, Hwalran; Kang, Jinseok; Kim, Ji-Hoon; Lee, Si Hyeock; Lee, Seunghwan; Hwang, Seung Yong

2013-12-01

Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology. DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples. A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management. © 2013 Society of Chemical Industry.

CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

PubMed

Bumm, Klaus; Zheng, Mingzhong; Bailey, Clyde; Zhan, Fenghuang; Chiriva-Internati, M; Eddlemon, Paul; Terry, Julian; Barlogie, Bart; Shaughnessy, John D

2002-02-01

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.

Design and validation of MEDRYS, a Mediterranean Sea reanalysis over the period 1992-2013

NASA Astrophysics Data System (ADS)

Hamon, Mathieu; Beuvier, Jonathan; Somot, Samuel; Lellouche, Jean-Michel; Greiner, Eric; Jordà, Gabriel; Bouin, Marie-Noëlle; Arsouze, Thomas; Béranger, Karine; Sevault, Florence; Dubois, Clotilde; Drevillon, Marie; Drillet, Yann

2016-04-01

The French research community in the Mediterranean Sea modeling and the French operational ocean forecasting center Mercator Océan have gathered their skill and expertise in physical oceanography, ocean modeling, atmospheric forcings and data assimilation to carry out a MEDiterranean sea ReanalYsiS (MEDRYS) at high resolution for the period 1992-2013. The ocean model used is NEMOMED12, a Mediterranean configuration of NEMO with a 1/12° ( ˜ 7 km) horizontal resolution and 75 vertical z levels with partial steps. At the surface, it is forced by a new atmospheric-forcing data set (ALDERA), coming from a dynamical downscaling of the ERA-Interim atmospheric reanalysis by the regional climate model ALADIN-Climate with a 12 km horizontal and 3 h temporal resolutions. This configuration is used to carry a 34-year hindcast simulation over the period 1979-2013 (NM12-FREE), which is the initial state of the reanalysis in October 1992. MEDRYS uses the existing Mercator Océan data assimilation system SAM2 that is based on a reduced-order Kalman filter with a three-dimensional (3-D) multivariate modal decomposition of the forecast error. Altimeter data, satellite sea surface temperature (SST) and temperature and salinity vertical profiles are jointly assimilated. This paper describes the configuration we used to perform MEDRYS. We then validate the skills of the data assimilation system. It is shown that the data assimilation restores a good average temperature and salinity at intermediate layers compared to the hindcast. No particular biases are identified in the bottom layers. However, the reanalysis shows slight positive biases of 0.02 psu and 0.15 °C above 150 m depth. In the validation stage, it is also shown that the assimilation allows one to better reproduce water, heat and salt transports through the Strait of Gibraltar. Finally, the ability of the reanalysis to represent the sea surface high-frequency variability is shown.

Cruella: developing a scalable tissue microarray data management system.

PubMed

Cowan, James D; Rimm, David L; Tuck, David P

2006-06-01

Compared with DNA microarray technology, relatively little information is available concerning the special requirements, design influences, and implementation strategies of data systems for tissue microarray technology. These issues include the requirement to accommodate new and different data elements for each new project as well as the need to interact with pre-existing models for clinical, biological, and specimen-related data. To design and implement a flexible, scalable tissue microarray data storage and management system that could accommodate information regarding different disease types and different clinical investigators, and different clinical investigation questions, all of which could potentially contribute unforeseen data types that require dynamic integration with existing data. The unpredictability of the data elements combined with the novelty of automated analysis algorithms and controlled vocabulary standards in this area require flexible designs and practical decisions. Our design includes a custom Java-based persistence layer to mediate and facilitate interaction with an object-relational database model and a novel database schema. User interaction is provided through a Java Servlet-based Web interface. Cruella has become an indispensable resource and is used by dozens of researchers every day. The system stores millions of experimental values covering more than 300 biological markers and more than 30 disease types. The experimental data are merged with clinical data that has been aggregated from multiple sources and is available to the researchers for management, analysis, and export. Cruella addresses many of the special considerations for managing tissue microarray experimental data and the associated clinical information. A metadata-driven approach provides a practical solution to many of the unique issues inherent in tissue microarray research, and allows relatively straightforward interoperability with and accommodation of new data models.

A Java-based tool for the design of classification microarrays.

PubMed

Meng, Da; Broschat, Shira L; Call, Douglas R

2008-08-04

Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for analysis of subsequent experimental data. Additionally, PLASMID can be used to construct virtual microarrays with genomes from public databases, which can then be used to identify an optimal set of probes.

Multi-task feature selection in microarray data by binary integer programming.

PubMed

Lan, Liang; Vucetic, Slobodan

2013-12-20

A major challenge in microarray classification is that the number of features is typically orders of magnitude larger than the number of examples. In this paper, we propose a novel feature filter algorithm to select the feature subset with maximal discriminative power and minimal redundancy by solving a quadratic objective function with binary integer constraints. To improve the computational efficiency, the binary integer constraints are relaxed and a low-rank approximation to the quadratic term is applied. The proposed feature selection algorithm was extended to solve multi-task microarray classification problems. We compared the single-task version of the proposed feature selection algorithm with 9 existing feature selection methods on 4 benchmark microarray data sets. The empirical results show that the proposed method achieved the most accurate predictions overall. We also evaluated the multi-task version of the proposed algorithm on 8 multi-task microarray datasets. The multi-task feature selection algorithm resulted in significantly higher accuracy than when using the single-task feature selection methods.

A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

PubMed

Yamamoto, F; Yamamoto, M

2004-07-01

We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

Stochastic models for inferring genetic regulation from microarray gene expression data.

PubMed

Tian, Tianhai

2010-03-01

Microarray expression profiles are inherently noisy and many different sources of variation exist in microarray experiments. It is still a significant challenge to develop stochastic models to realize noise in microarray expression profiles, which has profound influence on the reverse engineering of genetic regulation. Using the target genes of the tumour suppressor gene p53 as the test problem, we developed stochastic differential equation models and established the relationship between the noise strength of stochastic models and parameters of an error model for describing the distribution of the microarray measurements. Numerical results indicate that the simulated variance from stochastic models with a stochastic degradation process can be represented by a monomial in terms of the hybridization intensity and the order of the monomial depends on the type of stochastic process. The developed stochastic models with multiple stochastic processes generated simulations whose variance is consistent with the prediction of the error model. This work also established a general method to develop stochastic models from experimental information. 2009 Elsevier Ireland Ltd. All rights reserved.

Analysis of microarray leukemia data using an efficient MapReduce-based K-nearest-neighbor classifier.

PubMed

Kumar, Mukesh; Rath, Nitish Kumar; Rath, Santanu Kumar

2016-04-01

Microarray-based gene expression profiling has emerged as an efficient technique for classification, prognosis, diagnosis, and treatment of cancer. Frequent changes in the behavior of this disease generates an enormous volume of data. Microarray data satisfies both the veracity and velocity properties of big data, as it keeps changing with time. Therefore, the analysis of microarray datasets in a small amount of time is essential. They often contain a large amount of expression, but only a fraction of it comprises genes that are significantly expressed. The precise identification of genes of interest that are responsible for causing cancer are imperative in microarray data analysis. Most existing schemes employ a two-phase process such as feature selection/extraction followed by classification. In this paper, various statistical methods (tests) based on MapReduce are proposed for selecting relevant features. After feature selection, a MapReduce-based K-nearest neighbor (mrKNN) classifier is also employed to classify microarray data. These algorithms are successfully implemented in a Hadoop framework. A comparative analysis is done on these MapReduce-based models using microarray datasets of various dimensions. From the obtained results, it is observed that these models consume much less execution time than conventional models in processing big data. Copyright © 2016 Elsevier Inc. All rights reserved.

A biomimetic algorithm for the improved detection of microarray features

NASA Astrophysics Data System (ADS)

Nicolau, Dan V., Jr.; Nicolau, Dan V.; Maini, Philip K.

2007-02-01

One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface.

Ballet as a Career

ERIC Educational Resources Information Center

Sutherland, David Earl

1976-01-01

A reorganization and reanalysis of data gathered by Ronald Charles Frederico--who interviewed 146 dancers belonging to 12 ballet companies in the U.S.--to investigate the structural features of ballet as a profession. Four possibilities exist for a more general interpretative scheme for understanding ballet: social structural, phenomenological,…

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Autoregressive-model-based missing value estimation for DNA microarray time series data.

PubMed

Choong, Miew Keen; Charbit, Maurice; Yan, Hong

2009-01-01

Missing value estimation is important in DNA microarray data analysis. A number of algorithms have been developed to solve this problem, but they have several limitations. Most existing algorithms are not able to deal with the situation where a particular time point (column) of the data is missing entirely. In this paper, we present an autoregressive-model-based missing value estimation method (ARLSimpute) that takes into account the dynamic property of microarray temporal data and the local similarity structures in the data. ARLSimpute is especially effective for the situation where a particular time point contains many missing values or where the entire time point is missing. Experiment results suggest that our proposed algorithm is an accurate missing value estimator in comparison with other imputation methods on simulated as well as real microarray time series datasets.

Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples.

PubMed

McCoy, Gary R; Touzet, Nicolas; Fleming, Gerard T A; Raine, Robin

2015-07-01

The toxic microalgal species Prymnesium parvum and Prymnesium polylepis are responsible for numerous fish kills causing economic stress on the aquaculture industry and, through the consumption of contaminated shellfish, can potentially impact on human health. Monitoring of toxic phytoplankton is traditionally carried out by light microscopy. However, molecular methods of identification and quantification are becoming more common place. This study documents the optimisation of the novel Microarrays for the Detection of Toxic Algae (MIDTAL) microarray from its initial stages to the final commercial version now available from Microbia Environnement (France). Existing oligonucleotide probes used in whole-cell fluorescent in situ hybridisation (FISH) for Prymnesium species from higher group probes to species-level probes were adapted and tested on the first-generation microarray. The combination and interaction of numerous other probes specific for a whole range of phytoplankton taxa also spotted on the chip surface caused high cross reactivity, resulting in false-positive results on the microarray. The probe sequences were extended for the subsequent second-generation microarray, and further adaptations of the hybridisation protocol and incubation temperatures significantly reduced false-positive readings from the first to the second-generation chip, thereby increasing the specificity of the MIDTAL microarray. Additional refinement of the subsequent third-generation microarray protocols with the addition of a poly-T amino linker to the 5' end of each probe further enhanced the microarray performance but also highlighted the importance of optimising RNA labelling efficiency when testing with natural seawater samples from Killary Harbour, Ireland.

Content Representations in a Secondary Environmental Science Class.

ERIC Educational Resources Information Center

Tomanek, Debra

The purpose of this study was to determine what representations of content existed in a secondary environmental science class and what happended to those representations during curriculum occasions. Initial data construction involved attention to what was actually going on during class sessions. Following this, a reanalysis of the data corpus with…

Physical forcing of late summer chlorophyll a blooms in the oligotrophic eastern North Pacific

NASA Astrophysics Data System (ADS)

Toyoda, Takahiro; Okamoto, Suguru

2017-03-01

We investigated physical forcing of late summer chlorophyll a (chl a) blooms in the oligotrophic eastern North Pacific Ocean by using ocean reanalysis and satellite data. Relatively large chl a blooms as defined in this study occurred in August-October following sea surface temperature (SST) anomaly (SSTA) decreases, mixed layer deepening, and temperature and salinity increases at the bottom of the mixed layer. These physical conditions were apparently induced by the entrainment of subsurface water resulting from the destabilization of the surface layer caused by anomalous northward Ekman transport of subtropical waters of higher salinity. Salinity-normalized total alkalinity data provide supporting evidence for nutrient supply by the entrainment process. We next investigated the impact of including information about the entrainment on bloom identification. The results of analyses using reanalysis data and of those using only satellite data showed large SSTA decreases when the northward Ekman salinity transports were large, implying that the entrainment of subsurface water is well represented in both types of data. After surface-destabilizing conditions were established, relatively high surface chl a concentrations were observed. The use of SST information can further improve the detection of high chl a concentrations. Although the detection of high chl a concentrations would be enhanced by finer data resolution and the inclusion of biogeochemical parameters in the ocean reanalysis, our results obtained by using existing reanalysis data as well as recent satellite data are valuable for better understanding and prediction of lower trophic ecosystem variability.

A high-resolution regional reanalysis for the European CORDEX region

NASA Astrophysics Data System (ADS)

Bollmeyer, Christoph; Keller, Jan; Ohlwein, Christian; Wahl, Sabrina

2015-04-01

Within the Hans-Ertel-Centre for Weather Research (HErZ), the climate monitoring branch concentrates efforts on the assessment and analysis of regional climate in Germany and Europe. In joint cooperation with DWD (German Weather Service), a high-resolution reanalysis system based on the COSMO model has been developed. Reanalyses gain more and more importance as a source of meteorological information for many purposes and applications. Several global reanalyses projects (e.g., ERA, MERRA, CSFR, JMA9) produce and verify these data sets to provide time series as long as possible combined with a high data quality. Due to a spatial resolution down to 50-70km and 3-hourly temporal output, they are not suitable for small scale problems (e.g., regional climate assessment, meso-scale NWP verification, input for subsequent models such as river runoff simulations, renewable energy applications). The implementation of regional reanalyses based on a limited area model along with a data assimilation scheme is able to generate reanalysis data sets with high spatio-temporal resolution. The work presented here focuses on two regional reanalyses for Europe and Germany. The European reanalysis COSMO-REA6 matches the CORDEX EURO-11 specifications, albeit at a higher spatial resolution, i.e., 0.055° (6km) instead of 0.11° (12km). Nested into COSMO-REA6 is COSMO-REA2, a convective-scale reanalysis with 2km resolution for Germany. COSMO-REA6 comprises the assimilation of observational data using the existing nudging scheme of COSMO and is complemented by a special soil moisture analysis and boundary conditions given by ERA-Interim data. COSMO-REA2 also uses the nudging scheme complemented by a latent heat nudging of radar information. The reanalysis data set currently covers 17 years (1997-2013) for COSMO-REA6 and 4 years (2010-2013) for COSMO-REA2 with a very large set of output variables and a high temporal output step of hourly 3D-fields and quarter-hourly 2D-fields. The evaluation of the reanalyses is done using independent observations for the most important meteorological parameters with special emphasis on precipitation and high-impact weather situations.

Mobley et al. Turnover Model Reanalysis and Review of Existing Data.

ERIC Educational Resources Information Center

Dalessio, Anthony; And Others

Job satisfaction has been identified as one of the most important antecedents of turnover, although it rarely accounts for more than 16% of the variance in employee withdrawal. Several data sets collected on the Mobley, Horner, and Hollingsworth (1978) model of turnover were reanalyzed with path analytic techniques. Data analyses revealed support…

Reanalysis of the fragility of glycerol at very high pressures using new Tg data

NASA Astrophysics Data System (ADS)

Lyon, Kevin; Oliver, William

Direct measurements of the glass transition temperature of glycerol between 1 atm and 6.7 GPa from our lab allow reanalysis of high-pressure viscosity data, which were limited to approximately 107 poise. Previous attempts to determine Tg (P) and fragility by extrapolation of the viscosity data by many orders of magnitude led to inconclusive results. Tg (P) data constrain the value of viscosity at the glass transition providing for more accurate determinations of isobaric fragilities. Over most of the pressure range, a constant fragility is found in agreement with analysis of high-pressure dielectric data by Paluch et al.. Discrepancies in the pressure dependence of the fragility of glycerol at very low pressures exist in the literature and will also be discussed.

Who was the agent? The neural correlates of reanalysis processes during sentence comprehension.

PubMed

Hirotani, Masako; Makuuchi, Michiru; Rüschemeyer, Shirley-Ann; Friederici, Angela D

2011-11-01

Sentence comprehension is a complex process. Besides identifying the meaning of each word and processing the syntactic structure of a sentence, it requires the computation of thematic information, that is, information about who did what to whom. The present fMRI study investigated the neural basis for thematic reanalysis (reanalysis of the thematic roles initially assigned to noun phrases in a sentence) and its interplay with syntactic reanalysis (reanalysis of the underlying syntactic structure originally constructed for a sentence). Thematic reanalysis recruited a network consisting of Broca's area, that is, the left pars triangularis (LPT), and the left posterior superior temporal gyrus, whereas only LPT showed greater sensitivity to syntactic reanalysis. These data provide direct evidence for a functional neuroanatomical basis for two linguistically motivated reanalysis processes during sentence comprehension. Copyright © 2010 Wiley-Liss, Inc.

The Impact of Socio-Economic Status on Participation and Attainment in Science

ERIC Educational Resources Information Center

Gorard, Stephen; See, Beng Huat

2009-01-01

In this paper we combine the findings from two recent studies relating to participation and attainment in school science --a re-analysis of existing official data for England and a review of wider international research evidence in the literature relevant to the UK. Although the secondary data are drawn mainly from England, the comprehensiveness…

The MGED Ontology: a resource for semantics-based description of microarray experiments.

PubMed

Whetzel, Patricia L; Parkinson, Helen; Causton, Helen C; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Game, Laurence; Heiskanen, Mervi; Morrison, Norman; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; White, Joseph; Stoeckert, Christian J

2006-04-01

The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online.

Variations in the temperature and circulation of the atmosphere during the 11-year cycle of solar activity derived from the ERA-Interim reanalysis data

NASA Astrophysics Data System (ADS)

Gruzdev, A. N.

2017-07-01

Using the data of the ERA-Interim reanalysis, we have obtained estimates of changes in temperature, the geopotential and its large-scale zonal harmonics, wind velocity, and potential vorticity in the troposphere and stratosphere of the Northern and Southern hemispheres during the 11-year solar cycle. The estimates have been obtained using the method of multiple linear regression. Specific features of response of the indicated atmospheric parameters to the solar cycle have been revealed in particular regions of the atmosphere for a whole year and depending on the season. The results of the analysis indicate the existence of a reliable statistical relationship of large-scale dynamic and thermodynamic processes in the troposphere and stratosphere with the 11-year solar cycle.

MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus.

PubMed

Rode, Tone Mari; Berget, Ingunn; Langsrud, Solveig; Møretrø, Trond; Holck, Askild

2009-07-01

Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

MADGE: scalable distributed data management software for cDNA microarrays.

PubMed

McIndoe, Richard A; Lanzen, Aaron; Hurtz, Kimberly

2003-01-01

The human genome project and the development of new high-throughput technologies have created unparalleled opportunities to study the mechanism of diseases, monitor the disease progression and evaluate effective therapies. Gene expression profiling is a critical tool to accomplish these goals. The use of nucleic acid microarrays to assess the gene expression of thousands of genes simultaneously has seen phenomenal growth over the past five years. Although commercial sources of microarrays exist, investigators wanting more flexibility in the genes represented on the array will turn to in-house production. The creation and use of cDNA microarrays is a complicated process that generates an enormous amount of information. Effective data management of this information is essential to efficiently access, analyze, troubleshoot and evaluate the microarray experiments. We have developed a distributable software package designed to track and store the various pieces of data generated by a cDNA microarray facility. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system tuned to support a large number of transactions. The data services layer (2nd tier) is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user. This software is freely available to academic institutions and non-profit organizations at http://www.genomics.mcg.edu/niddkbtc.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.

PubMed

Taminau, Jonatan; Meganck, Stijn; Lazar, Cosmin; Steenhoff, David; Coletta, Alain; Molter, Colin; Duque, Robin; de Schaetzen, Virginie; Weiss Solís, David Y; Bersini, Hugues; Nowé, Ann

2012-12-24

With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

Characterization and simulation of cDNA microarray spots using a novel mathematical model

PubMed Central

Kim, Hye Young; Lee, Seo Eun; Kim, Min Jung; Han, Jin Il; Kim, Bo Kyung; Lee, Yong Sung; Lee, Young Seek; Kim, Jin Hyuk

2007-01-01

Background The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images. Results We developed a governing equation of cDNA deposition during evaporation of a drop in the microarray spotting process. The governing equation included four parameters: the surface site density on the support, the extrapolated equilibrium constant for the binding of cDNA molecules with surface sites on glass slides, the macromolecular interaction factor, and the volume constant of a drop of cDNA solution. We simulated cDNA deposition from the single model equation by varying the value of the parameters. The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape. The spot morphology can be changed into a flat shape by varying the experimental conditions while considering the parameters of the governing equation of cDNA deposition. The four parameters were estimated by fitting the governing equation to the real microarray images. With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated. Conclusion This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays. PMID:18096047

Introduction to the SPARC Reanalysis Intercomparison Project (S-RIP) and overview of the reanalysis systems

NASA Astrophysics Data System (ADS)

Fujiwara, Masatomo; Wright, Jonathon S.; Manney, Gloria L.; Gray, Lesley J.; Anstey, James; Birner, Thomas; Davis, Sean; Gerber, Edwin P.; Harvey, V. Lynn; Hegglin, Michaela I.; Homeyer, Cameron R.; Knox, John A.; Krüger, Kirstin; Lambert, Alyn; Long, Craig S.; Martineau, Patrick; Molod, Andrea; Monge-Sanz, Beatriz M.; Santee, Michelle L.; Tegtmeier, Susann; Chabrillat, Simon; Tan, David G. H.; Jackson, David R.; Polavarapu, Saroja; Compo, Gilbert P.; Dragani, Rossana; Ebisuzaki, Wesley; Harada, Yayoi; Kobayashi, Chiaki; McCarty, Will; Onogi, Kazutoshi; Pawson, Steven; Simmons, Adrian; Wargan, Krzysztof; Whitaker, Jeffrey S.; Zou, Cheng-Zhi

2017-01-01

The climate research community uses atmospheric reanalysis data sets to understand a wide range of processes and variability in the atmosphere, yet different reanalyses may give very different results for the same diagnostics. The Stratosphere-troposphere Processes And their Role in Climate (SPARC) Reanalysis Intercomparison Project (S-RIP) is a coordinated activity to compare reanalysis data sets using a variety of key diagnostics. The objectives of this project are to identify differences among reanalyses and understand their underlying causes, to provide guidance on appropriate usage of various reanalysis products in scientific studies, particularly those of relevance to SPARC, and to contribute to future improvements in the reanalysis products by establishing collaborative links between reanalysis centres and data users. The project focuses predominantly on differences among reanalyses, although studies that include operational analyses and studies comparing reanalyses with observations are also included when appropriate. The emphasis is on diagnostics of the upper troposphere, stratosphere, and lower mesosphere. This paper summarizes the motivation and goals of the S-RIP activity and extensively reviews key technical aspects of the reanalysis data sets that are the focus of this activity. The special issue The SPARC Reanalysis Intercomparison Project (S-RIP) in this journal serves to collect research with relevance to the S-RIP in preparation for the publication of the planned two (interim and full) S-RIP reports.

Multiclass classification of microarray data samples with a reduced number of genes

PubMed Central

2011-01-01

Background Multiclass classification of microarray data samples with a reduced number of genes is a rich and challenging problem in Bioinformatics research. The problem gets harder as the number of classes is increased. In addition, the performance of most classifiers is tightly linked to the effectiveness of mandatory gene selection methods. Critical to gene selection is the availability of estimates about the maximum number of genes that can be handled by any classification algorithm. Lack of such estimates may lead to either computationally demanding explorations of a search space with thousands of dimensions or classification models based on gene sets of unrestricted size. In the former case, unbiased but possibly overfitted classification models may arise. In the latter case, biased classification models unable to support statistically significant findings may be obtained. Results A novel bound on the maximum number of genes that can be handled by binary classifiers in binary mediated multiclass classification algorithms of microarray data samples is presented. The bound suggests that high-dimensional binary output domains might favor the existence of accurate and sparse binary mediated multiclass classifiers for microarray data samples. Conclusions A comprehensive experimental work shows that the bound is indeed useful to induce accurate and sparse multiclass classifiers for microarray data samples. PMID:21342522

Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips

PubMed Central

Lee, Yun-Shien; Chen, Chun-Houh; Tsai, Chi-Neu; Tsai, Chia-Lung; Chao, Angel; Wang, Tzu-Hao

2009-01-01

Interlaboratory comparison of microarray data, even when using the same platform, imposes several challenges to scientists. RNA quality, RNA labeling efficiency, hybridization procedures and data-mining tools can all contribute variations in each laboratory. In Affymetrix GeneChips, about 11–20 different 25-mer oligonucleotides are used to measure the level of each transcript. Here, we report that ‘labeling extension values (LEVs)’, which are correlation coefficients between probe intensities and probe positions, are highly correlated with the gene expression levels (GEVs) on eukayotic Affymetrix microarray data. By analyzing LEVs and GEVs in the publicly available 2414 cel files of 20 Affymetrix microarray types covering 13 species, we found that correlations between LEVs and GEVs only exist in eukaryotic RNAs, but not in prokaryotic ones. Surprisingly, Affymetrix results of the same specimens that were analyzed in different laboratories could be clearly differentiated only by LEVs, leading to the identification of ‘laboratory signatures’. In the examined dataset, GSE10797, filtering out high-LEV genes did not compromise the discovery of biological processes that are constructed by differentially expressed genes. In conclusion, LEVs provide a new filtering parameter for microarray analysis of gene expression and it may improve the inter- and intralaboratory comparability of Affymetrix GeneChips data. PMID:19295132

Discrimination of Influenza Infection (A/2009 H1N1) from Prior Exposure by Antibody Protein Microarray Analysis

PubMed Central

te Beest, Dennis; de Bruin, Erwin; Imholz, Sandra; Wallinga, Jacco; Teunis, Peter; Koopmans, Marion; van Boven, Michiel

2014-01-01

Reliable discrimination of recent influenza A infection from previous exposure using hemagglutination inhibition (HI) or virus neutralization tests is currently not feasible. This is due to low sensitivity of the tests and the interference of antibody responses generated by previous infections. Here we investigate the diagnostic characteristics of a newly developed antibody (HA1) protein microarray using data from cross-sectional serological studies carried out before and after the pandemic of 2009. The data are analysed by mixture models, providing a probabilistic classification of sera (susceptible, prior-exposed, recently infected). Estimated sensitivity and specificity for identifying A/2009 infections are low using HI (66% and 51%), and high when using A/2009 microarray data alone or together with A/1918 microarray data (96% and 95%). As a heuristic, a high A/2009 to A/1918 antibody ratio (>1.05) is indicative of recent infection, while a low ratio is indicative of a pre-existing response, even if the A/2009 titer is high. We conclude that highly sensitive and specific classification of individual sera is possible using the protein microarray, thereby enabling precise estimation of age-specific infection attack rates in the population even if sample sizes are small. PMID:25405997

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships

PubMed Central

2010-01-01

Background The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. Results In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. Conclusion High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data. PMID:20122245

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.

PubMed

Seok, Junhee; Kaushal, Amit; Davis, Ronald W; Xiao, Wenzhong

2010-01-18

The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data.

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

Multi-Reanalysis Comparison of Variability in Analysis Increment of Column-Integrated Water Vapor Associated with Madden-Julian Oscillation

NASA Astrophysics Data System (ADS)

Yokoi, S.

2014-12-01

This study conducts a comparison of three reanalysis products (JRA-55, JRA-25, and ERA-Interim) in representation of Madden-Julian Oscillation (MJO), focusing on column-integrated water vapor (CWV) that is considered as an essential variable for discussing MJO dynamics. Besides the analysis fields of CWV, which exhibit spatio-temporal distributions that are quite similar to satellite observations, CWV tendency simulated by forecast models and analysis increment calculated by data assimilation are examined. For JRA-55, it is revealed that, while its forecast model is able to simulate eastward propagation of the CWV anomaly, it tends to weaken the amplitude, and data assimilation process sustains the amplitude. The multi-reanalysis comparison of the analysis increment further reveals that this weakening bias is probably caused by excessively weak cloud-radiative feedback represented by the model. This bias in the feedback strength makes anomalous moisture supply by the vertical advection term in the CWV budget equation too insensitive to precipitation anomaly, resulting in reduction of the amplitude of CWV anomaly. ERA-Interim has a nearly opposite feature; the forecast model represents excessively strong feedback and unrealistically strengthens the amplitude, while the data assimilation weakens it. These results imply the necessity of accurate representation of the cloud-radiative feedback strength for a short-term MJO forecast, and may be evidence to support the argument that this feedback is essential for the existence of MJO. Furthermore, this study demonstrates that the multi-reanalysis comparison of the analysis increment will provide useful information for identifying model biases and, potentially, for estimating parameters that are difficult to estimate solely from observation data, such as gross moist stability.

Tuning a climate model using nudging to reanalysis.

NASA Astrophysics Data System (ADS)

Cheedela, S. K.; Mapes, B. E.

2014-12-01

Tuning a atmospheric general circulation model involves a daunting task of adjusting non-observable parameters to adjust the mean climate. These parameters arise from necessity to describe unresolved flow through parametrizations. Tuning a climate model is often done with certain set of priorities, such as global mean temperature, net top of the atmosphere radiation. These priorities are hard enough to reach let alone reducing systematic biases in the models. The goal of currently study is to explore alternate ways to tune a climate model to reduce some systematic biases that can be used in synergy with existing efforts. Nudging a climate model to a known state is a poor man's inverse of tuning process described above. Our approach involves nudging the atmospheric model to state of art reanalysis fields thereby providing a balanced state with respect to the global mean temperature and winds. The tendencies derived from nudging are negative of errors from physical parametrizations as the errors from dynamical core would be small. Patterns of nudging are compared to the patterns of different physical parametrizations to decipher the cause for certain biases in relation to tuning parameters. This approach might also help in understanding certain compensating errors that arise from tuning process. ECHAM6 is a comprehensive general model, also used in recent Coupled Model Intercomparision Project(CMIP5). The approach used to tune it and effect of certain parameters that effect its mean climate are reported clearly, hence it serves as a benchmark for our approach. Our planned experiments include nudging ECHAM6 atmospheric model to European Center Reanalysis (ERA-Interim) and reanalysis from National Center for Environmental Prediction (NCEP) and decipher choice of certain parameters that lead to systematic biases in its simulations. Of particular interest are reducing long standing biases related to simulation of Asian summer monsoon.

Functional Analyses of NSF1 in Wine Yeast Using Interconnected Correlation Clustering and Molecular Analyses

PubMed Central

Bessonov, Kyrylo; Walkey, Christopher J.; Shelp, Barry J.; van Vuuren, Hennie J. J.; Chiu, David; van der Merwe, George

2013-01-01

Analyzing time-course expression data captured in microarray datasets is a complex undertaking as the vast and complex data space is represented by a relatively low number of samples as compared to thousands of available genes. Here, we developed the Interdependent Correlation Clustering (ICC) method to analyze relationships that exist among genes conditioned on the expression of a specific target gene in microarray data. Based on Correlation Clustering, the ICC method analyzes a large set of correlation values related to gene expression profiles extracted from given microarray datasets. ICC can be applied to any microarray dataset and any target gene. We applied this method to microarray data generated from wine fermentations and selected NSF1, which encodes a C2H2 zinc finger-type transcription factor, as the target gene. The validity of the method was verified by accurate identifications of the previously known functional roles of NSF1. In addition, we identified and verified potential new functions for this gene; specifically, NSF1 is a negative regulator for the expression of sulfur metabolism genes, the nuclear localization of Nsf1 protein (Nsf1p) is controlled in a sulfur-dependent manner, and the transcription of NSF1 is regulated by Met4p, an important transcriptional activator of sulfur metabolism genes. The inter-disciplinary approach adopted here highlighted the accuracy and relevancy of the ICC method in mining for novel gene functions using complex microarray datasets with a limited number of samples. PMID:24130853

MASQOT: a method for cDNA microarray spot quality control

PubMed Central

Bylesjö, Max; Eriksson, Daniel; Sjödin, Andreas; Sjöström, Michael; Jansson, Stefan; Antti, Henrik; Trygg, Johan

2005-01-01

Background cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more. Results A novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies. Conclusion The proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process. PMID:16223442

Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis.

PubMed

Ma, Chuang; Wang, Xiangfeng

2012-09-01

One of the computational challenges in plant systems biology is to accurately infer transcriptional regulation relationships based on correlation analyses of gene expression patterns. Despite several correlation methods that are applied in biology to analyze microarray data, concerns regarding the compatibility of these methods with the gene expression data profiled by high-throughput RNA transcriptome sequencing (RNA-Seq) technology have been raised. These concerns are mainly due to the fact that the distribution of read counts in RNA-Seq experiments is different from that of fluorescence intensities in microarray experiments. Therefore, a comprehensive evaluation of the existing correlation methods and, if necessary, introduction of novel methods into biology is appropriate. In this study, we compared four existing correlation methods used in microarray analysis and one novel method called the Gini correlation coefficient on previously published microarray-based and sequencing-based gene expression data in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). The comparisons were performed on more than 11,000 regulatory relationships in Arabidopsis, including 8,929 pairs of transcription factors and target genes. Our analyses pinpointed the strengths and weaknesses of each method and indicated that the Gini correlation can compensate for the shortcomings of the Pearson correlation, the Spearman correlation, the Kendall correlation, and the Tukey's biweight correlation. The Gini correlation method, with the other four evaluated methods in this study, was implemented as an R package named rsgcc that can be utilized as an alternative option for biologists to perform clustering analyses of gene expression patterns or transcriptional network analyses.

A robust two-way semi-linear model for normalization of cDNA microarray data

PubMed Central

Wang, Deli; Huang, Jian; Xie, Hehuang; Manzella, Liliana; Soares, Marcelo Bento

2005-01-01

Background Normalization is a basic step in microarray data analysis. A proper normalization procedure ensures that the intensity ratios provide meaningful measures of relative expression values. Methods We propose a robust semiparametric method in a two-way semi-linear model (TW-SLM) for normalization of cDNA microarray data. This method does not make the usual assumptions underlying some of the existing methods. For example, it does not assume that: (i) the percentage of differentially expressed genes is small; or (ii) the numbers of up- and down-regulated genes are about the same, as required in the LOWESS normalization method. We conduct simulation studies to evaluate the proposed method and use a real data set from a specially designed microarray experiment to compare the performance of the proposed method with that of the LOWESS normalization approach. Results The simulation results show that the proposed method performs better than the LOWESS normalization method in terms of mean square errors for estimated gene effects. The results of analysis of the real data set also show that the proposed method yields more consistent results between the direct and the indirect comparisons and also can detect more differentially expressed genes than the LOWESS method. Conclusions Our simulation studies and the real data example indicate that the proposed robust TW-SLM method works at least as well as the LOWESS method and works better when the underlying assumptions for the LOWESS method are not satisfied. Therefore, it is a powerful alternative to the existing normalization methods. PMID:15663789

High-density, microsphere-based fiber optic DNA microarrays.

PubMed

Epstein, Jason R; Leung, Amy P K; Lee, Kyong Hoon; Walt, David R

2003-05-01

A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-microm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle. The fiber bundles are comprised of 6000-50000 fused optical fibers and each fiber terminates with an etched well. The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence. The array fabrication process results in random microsphere placement. Determining the position of microspheres in the random array requires an optical encoding scheme. This array platform provides many advantages over other array formats. The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy. Examining identical microspheres has a beneficial effect on the signal-to-noise ratio. As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities. These microarrays contain the smallest feature sizes (3 microm) of any DNA array, allowing interrogation of extremely small sample volumes. Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays. The microsphere array platform is also flexible in its applications; research has included DNA-protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons. Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis[W][OA

PubMed Central

Ma, Chuang; Wang, Xiangfeng

2012-01-01

One of the computational challenges in plant systems biology is to accurately infer transcriptional regulation relationships based on correlation analyses of gene expression patterns. Despite several correlation methods that are applied in biology to analyze microarray data, concerns regarding the compatibility of these methods with the gene expression data profiled by high-throughput RNA transcriptome sequencing (RNA-Seq) technology have been raised. These concerns are mainly due to the fact that the distribution of read counts in RNA-Seq experiments is different from that of fluorescence intensities in microarray experiments. Therefore, a comprehensive evaluation of the existing correlation methods and, if necessary, introduction of novel methods into biology is appropriate. In this study, we compared four existing correlation methods used in microarray analysis and one novel method called the Gini correlation coefficient on previously published microarray-based and sequencing-based gene expression data in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). The comparisons were performed on more than 11,000 regulatory relationships in Arabidopsis, including 8,929 pairs of transcription factors and target genes. Our analyses pinpointed the strengths and weaknesses of each method and indicated that the Gini correlation can compensate for the shortcomings of the Pearson correlation, the Spearman correlation, the Kendall correlation, and the Tukey’s biweight correlation. The Gini correlation method, with the other four evaluated methods in this study, was implemented as an R package named rsgcc that can be utilized as an alternative option for biologists to perform clustering analyses of gene expression patterns or transcriptional network analyses. PMID:22797655

Application of Immunosignatures for Diagnosis of Valley Fever

PubMed Central

Navalkar, Krupa Arun; Johnston, Stephen Albert; Woodbury, Neal; Galgiani, John N.; Magee, D. Mitchell; Chicacz, Zbigniew

2014-01-01

Valley fever (VF) is difficult to diagnose, partly because the symptoms of VF are confounded with those of other community-acquired pneumonias. Confirmatory diagnostics detect IgM and IgG antibodies against coccidioidal antigens via immunodiffusion (ID). The false-negative rate can be as high as 50% to 70%, with 5% of symptomatic patients never showing detectable antibody levels. In this study, we tested whether the immunosignature diagnostic can resolve VF false negatives. An immunosignature is the pattern of antibody binding to random-sequence peptides on a peptide microarray. A 10,000-peptide microarray was first used to determine whether valley fever patients can be distinguished from 3 other cohorts with similar infections. After determining the VF-specific peptides, a small 96-peptide diagnostic array was created and tested. The performances of the 10,000-peptide array and the 96-peptide diagnostic array were compared to that of the ID diagnostic standard. The 10,000-peptide microarray classified the VF samples from the other 3 infections with 98% accuracy. It also classified VF false-negative patients with 100% sensitivity in a blinded test set versus 28% sensitivity for ID. The immunosignature microarray has potential for simultaneously distinguishing valley fever patients from those with other fungal or bacterial infections. The same 10,000-peptide array can diagnose VF false-negative patients with 100% sensitivity. The smaller 96-peptide diagnostic array was less specific for diagnosing false negatives. We conclude that the performance of the immunosignature diagnostic exceeds that of the existing standard, and the immunosignature can distinguish related infections and might be used in lieu of existing diagnostics. PMID:24964807

Guanine Plus Cytosine Contents of the Deoxyribonucleic Acids of Some Sulfate-Reducing Bacteria: a Reassessment

PubMed Central

Skyring, G. W.; Jones, H. E.

1972-01-01

Guanine plus cytosine (GC) contents of the deoxyribonucleic acids of Desulfovibrio and Desulfotomaculum have been used as a basis for classification. Some of these data have been incorrectly calculated, resulting in errors of as much as 5% GC. This situation has been corrected by a reanalysis of existing data and by the contribution of new data. PMID:5011245

Recent advances in proteomic applications for schistosomiasis research: potential clinical impact.

PubMed

Sotillo, Javier; Doolan, Denise; Loukas, Alex

2017-02-01

Schistosomiasis is a neglected tropical disease affecting hundreds of millions of people worldwide. Recent advances in the field of proteomics and the development of new and highly sensitive mass spectrometers and quantitative techniques have provided new tools for advancing the molecular biology, cell biology, diagnosis and vaccine development for public health threats such as schistosomiasis. Areas covered: In this review we describe the latest advances in research that utilizes proteomics-based tools to address some of the key challenges to developing effective interventions against schistosomiasis. We also provide information about the potential of extracellular vesicles to advance the fight against this devastating disease. Expert commentary: Different proteins are already being tested as vaccines against schistosomiasis with promising results. The re-analysis of the Schistosoma spp. proteomes using new and more sensitive mass spectrometers as well as better separation approaches will help identify more vaccine targets in a rational and informed manner. In addition, the recent development of new proteome microarrays will facilitate characterisation of novel markers of infection as well as new vaccine and diagnostic candidate antigens.

Daily temperature and precipitation extremes in the Baltic Sea region derived from the BaltAn65+ reanalysis

NASA Astrophysics Data System (ADS)

Toll, Velle; Post, Piia

2018-04-01

Daily 2-m temperature and precipitation extremes in the Baltic Sea region for the time period of 1965-2005 is studied based on data from the BaltAn65 + high resolution atmospheric reanalysis. Moreover, the ability of regional reanalysis to capture extremes is analysed by comparing the reanalysis data to gridded observations. The shortcomings in the simulation of the minimum temperatures over the northern part of the region and in the simulation of the extreme precipitation over the Scandinavian mountains in the BaltAn65+ reanalysis data are detected and analysed. Temporal trends in the temperature and precipitation extremes in the Baltic Sea region, with the largest increases in temperature and precipitation in winter, are detected based on both gridded observations and the BaltAn65+ reanalysis data. However, the reanalysis is not able to capture all of the regional trends in the extremes in the observations due to the shortcomings in the simulation of the extremes.

Downscaling reanalysis data to high-resolution variables above a glacier surface (Cordillera Blanca, Peru)

NASA Astrophysics Data System (ADS)

Hofer, Marlis; Mölg, Thomas; Marzeion, Ben; Kaser, Georg

2010-05-01

Recently initiated observation networks in the Cordillera Blanca provide temporally high-resolution, yet short-term atmospheric data. The aim of this study is to extend the existing time series into the past. We present an empirical-statistical downscaling (ESD) model that links 6-hourly NCEP/NCAR reanalysis data to the local target variables, measured at the tropical glacier Artesonraju (Northern Cordillera Blanca). The approach is particular in the context of ESD for two reasons. First, the observational time series for model calibration are short (only about two years). Second, unlike most ESD studies in climate research, we focus on variables at a high temporal resolution (i.e., six-hourly values). Our target variables are two important drivers in the surface energy balance of tropical glaciers; air temperature and specific humidity. The selection of predictor fields from the reanalysis data is based on regression analyses and climatologic considerations. The ESD modelling procedure includes combined empirical orthogonal function and multiple regression analyses. Principal component screening is based on cross-validation using the Akaike Information Criterion as model selection criterion. Double cross-validation is applied for model evaluation. Potential autocorrelation in the time series is considered by defining the block length in the resampling procedure. Apart from the selection of predictor fields, the modelling procedure is automated and does not include subjective choices. We assess the ESD model sensitivity to the predictor choice by using both single- and mixed-field predictors of the variables air temperature (1000 hPa), specific humidity (1000 hPa), and zonal wind speed (500 hPa). The chosen downscaling domain ranges from 80 to 50 degrees west and from 0 to 20 degrees south. Statistical transfer functions are derived individually for different months and times of day (month/hour-models). The forecast skill of the month/hour-models largely depends on month and time of day, ranging from 0 to 0.8, but the mixed-field predictors generally perform better than the single-field predictors. At all time scales, the ESD model shows added value against two simple reference models; (i) the direct use of reanalysis grid point values, and (ii) mean diurnal and seasonal cycles over the calibration period. The ESD model forecast 1960 to 2008 clearly reflects interannual variability related to the El Niño/Southern Oscillation, but is sensitive to the chosen predictor type. So far, we have not assessed the performance of NCEP/NCAR reanalysis data against other reanalysis products. The developed ESD model is computationally cheap and applicable wherever measurements are available for model calibration.

Potential Seasonal Predictability of Water Cycle in Observations and Reanalysis

NASA Astrophysics Data System (ADS)

Feng, X.; Houser, P.

2012-12-01

Identification of predictability of water cycle variability is crucial for climate prediction, water resources availability, ecosystem management and hazard mitigation. An analysis that can assess the potential skill in seasonal prediction was proposed by the authors, named as analysis of covariance (ANOCOVA). This method tests whether interannual variability of seasonal means exceeds that due to weather noise under the null hypothesis that seasonal means are identical every year. It has the advantage of taking into account autocorrelation structure in the daily time series but also accounting for the uncertainty of the estimated parameters in the significance test. During the past several years, multiple reanalysis datasets have become available for studying climate variability and understanding climate system. We are motivated to compare the potential predictability of water cycle variation from different reanalysis datasets against observations using the newly proposed ANOCOVA method. The selected eight reanalyses include the National Centers for Environmental Prediction-National Center for Atmospheric Research (NCEP/NCAR) 40-year Reanalysis Project (NNRP), the National Centers for Environmental Prediction-Department of Energy (NCEP/DOE) Reanalysis Project (NDRP), the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-year Reanalysis, The Japan Meteorological Agency 25-year Reanalysis Project (JRA25), the ECMWF) Interim Reanalysis (ERAINT), the NCEP Climate Forecast System Reanalysis (CFSR), the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA), and the National Oceanic and Atmospheric Administration-Cooperative Institute for Research in Environmental Sciences (NOAA/CIRES) 20th Century Reanalysis Version 2 (20CR). For key water cycle components, precipitation and evaporation, all reanalyses consistently show high fraction of predictable variance in the tropics, low predictability over the extratropics, more potential predictability over the ocean than land, and a stronger seasonal variation in potential predictability over land than ocean. The substantial differences are observed especially over the extropical areas where boundary-forced signal is not as significant as in tropics. We further evaluate the accuracy of reanalysis in estimating seasonal predictability over several selected regions, where rain gauge measurement or land surface data assimilation product is available and accurate, to gain insight on the strength and weakness of reanalysis products.

Experimental design for three-color and four-color gene expression microarrays.

PubMed

Woo, Yong; Krueger, Winfried; Kaur, Anupinder; Churchill, Gary

2005-06-01

Three-color microarrays, compared with two-color microarrays, can increase design efficiency and power to detect differential expression without additional samples and arrays. Furthermore, three-color microarray technology is currently available at a reasonable cost. Despite the potential advantages, clear guidelines for designing and analyzing three-color experiments do not exist. We propose a three- and a four-color cyclic design (loop) and a complementary graphical representation to help design experiments that are balanced, efficient and robust to hybridization failures. In theory, three-color loop designs are more efficient than two-color loop designs. Experiments using both two- and three-color platforms were performed in parallel and their outputs were analyzed using linear mixed model analysis in R/MAANOVA. These results demonstrate that three-color experiments using the same number of samples (and fewer arrays) will perform as efficiently as two-color experiments. The improved efficiency of the design is somewhat offset by a reduced dynamic range and increased variability in the three-color experimental system. This result suggests that, with minor technological improvements, three-color microarrays using loop designs could detect differential expression more efficiently than two-color loop designs. http://www.jax.org/staff/churchill/labsite/software Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at http://www.jax.org/staff/churchill/labsite/pubs/yong.

MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering

PubMed Central

Kim, Eun-Youn; Kim, Seon-Young; Ashlock, Daniel; Nam, Dougu

2009-01-01

Background Uncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity of individual patients to specific therapies. Unsupervised clustering methods have been used to classify this type of data. However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance. Results We present a cluster-number-based ensemble clustering algorithm, called MULTI-K, for microarray sample classification, which demonstrates remarkable accuracy. The method amalgamates multiple k-means runs by varying the number of clusters and identifies clusters that manifest the most robust co-memberships of elements. In addition to the original algorithm, we newly devised the entropy-plot to control the separation of singletons or small clusters. MULTI-K, unlike the simple k-means or other widely used methods, was able to capture clusters with complex and high-dimensional structures accurately. MULTI-K outperformed other methods including a recently developed ensemble clustering algorithm in tests with five simulated and eight real gene-expression data sets. Conclusion The geometric complexity of clusters should be taken into account for accurate classification of microarray data, and ensemble clustering applied to the number of clusters tackles the problem very well. The C++ code and the data sets tested are available from the authors. PMID:19698124

Empirical-statistical downscaling of reanalysis data to high-resolution air temperature and specific humidity above a glacier surface (Cordillera Blanca, Peru)

NASA Astrophysics Data System (ADS)

Hofer, Marlis; MöLg, Thomas; Marzeion, Ben; Kaser, Georg

2010-06-01

Recently initiated observation networks in the Cordillera Blanca (Peru) provide temporally high-resolution, yet short-term, atmospheric data. The aim of this study is to extend the existing time series into the past. We present an empirical-statistical downscaling (ESD) model that links 6-hourly National Centers for Environmental Prediction (NCEP)/National Center for Atmospheric Research (NCAR) reanalysis data to air temperature and specific humidity, measured at the tropical glacier Artesonraju (northern Cordillera Blanca). The ESD modeling procedure includes combined empirical orthogonal function and multiple regression analyses and a double cross-validation scheme for model evaluation. Apart from the selection of predictor fields, the modeling procedure is automated and does not include subjective choices. We assess the ESD model sensitivity to the predictor choice using both single-field and mixed-field predictors. Statistical transfer functions are derived individually for different months and times of day. The forecast skill largely depends on month and time of day, ranging from 0 to 0.8. The mixed-field predictors perform better than the single-field predictors. The ESD model shows added value, at all time scales, against simpler reference models (e.g., the direct use of reanalysis grid point values). The ESD model forecast 1960-2008 clearly reflects interannual variability related to the El Niño/Southern Oscillation but is sensitive to the chosen predictor type.

A daily Azores-Iceland North Atlantic Oscillation index back to 1850.

PubMed

Cropper, Thomas; Hanna, Edward; Valente, Maria Antónia; Jónsson, Trausti

2015-07-01

We present the construction of a continuous, daily (09:00 UTC), station-based (Azores-Iceland) North Atlantic Oscillation (NAO) Index back to 1871 which is extended back to 1850 with additional daily mean data. The constructed index more than doubles the length of previously existing, widely available, daily NAO time series. The index is created using entirely observational sea-level pressure (SLP) data from Iceland and 73.5% of observational SLP data from the Azores - the remainder being filled in via reanalysis (Twentieth Century Reanalysis Project and European Mean Sea Level Pressure) SLP data. Icelandic data are taken from the Southwest Iceland pressure series. We construct and document a new Ponta Delgada SLP time series based on recently digitized and newly available data that extend back to 1872. The Ponta Delgada time series is created by splicing together several fractured records (from Ponta Delgada, Lajes, and Santa Maria) and filling in the major gaps (pre-1872, 1888-1905, and 1940-1941) and occasional days (145) with reanalysis data. Further homogeneity corrections are applied to the Azores record, and the daily (09:00 UTC) NAO index is then calculated. The resulting index, with its extended temporal length and daily resolution, is the first reconstruction of daily NAO back into the 19th Century and therefore is useful for researchers across multiple disciplines.

Global 3-D ionospheric electron density reanalysis based on multisource data assimilation

NASA Astrophysics Data System (ADS)

Yue, Xinan; Schreiner, William S.; Kuo, Ying-Hwa; Hunt, Douglas C.; Wang, Wenbin; Solomon, Stanley C.; Burns, Alan G.; Bilitza, Dieter; Liu, Jann-Yenq; Wan, Weixing; Wickert, Jens

2012-09-01

We report preliminary results of a global 3-D ionospheric electron density reanalysis demonstration study during 2002-2011 based on multisource data assimilation. The monthly global ionospheric electron density reanalysis has been done by assimilating the quiet days ionospheric data into a data assimilation model constructed using the International Reference Ionosphere (IRI) 2007 model and a Kalman filter technique. These data include global navigation satellite system (GNSS) observations of ionospheric total electron content (TEC) from ground-based stations, ionospheric radio occultations by CHAMP, GRACE, COSMIC, SAC-C, Metop-A, and the TerraSAR-X satellites, and Jason-1 and 2 altimeter TEC measurements. The output of the reanalysis are 3-D gridded ionospheric electron densities with temporal and spatial resolutions of 1 h in universal time, 5° in latitude, 10° in longitude, and ˜30 km in altitude. The climatological features of the reanalysis results, such as solar activity dependence, seasonal variations, and the global morphology of the ionosphere, agree well with those in the empirical models and observations. The global electron content derived from the international GNSS service global ionospheric maps, the observed electron density profiles from the Poker Flat Incoherent Scatter Radar during 2007-2010, and foF2 observed by the global ionosonde network during 2002-2011 are used to validate the reanalysis method. All comparisons show that the reanalysis have smaller deviations and biases than the IRI-2007 predictions. Especially after April 2006 when the six COSMIC satellites were launched, the reanalysis shows significant improvement over the IRI predictions. The obvious overestimation of the low-latitude ionospheric F region densities by the IRI model during the 23/24 solar minimum is corrected well by the reanalysis. The potential application and improvements of the reanalysis are also discussed.

Extending the reanalysis to the ionosphere based on ground and LEO based GNSS observations

NASA Astrophysics Data System (ADS)

Yue, X.; Schreiner, W. S.; Kuo, Y.

2012-12-01

We report preliminary results of a global 3-D ionospheric electron density reanalysis during 2002-2011 based on multi-source data assimilation. The monthly global ionospheric electron density reanalysis has been done by assimilating the quiet days ionospheric data into a data assimilation model constructed using the International Reference Ionosphere (IRI) 2007 model and a Kalman filter technique. These data include global navigation satellite system (GNSS) observations of ionospheric total electron content (TEC) from ground based stations, ionospheric radio occultations by CHAMP, GRACE, COSMIC, SAC-C, Metop-A, and the TerraSAR-X satellites, and Jason-1 and 2 altimeter TEC measurements. The output of the reanalysis are 3-D gridded ionospheric electron densities with temporal and spatial resolutions of 1 hr in universal time, 5o in latitude, 10o in longitude, and ~ 30 km in altitude. The climatological features of the reanalysis results, such as solar activity dependence, seasonal variations, and the global morphology of the ionosphere, agree well with those in the empirical models and observations. The global electron content (GEC) derived from the international GNSS service (IGS) global ionospheric maps (GIM), the observed electron density profiles from the Poker Flat Incoherent Scatter Radar (PFISR) during 2007-2010, and foF2 observed by the global ionosonde network during 2002-2011 are used to validate the reanalysis method. All comparisons show that the reanalysis have smaller deviations and biases than the IRI-2007 predictions. Especially after April 2006 when the six COSMIC satellites were launched, the reanalysis shows significant improvement over the IRI predictions. The obvious overestimation of the low-latitude ionospheric F-region densities by the IRI model during the 23/24 solar minimum is corrected well by the reanalysis. The potential application and improvements of the reanalysis are also discussed.

Microarray missing data imputation based on a set theoretic framework and biological knowledge.

PubMed

Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

2006-01-01

Gene expressions measured using microarrays usually suffer from the missing value problem. However, in many data analysis methods, a complete data matrix is required. Although existing missing value imputation algorithms have shown good performance to deal with missing values, they also have their limitations. For example, some algorithms have good performance only when strong local correlation exists in data while some provide the best estimate when data is dominated by global structure. In addition, these algorithms do not take into account any biological constraint in their imputation. In this paper, we propose a set theoretic framework based on projection onto convex sets (POCS) for missing data imputation. POCS allows us to incorporate different types of a priori knowledge about missing values into the estimation process. The main idea of POCS is to formulate every piece of prior knowledge into a corresponding convex set and then use a convergence-guaranteed iterative procedure to obtain a solution in the intersection of all these sets. In this work, we design several convex sets, taking into consideration the biological characteristic of the data: the first set mainly exploit the local correlation structure among genes in microarray data, while the second set captures the global correlation structure among arrays. The third set (actually a series of sets) exploits the biological phenomenon of synchronization loss in microarray experiments. In cyclic systems, synchronization loss is a common phenomenon and we construct a series of sets based on this phenomenon for our POCS imputation algorithm. Experiments show that our algorithm can achieve a significant reduction of error compared to the KNNimpute, SVDimpute and LSimpute methods.

Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model

PubMed Central

Suh, Yeunsu; Davis, Michael E.; Lee, Kichoon

2013-01-01

Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI′s Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved. PMID:23741331

High density DNA microarrays: algorithms and biomedical applications.

PubMed

Liu, Wei-Min

2004-08-01

DNA microarrays are devices capable of detecting the identity and abundance of numerous DNA or RNA segments in samples. They are used for analyzing gene expressions, identifying genetic markers and detecting mutations on a genomic scale. The fundamental chemical mechanism of DNA microarrays is the hybridization between probes and targets due to the hydrogen bonds of nucleotide base pairing. Since the cross hybridization is inevitable, and probes or targets may form undesirable secondary or tertiary structures, the microarray data contain noise and depend on experimental conditions. It is crucial to apply proper statistical algorithms to obtain useful signals from noisy data. After we obtained the signals of a large amount of probes, we need to derive the biomedical information such as the existence of a transcript in a cell, the difference of expression levels of a gene in multiple samples, and the type of a genetic marker. Furthermore, after the expression levels of thousands of genes or the genotypes of thousands of single nucleotide polymorphisms are determined, it is usually important to find a small number of genes or markers that are related to a disease, individual reactions to drugs, or other phenotypes. All these applications need careful data analyses and reliable algorithms.

Development and application of a DNA microarray-based yeast two-hybrid system

PubMed Central

Suter, Bernhard; Fontaine, Jean-Fred; Yildirimman, Reha; Raskó, Tamás; Schaefer, Martin H.; Rasche, Axel; Porras, Pablo; Vázquez-Álvarez, Blanca M.; Russ, Jenny; Rau, Kirstin; Foulle, Raphaele; Zenkner, Martina; Saar, Kathrin; Herwig, Ralf; Andrade-Navarro, Miguel A.; Wanker, Erich E.

2013-01-01

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms. PMID:23275563

Apparently low reproducibility of true differential expression discoveries in microarray studies.

PubMed

Zhang, Min; Yao, Chen; Guo, Zheng; Zou, Jinfeng; Zhang, Lin; Xiao, Hui; Wang, Dong; Yang, Da; Gong, Xue; Zhu, Jing; Li, Yanhui; Li, Xia

2008-09-15

Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is often believed that current small microarray studies will largely introduce false discoveries. Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low reproducibility of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall reproducibility of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the reproducibility of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.

UCLA-LANL Reanalysis Project

NASA Astrophysics Data System (ADS)

Shprits, Y.; Chen, Y.; Friedel, R.; Kondrashov, D.; Ni, B.; Subbotin, D.; Reeves, G.; Ghil, M.

2009-04-01

We present first results of the UCLA-LANL Reanalysis Project. Radiation belt relativistic electron Phase Space Density is obtained using the data assimilative VERB code combined with observations from GEO, CRRES, and Akebono data. Reanalysis of data shows the pronounced peaks in the phase space density and pronounced dropouts of fluxes during the main phase of a storm. The results of the reanalysis are discussed and compared to the simulations with the recently developed VERB 3D code.

Global Eddy-Permitting Ocean Reanalyses and Simulations of the Period 1992 to Present

NASA Astrophysics Data System (ADS)

Parent, L.; Ferry, N.; Barnier, B.; Garric, G.; Bricaud, C.; Testut, C.-E.; Le Galloudec, O.; Lellouche, J.-M.; Greiner, E.; Drevillon, M.; Remy, E.; Moulines, J.-M.; Guinehut, S.; Cabanes, C.

2013-09-01

We present GLORYS2V1 global ocean and sea-ice eddy permitting reanalysis over the altimetric era (1993- 2009). This reanalysis is based on an ocean and sea-ice general circulation model at 1⁄4° horizontal resolution assimilating sea surface temperature, in situ profiles of temperature and salinity and along-track sea level anomaly observations. The reanalysis has been produced along with a reference simulation called MJM95 which allows evaluating the benefits of the data assimilation. In the introduction, we briefly describe the GLORYS2V1 reanalysis system. In sections 2, 3 and 4, the reanalysis skill is presented. Data assimilation diagnostics reveal that the reanalysis is stable all along the time period, with however an improved skill when Argo observation network establishes. GLORYS2V1 captures well climate signals and trends and describes meso-scale variability in a realistic manner.

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

Berg, Larry K.; Riihimaki, Laura D.; Qian, Yun

This study utilizes five commonly used reanalysis products, including the NCEP-DOE Reanalysis 2 (NCEP2), ECMWF Re-Analysis (ERA)-Interim, Japanese 25-year Reanalysis (JRA-25), Modern-Era Retrospective Analysis for Research and Applications (MERRA), and North American Regional Reanalysis (NARR) to evaluate features of the Southern Great Plains Low Level Jet (LLJ) above the Atmospheric Radiation Measurement (ARM) Climate Research Facility (ACRF) Southern Great Plains site. Two sets of radiosonde data are utilized: the six-week Midlatitude Continental Convective Clouds Experiment (MC3E), and a ten-year period spanning 2001-2010. All five reanalysis are compared to MC3E data, while only the NARR and MERRA are compared to themore » ten-year data. Each reanalysis is able to represent most aspects of the composite LLJ profile, although there is a tendency for each reanalysis to overestimate the wind speed between the nose of the LLJ and 700 mb. There are large discrepancies in the number of LLJ observed and derived from the reanalysis, particularly for strong LLJs that leads to an underestimate of the water vapor transport associated with LLJs. When the ten-year period is considered, the NARR overestimates and MERRA underestimates the total moisture transport, but both underestimate the transport associated with strong LLJs by factors of 2.0 and 2.7 for the NARR and MERR, respectively. During MC3E there were differences in the patterns of moisture convergence and divergence, with the MERRA having an area of moisture divergence over Oklahoma, while the NARR has moisture convergence. The patterns of moisture convergence and divergence are more consistent during the ten-year period.« less

A First Look at Surface Meteorology in the Arctic System Reanalysis

NASA Astrophysics Data System (ADS)

Slater, A. G.; Serreze, M. C.; Asr-Team, A.

2010-12-01

The Arctic System Reanalysis (ASR) is a joint venture between several universities (Ohio-State Uni., Uni. Colorado, Uni. Illinois UC, Uni. Alaska) and NCAR. It is a regional reanalysis that will span the period 2000-2010, possibly continuing into the future. Compared to current regional or global reanalyses it will have a spatial resolution twice that of prior efforts; a final product is expected to be an equal area projection of 15km grid boxes. The domain encompasses all the Arctic Ocean drainage areas. Several new reanalysis applications have been implemented, with some being Arctic specific - for example satellite derived sea ice age is translated into thickness and MODIS surface albedo is to be ingested. A preliminary ASR run has been performed for the period June 2007 - December 2008 at a reduced resolution of 30km. Here we make a comparison of all recent reanalysis products (NARR, MERRA, ERA-I, CFSRR) to both the ASR and observations at 350 surface stations in the Western Arctic; there is a major focus on Alaska. An intercomparison of surface variables (which are perhaps the most used reanalysis data) has been undertaken including temperature, humidity and solar radiation. Results indicate that the level of discrepancy between reanalysis data and observations is of similar magnitude as it is between all the reanalysis products; possibly suggesting that we have reached the limit of repersentativeness when comparing grid boxes to point measurements.

JRAero: the Japanese Reanalysis for Aerosol v1.0

NASA Astrophysics Data System (ADS)

Yumimoto, Keiya; Tanaka, Taichu Y.; Oshima, Naga; Maki, Takashi

2017-09-01

A global aerosol reanalysis product named the Japanese Reanalysis for Aerosol (JRAero) was constructed by the Meteorological Research Institute (MRI) of the Japan Meteorological Agency. The reanalysis employs a global aerosol transport model developed by MRI and a two-dimensional variational data assimilation method. It assimilates maps of aerosol optical depth (AOD) from MODIS onboard the Terra and Aqua satellites every 6 h and has a TL159 horizontal resolution (approximately 1.1° × 1.1°). This paper describes the aerosol transport model, the data assimilation system, the observation data, and the setup of the reanalysis and examines its quality with AOD observations. Comparisons with MODIS AODs that were used for the assimilation showed that the reanalysis showed much better agreement than the free run (without assimilation) of the aerosol model and improved under- and overestimation in the free run, thus confirming the accuracy of the data assimilation system. The reanalysis had a root mean square error (RMSE) of 0.05, a correlation coefficient (R) of 0.96, a mean fractional error (MFE) of 23.7 %, a mean fractional bias (MFB) of 2.8 %, and an index of agreement (IOA) of 0.98. The better agreement of the first guess, compared to the free run, indicates that aerosol fields obtained by the reanalysis can improve short-term forecasts. AOD fields from the reanalysis also agreed well with monthly averaged global AODs obtained by the Aerosol Robotic Network (AERONET) (RMSE = 0.08, R = 0. 90, MFE = 28.1 %, MFB = 0.6 %, and IOA = 0.93). Site-by-site comparison showed that the reanalysis was considerably better than the free run; RMSE was less than 0.10 at 86.4 % of the 181 AERONET sites, R was greater than 0.90 at 40.7 % of the sites, and IOA was greater than 0.90 at 43.4 % of the sites. However, the reanalysis tended to have a negative bias at urban sites (in particular, megacities in industrializing countries) and a positive bias at mountain sites, possibly because of insufficient anthropogenic emissions data, the coarse model resolution, and the difference in representativeness between satellite and ground-based observations.

Evaluation of artificial time series microarray data for dynamic gene regulatory network inference.

PubMed

Xenitidis, P; Seimenis, I; Kakolyris, S; Adamopoulos, A

2017-08-07

High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process. We examined the effect of various factors on the inference performance such as the network size, the presence of noise in microarray data, and the network sparseness. We used a system theory approach and examined the relationship between the pole placement of the inferred system and the inference performance. We examined the relationship between the inference performance in the time domain and the true system parameter identification. Simulation results indicated that time separation and the percentage of directly triggered genes are crucial factors. Also, network sparseness, the triggering function type and noise in input data affect the inference performance. When two factors were simultaneously varied, it was found that variation of one parameter significantly affects the dynamic response of the other. Crucial factors were also examined using a real GRN and acquired results confirmed simulation findings with artificial data. Different initial conditions were also used as an alternative triggering approach. Relevant results confirmed that the number of datasets constitutes the most significant parameter with regard to the inference performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the improvement of wave and storm surge hindcasts by downscaled atmospheric forcing: application to historical storms

NASA Astrophysics Data System (ADS)

Bresson, Émilie; Arbogast, Philippe; Aouf, Lotfi; Paradis, Denis; Kortcheva, Anna; Bogatchev, Andrey; Galabov, Vasko; Dimitrova, Marieta; Morvan, Guillaume; Ohl, Patrick; Tsenova, Boryana; Rabier, Florence

2018-04-01

Winds, waves and storm surges can inflict severe damage in coastal areas. In order to improve preparedness for such events, a better understanding of storm-induced coastal flooding episodes is necessary. To this end, this paper highlights the use of atmospheric downscaling techniques in order to improve wave and storm surge hindcasts. The downscaling techniques used here are based on existing European Centre for Medium-Range Weather Forecasts reanalyses (ERA-20C, ERA-40 and ERA-Interim). The results show that the 10 km resolution data forcing provided by a downscaled atmospheric model gives a better wave and surge hindcast compared to using data directly from the reanalysis. Furthermore, the analysis of the most extreme mid-latitude cyclones indicates that a four-dimensional blending approach improves the whole process, as it assimilates more small-scale processes in the initial conditions. Our approach has been successfully applied to ERA-20C (the 20th century reanalysis).

An Update on the VAMOS Extremes Working Group Activities

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Cavalcanti, Iracema

2011-01-01

We review here the progress of the Variability of the American MOnsoon Systems (VAMOS) extremes working group since it was formed in February of 2010. The goals of the working group are to 1) develop an atlas of warm-season extremes over the Americas, 2) evaluate existing and planned simulations, and 3) suggest new model runs to address mechanisms and predictability of extremes. Substantial progress has been made in the development of an extremes atlas based on gridded observations and several reanalysis products including Modern Era Retrospective-Analysis for Research and Applications (MERRA) and Climate Forecast System Reanalysis (CFSR). The status of the atlas, remaining issues and plans for its expansion to include model data will be discussed. This includes the possibility of adding a companion atlas based on station observations based on the software developed under the World Climate Research Programme (WCRP) Expert Team on Climate Change. Detection and Indices (ETCCDI) activity. We will also review progress on relevant research and plans for the use and validation of the atlas results.

Quantifying How Observations Inform a Numerical Reanalysis of Hawaii

NASA Astrophysics Data System (ADS)

Powell, B. S.

2017-11-01

When assimilating observations into a model via state-estimation, it is possible to quantify how each observation changes the modeled estimate of a chosen oceanic metric. Using an existing 2 year reanalysis of Hawaii that includes more than 31 million observations from satellites, ships, SeaGliders, and autonomous floats, I assess which observations most improve the estimates of the transport and eddy kinetic energy. When the SeaGliders were in the water, they comprised less than 2.5% of the data, but accounted for 23% of the transport adjustment. Because the model physics constrains advanced state-estimation, the prescribed covariances are propagated in time to identify observation-model covariance. I find that observations that constrain the isopycnal tilt across the transport section provide the greatest impact in the analysis. In the case of eddy kinetic energy, observations that constrain the surface-driven upper ocean have more impact. This information can help to identify optimal sampling strategies to improve both state-estimates and forecasts.

Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.

PubMed

Bonàs-Guarch, Sílvia; Guindo-Martínez, Marta; Miguel-Escalada, Irene; Grarup, Niels; Sebastian, David; Rodriguez-Fos, Elias; Sánchez, Friman; Planas-Fèlix, Mercè; Cortes-Sánchez, Paula; González, Santi; Timshel, Pascal; Pers, Tune H; Morgan, Claire C; Moran, Ignasi; Atla, Goutham; González, Juan R; Puiggros, Montserrat; Martí, Jonathan; Andersson, Ehm A; Díaz, Carlos; Badia, Rosa M; Udler, Miriam; Leong, Aaron; Kaur, Varindepal; Flannick, Jason; Jørgensen, Torben; Linneberg, Allan; Jørgensen, Marit E; Witte, Daniel R; Christensen, Cramer; Brandslund, Ivan; Appel, Emil V; Scott, Robert A; Luan, Jian'an; Langenberg, Claudia; Wareham, Nicholas J; Pedersen, Oluf; Zorzano, Antonio; Florez, Jose C; Hansen, Torben; Ferrer, Jorge; Mercader, Josep Maria; Torrents, David

2018-01-22

The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association studies (GWAS) data for 70,127 subjects, we identify seven novel associated regions, five driven by common variants (LYPLAL1, NEUROG3, CAMKK2, ABO, and GIP genes), one by a low-frequency (EHMT2), and one driven by a rare variant in chromosome Xq23, rs146662057, associated with a twofold increased risk for T2D in males. rs146662057 is located within an active enhancer associated with the expression of Angiotensin II Receptor type 2 gene (AGTR2), a modulator of insulin sensitivity, and exhibits allelic specific activity in muscle cells. Beyond providing insights into the genetics and pathophysiology of T2D, these results also underscore the value of reanalyzing publicly available data using novel genetic resources and analytical approaches.

Evaluation of MERRAero (MERRA Aerosol Reanalysis)

NASA Technical Reports Server (NTRS)

Buchard, Virginie; da Silva, Arlindo; Randles, Cynthia; Colarco, Peter; Darmenov, Anton; Govindaraju, Ravi

2016-01-01

This presentation focuses on MERRA Aerosol Reanalysis (MERRAero) which is the first aerosol reanalysis produced at GMAO. This presentation involve an overview of MERRAero. The evaluation of MERRAero absorption and the evaluation of MERRAero Surface PM 2.5 will also be discussed.

Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species

PubMed Central

Poeschl, Yvonne; Delker, Carolin; Trenner, Jana; Ullrich, Kristian Karsten; Quint, Marcel; Grosse, Ivo

2013-01-01

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses. PMID:24260119

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.

PubMed

Chitturi, Neelima; Balagannavar, Govindkumar; Chandrashekar, Darshan S; Abinaya, Sadashivam; Srini, Vasan S; Acharya, Kshitish K

2013-12-27

Standard 3' Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this. We report a web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. 'Good probes' with complete coverage and identity to latest reference transcript sequences were first identified. Using them, 'Transcript specific probe-clusters' were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as 'transcribed', 'not-detected' or 'differentially regulated'. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP. The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms--at least in some cases.

sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters.

PubMed

Casel, Pierrot; Moreews, François; Lagarrigue, Sandrine; Klopp, Christophe

2009-07-16

Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a set of transcripts as possible in order to monitor as many genes as possible. Depending on the genome sequencing state and on the assembly state the knowledge of the existing transcripts can be very different. This knowledge evolves with the different genome builds and gene builds. Once the design is done the microarrays are often used for several years. The biologists working in EADGENE expressed the need of up-to-dated annotation files for the oligo-sets they share including information about the orthologous genes of model species, the Gene Ontology, the corresponding pathways and the chromosomal location. The results of SigReannot on a chicken micro-array used in the EADGENE project compared to the initial annotations show that 23% of the oligo-nucleotide gene annotations were not confirmed, 2% were modified and 1% were added. The interest of this up-to-date annotation procedure is demonstrated through the analysis of real data previously published. SigReannot uses the oligo-nucleotide design procedure criteria to validate the probe-gene link and the Ensembl transcripts as reference for annotation. It therefore produces a high quality annotation based on reference gene sets.

Extending Climate Analytics as a Service to the Earth System Grid Federation Progress Report on the Reanalysis Ensemble Service

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; Li, J.; Strong, S.; Thompson, J. H.

2016-12-01

We are extending climate analytics-as-a-service, including: (1) A high-performance Virtual Real-Time Analytics Testbed supporting six major reanalysis data sets using advanced technologies like the Cloudera Impala-based SQL and Hadoop-based MapReduce analytics over native NetCDF files. (2) A Reanalysis Ensemble Service (RES) that offers a basic set of commonly used operations over the reanalysis collections that are accessible through NASA's climate data analytics Web services and our client-side Climate Data Services Python library, CDSlib. (3) An Open Geospatial Consortium (OGC) WPS-compliant Web service interface to CDSLib to accommodate ESGF's Web service endpoints. This presentation will report on the overall progress of this effort, with special attention to recent enhancements that have been made to the Reanalysis Ensemble Service, including the following: - An CDSlib Python library that supports full temporal, spatial, and grid-based resolution services - A new reanalysis collections reference model to enable operator design and implementation - An enhanced library of sample queries to demonstrate and develop use case scenarios - Extended operators that enable single- and multiple reanalysis area average, vertical average, re-gridding, and trend, climatology, and anomaly computations - Full support for the MERRA-2 reanalysis and the initial integration of two additional reanalyses - A prototype Jupyter notebook-based distribution mechanism that combines CDSlib documentation with interactive use case scenarios and personalized project management - Prototyped uncertainty quantification services that combine ensemble products with comparative observational products - Convenient, one-stop shopping for commonly used data products from multiple reanalyses, including basic subsetting and arithmetic operations over the data and extractions of trends, climatologies, and anomalies - The ability to compute and visualize multiple reanalysis intercomparisons

Atmospheric response to Saharan dust deduced from ECMWF reanalysis (ERA) temperature increments

NASA Astrophysics Data System (ADS)

Kishcha, P.; Alpert, P.; Barkan, J.; Kirchner, I.; Machenhauer, B.

2003-09-01

This study focuses on the atmospheric temperature response to dust deduced from a new source of data the European Reanalysis (ERA) increments. These increments are the systematic errors of global climate models, generated in the reanalysis procedure. The model errors result not only from the lack of desert dust but also from a complex combination of many kinds of model errors. Over the Sahara desert the lack of dust radiative effect is believed to be a predominant model defect which should significantly affect the increments. This dust effect was examined by considering correlation between the increments and remotely sensed dust. Comparisons were made between April temporal variations of the ERA analysis increments and the variations of the Total Ozone Mapping Spectrometer aerosol index (AI) between 1979 and 1993. The distinctive structure was identified in the distribution of correlation composed of three nested areas with high positive correlation (>0.5), low correlation and high negative correlation (<-0.5). The innermost positive correlation area (PCA) is a large area near the center of the Sahara desert. For some local maxima inside this area the correlation even exceeds 0.8. The outermost negative correlation area (NCA) is not uniform. It consists of some areas over the eastern and western parts of North Africa with a relatively small amount of dust. Inside those areas both positive and negative high correlations exist at pressure levels ranging from 850 to 700 hPa, with the peak values near 775 hPa. Dust-forced heating (cooling) inside the PCA (NCA) is accompanied by changes in the static instability of the atmosphere above the dust layer. The reanalysis data of the European Center for Medium Range Weather Forecast (ECMWF) suggest that the PCA (NCA) corresponds mainly to anticyclonic (cyclonic) flow, negative (positive) vorticity and downward (upward) airflow. These findings are associated with the interaction between dust-forced heating/cooling and atmospheric circulation. This paper contributes to a better understanding of dust radiative processes missed in the model.

Connecting Observations and Reanalysis of the MJO with Theory

NASA Astrophysics Data System (ADS)

Powell, S. W.

2017-12-01

Over the past few years, refined theories have been advanced the explain the onset and/or propagation of the Madden-Julian Oscillation over the tropical warm pool. For example, Adames and Kim (2016) built on Sobel and Maloney (2012, 2013) to describe the MJO as a dispersive moisture wave whose instability mechanism is a radiative-convective instability supported by anvils of large mesoscale systems. Wang and Chen (2016) describe a similar frictionally coupled moisture mode that captures many basic features of the canonically observed MJO. Arnold and Randall (2015) hypothesize that the MJO might be described as self-aggregation of convection over the Indian Ocean. Fuchs and Raymond (2017) describe the MJO as a first baroclinic dispersive mode in a simplified model with a linear WISHE instability that shows decreased propagation speeds for lower wavelengths. Not all of these theories can be correct, and quite possibly none of them are fully. Intelligent use of observations and reanalysis of past MJO events can help guide development of MJO theory. For example, Powell (2017) shows that in MERRA-2 reanalysis, the MJO propagates as a convectively coupled Kelvin wave over the Western Hemisphere then transitions abruptly into a slower moving mode over the Indian Ocean. A complete MJO theory must account for both forms as, and when, the MJO circumnavigates. Observations (like TRMM and GPM data) and reanalysis can reveal the relative roles of cloud-scale processes and large-scale free tropospheric horizontal advection in "pre-moistening" the troposphere in the location of MJO initiation where subsequent propagation of an existing MJO occurs. This can, for example, help validate or refute aspects of moisture mode theory that require large-scale dynamics to moisten an area ahead of an active envelope of MJO-related convection before the MJO can propagate eastward. Radar and satellite observations might yield some insight into whether convective self-aggregation is a real phenomenon or if upscale growth of cloud elements into mesoscale systems is actually more responsible for the apparent large-scale organization of convection in the tropics, let alone within the MJO. I will present a few such examples of how careful exploration of observations and reanalysis might help guide MJO theory during the next several years.

Towards a reanalysis covering the last millennia

NASA Astrophysics Data System (ADS)

Goosse, H.; Dubinkina, S.

2012-04-01

The reanalysis, extending over several decades or longer, provide a comprehensive record of the recent variability and changes of the climate system by objectively combining observations and a numerical model. They are now considered as an essential source of information on the state of the ocean and the atmosphere used, among many other applications, to study the dynamics of the system and the interactions between its different components, to analyze the characteristics of the recent changes as well as the interannual climate variability. However, in order to study processes with a characteristic period from some decades to several centuries, the period covered by the presently available reanalysis is too short. It is therefore necessary to use paleoclimatic proxy data, which provide longer time series, in order to extent the period covered by reanalyses . Those paleoclimatic data, however, are much less numerous, more noisy, and have a lower spatial and temporal resolution than the ones available for the reanalyses over the 20th century. In order to obtain reanalyses covering the last millennia, several steps are thus still required. It is first necessary to develop data assimilation methods adapted to this specific problem. Some data synthesis for this period are available but a reanalysis requires a comprehensive evaluation of the quality of existing data, in all the regions and for all the proxies. Reanalyses are very demanding in computer time, the model selected in the procedure must thus be efficient enough but should also include the right dynamics in order to reproduce the teleconnections between areas where data are available and to extrapolate the information towards regions with no data. Finally, proxies and models do not provide the same variables and comparing them requires a sophisticated approach, ideally implying the inclusion of forward proxy models in the data assimilation system. Here, we propose to review the present status of the field and to identify how significant steps can be made in the way towards a reanalysis over the last millennia. This is illustrated by examples from recent studies in which data assimilation is applied over the last millennia using reconstructions at continental and nearly hemispheric-scale as well as grid-scale temperatures derived directly from the local calibration of proxies.

Method and Early Results of Applying the Global Land Data Assimilation System (GLDAS) in the Third Global Reanalysis of NCEP

NASA Astrophysics Data System (ADS)

Meng, J.; Mitchell, K.; Wei, H.; Yang, R.; Kumar, S.; Geiger, J.; Xie, P.

2008-05-01

Over the past several years, the Environmental Modeling Center (EMC) of the National Centers for Environmental Prediction (NCEP) of the U.S. National Weather Service has developed a Global Land Data Assimilation System (GLDAS). For its computational infrastructure, the GLDAS applies the NASA Land Information System (LIS), developed by the Hydrological Science Branch of NASA Goddard Space Flight Center. The land model utilized in the NCEP GLDAS is the NCEP Noah Land Surface Model (Noah LSM). This presentation will 1) describe how the GLDAS component has been included in the development of NCEP's third global reanalysis (with special attention to the input sources of global precipitation), and 2) will present results from the GLDAS component of pilot tests of the new NCEP global reanalysis. Unlike NCEP's past two global reanalysis projects, this new NCEP global reanalysis includes both a global land data assimilation system (GLDAS) and a global ocean data assimilation system (GODAS). The new global reanalysis will span 30-years (1979-2008) and will include a companion realtime operational component. The atmospheric, ocean, and land states of this global reanalysis will provide the initial conditions for NCEP's 3rd- generation global coupled Climate Forecast System (CFS). NCEP is now preparing to launch a 28-year seasonal reforecast project with its new CFS, to provide the reforecast foundation for operational NCEP seasonal climate forecasts using the new CFS. Together, the new global reanalysis and companion CFS reforecasts constitute what NCEP calls the Climate Forecast System Reanalysis and Reforecast (CFSRR) project. Compared to the previous two generations of NCEP global reanalysis, the hallmark of the GLDAS component of CFSRR is GLDAS use of global analyses of observed precipitation to drive the land surface component of the reanalysis (rather than the typical reanalysis approach of using precipitation from the assimilating background atmospheric model). Specifically, the GLDAS merges two global analyses of observed precipitation produced by the Climate Prediction Center (CPC) of NCEP, as follows: 1) a new CPC daily gauge-only land-only global precipitation analysis at 0.5-degree resolution and 2) the well-known CPC CMAP global 2.0 x 2.5 degree 5-day precipitation analysis, which utilizes satellite estimates of precipitation, as well as some gauge observations. The presentation will describe how these two analyses are merged with latitude-dependent weights that favor the gauge-only analysis in mid-latitudes and the satellite-dominated CMAP analysis in tropical latitudes. Finally, we will show some impacts of using GLDAS to initialize the land states of seasonal CFS reforecasts, versus using the previous generation of NCEP global reanalysis as the source for CFS initial land states.

High-Resolution Regional Reanalysis in China: Evaluation of 1 Year Period Experiments

NASA Astrophysics Data System (ADS)

Zhang, Qi; Pan, Yinong; Wang, Shuyu; Xu, Jianjun; Tang, Jianping

2017-10-01

Globally, reanalysis data sets are widely used in assessing climate change, validating numerical models, and understanding the interactions between the components of a climate system. However, due to the relatively coarse resolution, most global reanalysis data sets are not suitable to apply at the local and regional scales directly with the inadequate descriptions of mesoscale systems and climatic extreme incidents such as mesoscale convective systems, squall lines, tropical cyclones, regional droughts, and heat waves. In this study, by using a data assimilation system of Gridpoint Statistical Interpolation, and a mesoscale atmospheric model of Weather Research and Forecast model, we build a regional reanalysis system. This is preliminary and the first experimental attempt to construct a high-resolution reanalysis for China main land. Four regional test bed data sets are generated for year 2013 via three widely used methods (classical dynamical downscaling, spectral nudging, and data assimilation) and a hybrid method with data assimilation coupled with spectral nudging. Temperature at 2 m, precipitation, and upper level atmospheric variables are evaluated by comparing against observations for one-year-long tests. It can be concluded that the regional reanalysis with assimilation and nudging methods can better produce the atmospheric variables from surface to upper levels, and regional extreme events such as heat waves, than the classical dynamical downscaling. Compared to the ERA-Interim global reanalysis, the hybrid nudging method performs slightly better in reproducing upper level temperature and low-level moisture over China, which improves regional reanalysis data quality.

Performance evaluation of CESM in simulating the dust cycle

NASA Astrophysics Data System (ADS)

Parajuli, S. P.; Yang, Z. L.; Kocurek, G.; Lawrence, D. M.

2014-12-01

Mineral dust in the atmosphere has implications for Earth's radiation budget, biogeochemical cycles, hydrological cycles, human health and visibility. Mineral dust is injected into the atmosphere during dust storms when the surface winds are sufficiently strong and the land surface conditions are favorable. Dust storms are very common in specific regions of the world including the Middle East and North Africa (MENA) region, which contains more than 50% of the global dust sources. In this work, we present simulation of the dust cycle under the framework of CESM1.2.2 and evaluate how well the model captures the spatio-temporal characteristics of dust sources, transport and deposition at global scale, especially in dust source regions. We conducted our simulations using two existing erodibility maps (geomorphic and topographic) and a new erodibility map, which is based on the correlation between observed wind and dust. We compare the simulated results with MODIS satellite data, MACC reanalysis data, and AERONET station data. Comparison with MODIS satellite data and MACC reanalysis data shows that all three erodibility maps generally reproduce the spatio-temporal characteristics of dust optical depth globally. However, comparison with AERONET station data shows that the simulated dust optical depth is generally overestimated for all erodibility maps. Results vary greatly by region and scale of observational data. Our results also show that the simulations forced by reanalysis meteorology capture the overall dust cycle more realistically compared to the simulations done using online meteorology.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

PubMed

Geeleher, Paul; Morris, Dermot; Hinde, John P; Golden, Aaron

2009-06-01

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets. BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from (http://bioinf.nuigalway.ie).

Sensitivity of Simulated Global Ocean Carbon Flux Estimates to Forcing by Reanalysis Products

NASA Technical Reports Server (NTRS)

Gregg, Watson W.; Casey, Nancy W.; Rousseaux, Cecile S.

2015-01-01

Reanalysis products from MERRA, NCEP2, NCEP1, and ECMWF were used to force an established ocean biogeochemical model to estimate air-sea carbon fluxes (FCO2) and partial pressure of carbon dioxide (pCO2) in the global oceans. Global air-sea carbon fluxes and pCO2 were relatively insensitive to the choice of forcing reanalysis. All global FCO2 estimates from the model forced by the four different reanalyses were within 20% of in situ estimates (MERRA and NCEP1 were within 7%), and all models exhibited statistically significant positive correlations with in situ estimates across the 12 major oceanographic basins. Global pCO2 estimates were within 1% of in situ estimates with ECMWF being the outlier at 0.6%. Basin correlations were similar to FCO2. There were, however, substantial departures among basin estimates from the different reanalysis forcings. The high latitudes and tropics had the largest ranges in estimated fluxes among the reanalyses. Regional pCO2 differences among the reanalysis forcings were muted relative to the FCO2 results. No individual reanalysis was uniformly better or worse in the major oceanographic basins. The results provide information on the characterization of uncertainty in ocean carbon models due to choice of reanalysis forcing.

Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes.

PubMed

Zhang, Min; Zhang, Lin; Zou, Jinfeng; Yao, Chen; Xiao, Hui; Liu, Qing; Wang, Jing; Wang, Dong; Wang, Chenguang; Guo, Zheng

2009-07-01

According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies. We proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular changes rather than only counting gene overlaps between the lists. Based on microarray datasets of three diseases, we showed that though the POG scores for DEG lists from different studies for each disease are extremely low, the POGR and nPOGR scores can be rather high, suggesting that the apparently inconsistent DEG lists may be highly reproducible in the sense that they are actually significantly correlated. Observing different discovery results for a disease by the POGR and nPOGR scores will obviously reduce the uncertainty of the microarray studies. The proposed metrics could also be applicable in many other high-throughput post-genomic areas.

Droplet Microarray Based on Superhydrophobic-Superhydrophilic Patterns for Single Cell Analysis.

PubMed

Jogia, Gabriella E; Tronser, Tina; Popova, Anna A; Levkin, Pavel A

2016-12-09

Single-cell analysis provides fundamental information on individual cell response to different environmental cues and is a growing interest in cancer and stem cell research. However, current existing methods are still facing challenges in performing such analysis in a high-throughput manner whilst being cost-effective. Here we established the Droplet Microarray (DMA) as a miniaturized screening platform for high-throughput single-cell analysis. Using the method of limited dilution and varying cell density and seeding time, we optimized the distribution of single cells on the DMA. We established culturing conditions for single cells in individual droplets on DMA obtaining the survival of nearly 100% of single cells and doubling time of single cells comparable with that of cells cultured in bulk cell population using conventional methods. Our results demonstrate that the DMA is a suitable platform for single-cell analysis, which carries a number of advantages compared with existing technologies allowing for treatment, staining and spot-to-spot analysis of single cells over time using conventional analysis methods such as microscopy.

Gene regulatory network identification from the yeast cell cycle based on a neuro-fuzzy system.

PubMed

Wang, B H; Lim, J W; Lim, J S

2016-08-30

Many studies exist for reconstructing gene regulatory networks (GRNs). In this paper, we propose a method based on an advanced neuro-fuzzy system, for gene regulatory network reconstruction from microarray time-series data. This approach uses a neural network with a weighted fuzzy function to model the relationships between genes. Fuzzy rules, which determine the regulators of genes, are very simplified through this method. Additionally, a regulator selection procedure is proposed, which extracts the exact dynamic relationship between genes, using the information obtained from the weighted fuzzy function. Time-series related features are extracted from the original data to employ the characteristics of temporal data that are useful for accurate GRN reconstruction. The microarray dataset of the yeast cell cycle was used for our study. We measured the mean squared prediction error for the efficiency of the proposed approach and evaluated the accuracy in terms of precision, sensitivity, and F-score. The proposed method outperformed the other existing approaches.

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

Probabilistic segmentation and intensity estimation for microarray images.

PubMed

Gottardo, Raphael; Besag, Julian; Stephens, Matthew; Murua, Alejandro

2006-01-01

We describe a probabilistic approach to simultaneous image segmentation and intensity estimation for complementary DNA microarray experiments. The approach overcomes several limitations of existing methods. In particular, it (a) uses a flexible Markov random field approach to segmentation that allows for a wider range of spot shapes than existing methods, including relatively common 'doughnut-shaped' spots; (b) models the image directly as background plus hybridization intensity, and estimates the two quantities simultaneously, avoiding the common logical error that estimates of foreground may be less than those of the corresponding background if the two are estimated separately; and (c) uses a probabilistic modeling approach to simultaneously perform segmentation and intensity estimation, and to compute spot quality measures. We describe two approaches to parameter estimation: a fast algorithm, based on the expectation-maximization and the iterated conditional modes algorithms, and a fully Bayesian framework. These approaches produce comparable results, and both appear to offer some advantages over other methods. We use an HIV experiment to compare our approach to two commercial software products: Spot and Arrayvision.

Evaluation and inter-comparison of modern day reanalysis datasets over Africa and the Middle East

NASA Astrophysics Data System (ADS)

Shukla, S.; Arsenault, K. R.; Hobbins, M.; Peters-Lidard, C. D.; Verdin, J. P.

2015-12-01

Reanalysis datasets are potentially very valuable for otherwise data-sparse regions such as Africa and the Middle East. They are potentially useful for long-term climate and hydrologic analyses and, given their availability in real-time, they are particularity attractive for real-time hydrologic monitoring purposes (e.g. to monitor flood and drought events). Generally in data-sparse regions, reanalysis variables such as precipitation, temperature, radiation and humidity are used in conjunction with in-situ and/or satellite-based datasets to generate long-term gridded atmospheric forcing datasets. These atmospheric forcing datasets are used to drive offline land surface models and simulate soil moisture and runoff, which are natural indicators of hydrologic conditions. Therefore, any uncertainty or bias in the reanalysis datasets contributes to uncertainties in hydrologic monitoring estimates. In this presentation, we report on a comprehensive analysis that evaluates several modern-day reanalysis products (such as NASA's MERRA-1 and -2, ECMWF's ERA-Interim and NCEP's CFS Reanalysis) over Africa and the Middle East region. We compare the precipitation and temperature from the reanalysis products with other independent gridded datasets such as GPCC, CRU, and USGS/UCSB's CHIRPS precipitation datasets, and CRU's temperature datasets. The evaluations are conducted at a monthly time scale, since some of these independent datasets are only available at this temporal resolution. The evaluations range from the comparison of the monthly mean climatology to inter-annual variability and long-term changes. Finally, we also present the results of inter-comparisons of radiation and humidity variables from the different reanalysis datasets.

Evaluation of reanalysis datasets against observational soil temperature data over China

NASA Astrophysics Data System (ADS)

Yang, Kai; Zhang, Jingyong

2018-01-01

Soil temperature is a key land surface variable, and is a potential predictor for seasonal climate anomalies and extremes. Using observational soil temperature data in China for 1981-2005, we evaluate four reanalysis datasets, the land surface reanalysis of the European Centre for Medium-Range Weather Forecasts (ERA-Interim/Land), the second modern-era retrospective analysis for research and applications (MERRA-2), the National Center for Environmental Prediction Climate Forecast System Reanalysis (NCEP-CFSR), and version 2 of the Global Land Data Assimilation System (GLDAS-2.0), with a focus on 40 cm soil layer. The results show that reanalysis data can mainly reproduce the spatial distributions of soil temperature in summer and winter, especially over the east of China, but generally underestimate their magnitudes. Owing to the influence of precipitation on soil temperature, the four datasets perform better in winter than in summer. The ERA-Interim/Land and GLDAS-2.0 produce spatial characteristics of the climatological mean that are similar to observations. The interannual variability of soil temperature is well reproduced by the ERA-Interim/Land dataset in summer and by the CFSR dataset in winter. The linear trend of soil temperature in summer is well rebuilt by reanalysis datasets. We demonstrate that soil heat fluxes in April-June and in winter are highly correlated with the soil temperature in summer and winter, respectively. Different estimations of surface energy balance components can contribute to different behaviors in reanalysis products in terms of estimating soil temperature. In addition, reanalysis datasets can mainly rebuild the northwest-southeast gradient of soil temperature memory over China.

A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays

PubMed Central

Zuckerman, Neta S.; Noam, Yair; Goldsmith, Andrea J.; Lee, Peter P.

2013-01-01

Gene expression analysis is generally performed on heterogeneous tissue samples consisting of multiple cell types. Current methods developed to separate heterogeneous gene expression rely on prior knowledge of the cell-type composition and/or signatures - these are not available in most public datasets. We present a novel method to identify the cell-type composition, signatures and proportions per sample without need for a-priori information. The method was successfully tested on controlled and semi-controlled datasets and performed as accurately as current methods that do require additional information. As such, this method enables the analysis of cell-type specific gene expression using existing large pools of publically available microarray datasets. PMID:23990767

eQTL Mapping Using RNA-seq Data

PubMed Central

Hu, Yijuan

2012-01-01

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping. PMID:23667399

Where's the Beef? A Comment on Ferguson and Donnellan (2014)

ERIC Educational Resources Information Center

Zimmerman, Frederick J.

2014-01-01

To make a scientific contribution, a reanalysis must be firmly rooted in the identification of a clearly superior methodological innovation over the original research. By contrast, a reanalysis rooted in dissatisfaction with previous results will necessarily be biased and can only obscure scientific discoveries. The reanalysis published by…

MERRA-2 Input Observations: Summary and Assessment

NASA Technical Reports Server (NTRS)

Koster, Randal D. (Editor); McCarty, Will; Coy, Lawrence; Gelaro, Ronald; Huang, Albert; Merkova, Dagmar; Smith, Edmond B.; Sienkiewicz, Meta; Wargan, Krzysztof

2016-01-01

The Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA-2) is an atmospheric reanalysis, spanning 1980 through near-realtime, that uses state-of-the-art processing of observations from the continually evolving global observing system. The effectiveness of any reanalysis is a function not only of the input observations themselves, but also of how the observations are handled in the assimilation procedure. Relevant issues to consider include, but are not limited to, data selection, data preprocessing, quality control, bias correction procedures, and blacklisting. As the assimilation algorithm and earth system models are fundamentally fixed in a reanalysis, it is often a change in the character of the observations, and their feedbacks on the system, that cause changes in the character of the reanalysis. It is therefore important to provide documentation of the observing system so that its discontinuities and transitions can be readily linked to discontinuities seen in the gridded atmospheric fields of the reanalysis. With this in mind, this document provides an exhaustive list of the input observations, the context under which they are assimilated, and an initial assessment of selected core observations fundamental to the reanalysis.

Technical Report Series on Global Modeling and Data Assimilation. Volume 13; Interannual Variability and Potential Predictability in Reanalysis Products

NASA Technical Reports Server (NTRS)

Min, Wei; Schubert, Siegfried D.; Suarez, Max J. (Editor)

1997-01-01

The Data Assimilation Office (DAO) at Goddard Space Flight Center and the National Center for Environmental Prediction and National Center for Atmospheric Research (NCEP/NCAR) have produced multi-year global assimilations of historical data employing fixed analysis systems. These "reanalysis" products are ideally suited for studying short-term climatic variations. The availability of multiple reanalysis products also provides the opportunity to examine the uncertainty in the reanalysis data. The purpose of this document is to provide an updated estimate of seasonal and interannual variability based on the DAO and NCEP/NCAR reanalyses for the 15-year period 1980-1995. Intercomparisons of the seasonal means and their interannual variations are presented for a variety of prognostic and diagnostic fields. In addition, atmospheric potential predictability is re-examined employing selected DAO reanalysis variables.

The NASA Reanalysis Ensemble Service - Advanced Capabilities for Integrated Reanalysis Access and Intercomparison

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; Li, J.; Strong, S.; Thompson, J. H.

2017-12-01

NASA's efforts to advance climate analytics-as-a-service are making new capabilities available to the research community: (1) A full-featured Reanalysis Ensemble Service (RES) comprising monthly means data from multiple reanalysis data sets, accessible through an enhanced set of extraction, analytic, arithmetic, and intercomparison operations. The operations are made accessible through NASA's climate data analytics Web services and our client-side Climate Data Services Python library, CDSlib; (2) A cloud-based, high-performance Virtual Real-Time Analytics Testbed supporting a select set of climate variables. This near real-time capability enables advanced technologies like Spark and Hadoop-based MapReduce analytics over native NetCDF files; and (3) A WPS-compliant Web service interface to our climate data analytics service that will enable greater interoperability with next-generation systems such as ESGF. The Reanalysis Ensemble Service includes the following: - New API that supports full temporal, spatial, and grid-based resolution services with sample queries - A Docker-ready RES application to deploy across platforms - Extended capabilities that enable single- and multiple reanalysis area average, vertical average, re-gridding, standard deviation, and ensemble averages - Convenient, one-stop shopping for commonly used data products from multiple reanalyses including basic sub-setting and arithmetic operations (e.g., avg, sum, max, min, var, count, anomaly) - Full support for the MERRA-2 reanalysis dataset in addition to, ECMWF ERA-Interim, NCEP CFSR, JMA JRA-55 and NOAA/ESRL 20CR… - A Jupyter notebook-based distribution mechanism designed for client use cases that combines CDSlib documentation with interactive scenarios and personalized project management - Supporting analytic services for NASA GMAO Forward Processing datasets - Basic uncertainty quantification services that combine heterogeneous ensemble products with comparative observational products (e.g., reanalysis, observational, visualization) - The ability to compute and visualize multiple reanalysis for ease of inter-comparisons - Automated tools to retrieve and prepare data collections for analytic processing

Surface Glycosylation Profiles of Urine Extracellular Vesicles

PubMed Central

Gerlach, Jared Q.; Krüger, Anja; Gallogly, Susan; Hanley, Shirley A.; Hogan, Marie C.; Ward, Christopher J.

2013-01-01

Urinary extracellular vesicles (uEVs) are released by cells throughout the nephron and contain biomolecules from their cells of origin. Although uEV-associated proteins and RNA have been studied in detail, little information exists regarding uEV glycosylation characteristics. Surface glycosylation profiling by flow cytometry and lectin microarray was applied to uEVs enriched from urine of healthy adults by ultracentrifugation and centrifugal filtration. The carbohydrate specificity of lectin microarray profiles was confirmed by competitive sugar inhibition and carbohydrate-specific enzyme hydrolysis. Glycosylation profiles of uEVs and purified Tamm Horsfall protein were compared. In both flow cytometry and lectin microarray assays, uEVs demonstrated surface binding, at low to moderate intensities, of a broad range of lectins whether prepared by ultracentrifugation or centrifugal filtration. In general, ultracentrifugation-prepared uEVs demonstrated higher lectin binding intensities than centrifugal filtration-prepared uEVs consistent with lesser amounts of co-purified non-vesicular proteins. The surface glycosylation profiles of uEVs showed little inter-individual variation and were distinct from those of Tamm Horsfall protein, which bound a limited number of lectins. In a pilot study, lectin microarray was used to compare uEVs from individuals with autosomal dominant polycystic kidney disease to those of age-matched controls. The lectin microarray profiles of polycystic kidney disease and healthy uEVs showed differences in binding intensity of 6/43 lectins. Our results reveal a complex surface glycosylation profile of uEVs that is accessible to lectin-based analysis following multiple uEV enrichment techniques, is distinct from co-purified Tamm Horsfall protein and may demonstrate disease-specific modifications. PMID:24069349

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

PubMed Central

Rahmatallah, Yasir; Emmert-Streib, Frank

2016-01-01

Transcriptome sequencing (RNA-seq) is gradually replacing microarrays for high-throughput studies of gene expression. The main challenge of analyzing microarray data is not in finding differentially expressed genes, but in gaining insights into the biological processes underlying phenotypic differences. To interpret experimental results from microarrays, gene set analysis (GSA) has become the method of choice, in particular because it incorporates pre-existing biological knowledge (in a form of functionally related gene sets) into the analysis. Here we provide a brief review of several statistically different GSA approaches (competitive and self-contained) that can be adapted from microarrays practice as well as those specifically designed for RNA-seq. We evaluate their performance (in terms of Type I error rate, power, robustness to the sample size and heterogeneity, as well as the sensitivity to different types of selection biases) on simulated and real RNA-seq data. Not surprisingly, the performance of various GSA approaches depends only on the statistical hypothesis they test and does not depend on whether the test was developed for microarrays or RNA-seq data. Interestingly, we found that competitive methods have lower power as well as robustness to the samples heterogeneity than self-contained methods, leading to poor results reproducibility. We also found that the power of unsupervised competitive methods depends on the balance between up- and down-regulated genes in tested gene sets. These properties of competitive methods have been overlooked before. Our evaluation provides a concise guideline for selecting GSA approaches, best performing under particular experimental settings in the context of RNA-seq. PMID:26342128

Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data.

PubMed

Ooi, Chia Huey; Chetty, Madhu; Teng, Shyh Wei

2006-06-23

Due to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification while improving accuracy at the same time. Surprisingly, this does not appear to be the case for all multiclass microarray datasets. The reason is that many feature selection techniques applied on microarray datasets are either rank-based and hence do not take into account correlations between genes, or are wrapper-based, which require high computational cost, and often yield difficult-to-reproduce results. In studies where correlations between genes are considered, attempts to establish the merit of the proposed techniques are hampered by evaluation procedures which are less than meticulous, resulting in overly optimistic estimates of accuracy. We present two realistically evaluated correlation-based feature selection techniques which incorporate, in addition to the two existing criteria involved in forming a predictor set (relevance and redundancy), a third criterion called the degree of differential prioritization (DDP). DDP functions as a parameter to strike the balance between relevance and redundancy, providing our techniques with the novel ability to differentially prioritize the optimization of relevance against redundancy (and vice versa). This ability proves useful in producing optimal classification accuracy while using reasonably small predictor set sizes for nine well-known multiclass microarray datasets. For multiclass microarray datasets, especially the GCM and NCI60 datasets, DDP enables our filter-based techniques to produce accuracies better than those reported in previous studies which employed similarly realistic evaluation procedures.

Linking microarray reporters with protein functions.

PubMed

Gaj, Stan; van Erk, Arie; van Haaften, Rachel I M; Evelo, Chris T A

2007-09-26

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.

Northern Hemisphere winter storm track trends since 1959 derived from multiple reanalysis datasets

NASA Astrophysics Data System (ADS)

Chang, Edmund K. M.; Yau, Albert M. W.

2016-09-01

In this study, a comprehensive comparison of Northern Hemisphere winter storm track trend since 1959 derived from multiple reanalysis datasets and rawinsonde observations has been conducted. In addition, trends in terms of variance and cyclone track statistics have been compared. Previous studies, based largely on the National Center for Environmental Prediction-National Center for Atmospheric Research Reanalysis (NNR), have suggested that both the Pacific and Atlantic storm tracks have significantly intensified between the 1950s and 1990s. Comparison with trends derived from rawinsonde observations suggest that the trends derived from NNR are significantly biased high, while those from the European Center for Medium Range Weather Forecasts 40-year Reanalysis and the Japanese 55-year Reanalysis are much less biased but still too high. Those from the two twentieth century reanalysis datasets are most consistent with observations but may exhibit slight biases of opposite signs. Between 1959 and 2010, Pacific storm track activity has likely increased by 10 % or more, while Atlantic storm track activity has likely increased by <10 %. Our analysis suggests that trends in Pacific and Atlantic basin wide storm track activity prior to the 1950s derived from the two twentieth century reanalysis datasets are unlikely to be reliable due to changes in density of surface observations. Nevertheless, these datasets may provide useful information on interannual variability, especially over the Atlantic.

76 FR 26290 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-06

... report entitled ``SAB Review of EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to... of EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments.'' The SAB... Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments.'' To conduct this review...

Missing value imputation for microarray data: a comprehensive comparison study and a web tool.

PubMed

Chiu, Chia-Chun; Chan, Shih-Yao; Wang, Chung-Ching; Wu, Wei-Sheng

2013-01-01

Microarray data are usually peppered with missing values due to various reasons. However, most of the downstream analyses for microarray data require complete datasets. Therefore, accurate algorithms for missing value estimation are needed for improving the performance of microarray data analyses. Although many algorithms have been developed, there are many debates on the selection of the optimal algorithm. The studies about the performance comparison of different algorithms are still incomprehensive, especially in the number of benchmark datasets used, the number of algorithms compared, the rounds of simulation conducted, and the performance measures used. In this paper, we performed a comprehensive comparison by using (I) thirteen datasets, (II) nine algorithms, (III) 110 independent runs of simulation, and (IV) three types of measures to evaluate the performance of each imputation algorithm fairly. First, the effects of different types of microarray datasets on the performance of each imputation algorithm were evaluated. Second, we discussed whether the datasets from different species have different impact on the performance of different algorithms. To assess the performance of each algorithm fairly, all evaluations were performed using three types of measures. Our results indicate that the performance of an imputation algorithm mainly depends on the type of a dataset but not on the species where the samples come from. In addition to the statistical measure, two other measures with biological meanings are useful to reflect the impact of missing value imputation on the downstream data analyses. Our study suggests that local-least-squares-based methods are good choices to handle missing values for most of the microarray datasets. In this work, we carried out a comprehensive comparison of the algorithms for microarray missing value imputation. Based on such a comprehensive comparison, researchers could choose the optimal algorithm for their datasets easily. Moreover, new imputation algorithms could be compared with the existing algorithms using this comparison strategy as a standard protocol. In addition, to assist researchers in dealing with missing values easily, we built a web-based and easy-to-use imputation tool, MissVIA (http://cosbi.ee.ncku.edu.tw/MissVIA), which supports many imputation algorithms. Once users upload a real microarray dataset and choose the imputation algorithms, MissVIA will determine the optimal algorithm for the users' data through a series of simulations, and then the imputed results can be downloaded for the downstream data analyses.

Translating standards into practice - one Semantic Web API for Gene Expression.

PubMed

Deus, Helena F; Prud'hommeaux, Eric; Miller, Michael; Zhao, Jun; Malone, James; Adamusiak, Tomasz; McCusker, Jim; Das, Sudeshna; Rocca Serra, Philippe; Fox, Ronan; Marshall, M Scott

2012-08-01

Sharing and describing experimental results unambiguously with sufficient detail to enable replication of results is a fundamental tenet of scientific research. In today's cluttered world of "-omics" sciences, data standards and standardized use of terminologies and ontologies for biomedical informatics play an important role in reporting high-throughput experiment results in formats that can be interpreted by both researchers and analytical tools. Increasing adoption of Semantic Web and Linked Data technologies for the integration of heterogeneous and distributed health care and life sciences (HCLSs) datasets has made the reuse of standards even more pressing; dynamic semantic query federation can be used for integrative bioinformatics when ontologies and identifiers are reused across data instances. We present here a methodology to integrate the results and experimental context of three different representations of microarray-based transcriptomic experiments: the Gene Expression Atlas, the W3C BioRDF task force approach to reporting Provenance of Microarray Experiments, and the HSCI blood genomics project. Our approach does not attempt to improve the expressivity of existing standards for genomics but, instead, to enable integration of existing datasets published from microarray-based transcriptomic experiments. SPARQL Construct is used to create a posteriori mappings of concepts and properties and linking rules that match entities based on query constraints. We discuss how our integrative approach can encourage reuse of the Experimental Factor Ontology (EFO) and the Ontology for Biomedical Investigations (OBIs) for the reporting of experimental context and results of gene expression studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Improving nuclear data accuracy of 241Am and 237Np capture cross sections

NASA Astrophysics Data System (ADS)

Žerovnik, Gašper; Schillebeeckx, Peter; Cano-Ott, Daniel; Jandel, Marian; Hori, Jun-ichi; Kimura, Atsushi; Rossbach, Matthias; Letourneau, Alain; Noguere, Gilles; Leconte, Pierre; Sano, Tadafumi; Kellett, Mark A.; Iwamoto, Osamu; Ignatyuk, Anatoly V.; Cabellos, Oscar; Genreith, Christoph; Harada, Hideo

2017-09-01

In the framework of the OECD/NEA WPEC subgroup 41, ways to improve neutron induced capture cross sections for 241Am and 237Np are being sought. Decay data, energy dependent cross section data and neutron spectrum averaged data are important for that purpose and were investigated. New time-of-flight measurements were performed and analyzed, and considerable effort was put into development of methods for analysis of spectrum averaged data and re-analysis of existing experimental data.

Analysis and High-Resolution Modeling of Tropical Cyclogenesis During the TCS-08 and TPARC Field Campaign

DTIC Science & Technology

2014-10-13

synoptic and dynamic aspects of cyclogenesis, a multi-nested WRF model (with 2 km resolution in the innermost mesh) will be used to simulate both...intraseasonal and interannual variability of TC activity in the WNP. For the data assimilation task, WRF 3DVar assimilation system will be employed...simulated using WRF . This genesis is associated with Rossby wave energy dispersion of a pre- existing TC Bills (2000). Using the reanalysis data as an

Application of a substructuring technique to the problem of crack extension and closure

NASA Technical Reports Server (NTRS)

Armen, H., Jr.

1974-01-01

A substructuring technique, originally developed for the efficient reanalysis of structures, is incorporated into the methodology associated with the plastic analysis of structures. An existing finite-element computer program that accounts for elastic-plastic material behavior under cyclic loading was modified to account for changing kinematic constraint conditions - crack growth and intermittent contact of crack surfaces in two dimensional regions. Application of the analysis is presented for a problem of a centercrack panel to demonstrate the efficiency and accuracy of the technique.

Comparison of surface sensible and latent heat fluxes over the Tibetan Plateau from reanalysis and observations

NASA Astrophysics Data System (ADS)

Xie, Jin; Yu, Ye; Li, Jiang-lin; Ge, Jun; Liu, Chuan

2018-02-01

Surface sensible and latent heat fluxes (SH and LE) over the Tibetan Plateau (TP) have been under research since 1950s, especially for recent several years, by mainly using observation, reanalysis, and satellite data. However, the spatiotemporal changes are not consistent among different studies. This paper focuses on the spatiotemporal variation of SH and LE over the TP from 1981 to 2013 using reanalysis data sets (ERA-Interim, JRA-55, and MERRA) and observations. Results show that the spatiotemporal changes from the three reanalysis data sets are significantly different and the probable causes are discussed. Averaged for the whole TP, both SH and LE from MERRA are obviously higher than the other two reanalysis data sets. ERA-Interim shows a significant downward trend for SH and JRA-55 shows a significant increase of LE during the 33 years with other data sets having no obvious changes. By comparing the heat fluxes and some climate factors from the reanalysis with observations, it is found that the differences of heat fluxes among the three reanalysis data sets are closely related to their differences in meteorological conditions as well as the different parameterizations for surface transfer coefficients. In general, the heat fluxes from the three reanalysis have a better representation in the western TP than that in the eastern TP under inter-annual scale. While in terms of monthly variation, ERA-Interim may have better applicability in the eastern TP with dense vegetation conditions, while SH of JRA-55 and LE of MERRA are probably more representative for the middle and western TP with poor vegetation conditions.

Structural reanalysis via a mixed method. [using Taylor series for accuracy improvement

NASA Technical Reports Server (NTRS)

Noor, A. K.; Lowder, H. E.

1975-01-01

A study is made of the approximate structural reanalysis technique based on the use of Taylor series expansion of response variables in terms of design variables in conjunction with the mixed method. In addition, comparisons are made with two reanalysis techniques based on the displacement method. These techniques are the Taylor series expansion and the modified reduced basis. It is shown that the use of the reciprocals of the sizing variables as design variables (which is the natural choice in the mixed method) can result in a substantial improvement in the accuracy of the reanalysis technique. Numerical results are presented for a space truss structure.

Comparison of MERRA-2 and ECCO-v4 ocean surface heat fluxes: Consequences of different forcing feedbacks on ocean circulation and implications for climate data assimilation.

NASA Astrophysics Data System (ADS)

Strobach, E.; Molod, A.; Menemenlis, D.; Forget, G.; Hill, C. N.; Campin, J. M.; Heimbach, P.

2017-12-01

Forcing ocean models with reanalysis data is a common practice in ocean modeling. As part of this practice, prescribed atmospheric state variables and interactive ocean SST are used to calculate fluxes between the ocean and the atmosphere. When forcing an ocean model with reanalysis fields, errors in the reanalysis data, errors in the ocean model and errors in the forcing formulation will generate a different solution compared to other ocean reanalysis solutions (which also have their own errors). As a first step towards a consistent coupled ocean-atmosphere reanalysis, we compare surface heat fluxes from a state-of-the-art atmospheric reanalysis, the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), to heat fluxes from a state-of-the-art oceanic reanalysis, the Estimating the Circulation and Climate of the Ocean Version 4, Release 2 (ECCO-v4). Then, we investigate the errors associated with the MITgcm ocean model in its ECCO-v4 ocean reanalysis configuration (1992-2011) when it is forced with MERRA-2 atmospheric reanalysis fields instead of with the ECCO-v4 adjoint optimized ERA-interim state variables. This is done by forcing ECCO-v4 ocean with and without feedbacks from MERRA-2 related to turbulent fluxes of heat and moisture and the outgoing long wave radiation. In addition, we introduce an intermediate forcing method that includes only the feedback from the interactive outgoing long wave radiation. The resulting ocean circulation is compared with ECCO-v4 reanalysis and in-situ observations. We show that, without feedbacks, imbalances in the energy and the hydrological cycles of MERRA-2 (which are directly related to the fact it was created without interactive ocean) result in considerable SST drifts and a large reduction in sea level. The bulk formulae and interactive outgoing long wave radiation, although providing air-sea feedbacks and reducing model-data misfit, strongly relax the ocean to observed SST and may result in unwanted features such as large change in the water budget. These features have implications in on desired forcing recipe to be used. The results strongly and unambiguously argue for next generation data assimilation climate studies to involve fully coupled systems.

An integrated approach for identifying wrongly labelled samples when performing classification in microarray data.

PubMed

Leung, Yuk Yee; Chang, Chun Qi; Hung, Yeung Sam

2012-01-01

Using hybrid approach for gene selection and classification is common as results obtained are generally better than performing the two tasks independently. Yet, for some microarray datasets, both classification accuracy and stability of gene sets obtained still have rooms for improvement. This may be due to the presence of samples with wrong class labels (i.e. outliers). Outlier detection algorithms proposed so far are either not suitable for microarray data, or only solve the outlier detection problem on their own. We tackle the outlier detection problem based on a previously proposed Multiple-Filter-Multiple-Wrapper (MFMW) model, which was demonstrated to yield promising results when compared to other hybrid approaches (Leung and Hung, 2010). To incorporate outlier detection and overcome limitations of the existing MFMW model, three new features are introduced in our proposed MFMW-outlier approach: 1) an unbiased external Leave-One-Out Cross-Validation framework is developed to replace internal cross-validation in the previous MFMW model; 2) wrongly labeled samples are identified within the MFMW-outlier model; and 3) a stable set of genes is selected using an L1-norm SVM that removes any redundant genes present. Six binary-class microarray datasets were tested. Comparing with outlier detection studies on the same datasets, MFMW-outlier could detect all the outliers found in the original paper (for which the data was provided for analysis), and the genes selected after outlier removal were proven to have biological relevance. We also compared MFMW-outlier with PRAPIV (Zhang et al., 2006) based on same synthetic datasets. MFMW-outlier gave better average precision and recall values on three different settings. Lastly, artificially flipped microarray datasets were created by removing our detected outliers and flipping some of the remaining samples' labels. Almost all the 'wrong' (artificially flipped) samples were detected, suggesting that MFMW-outlier was sufficiently powerful to detect outliers in high-dimensional microarray datasets.

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data

PubMed Central

Glez-Peña, Daniel; Álvarez, Rodrigo; Díaz, Fernando; Fdez-Riverola, Florentino

2009-01-01

Background Expression profiling assays done by using DNA microarray technology generate enormous data sets that are not amenable to simple analysis. The greatest challenge in maximizing the use of this huge amount of data is to develop algorithms to interpret and interconnect results from different genes under different conditions. In this context, fuzzy logic can provide a systematic and unbiased way to both (i) find biologically significant insights relating to meaningful genes, thereby removing the need for expert knowledge in preliminary steps of microarray data analyses and (ii) reduce the cost and complexity of later applied machine learning techniques being able to achieve interpretable models. Results DFP is a new Bioconductor R package that implements a method for discretizing and selecting differentially expressed genes based on the application of fuzzy logic. DFP takes advantage of fuzzy membership functions to assign linguistic labels to gene expression levels. The technique builds a reduced set of relevant genes (FP, Fuzzy Pattern) able to summarize and represent each underlying class (pathology). A last step constructs a biased set of genes (DFP, Discriminant Fuzzy Pattern) by intersecting existing fuzzy patterns in order to detect discriminative elements. In addition, the software provides new functions and visualisation tools that summarize achieved results and aid in the interpretation of differentially expressed genes from multiple microarray experiments. Conclusion DFP integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It has the advantage that its parameters are highly configurable, facilitating the discovery of biologically relevant connections between sets of genes belonging to different pathologies. This information makes it possible to automatically filter irrelevant genes thereby reducing the large volume of data supplied by microarray experiments. Based on these contributions GENECBR, a successful tool for cancer diagnosis using microarray datasets, has recently been released. PMID:19178723

Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method.

PubMed

Bengtsson, Henrik; Hössjer, Ola

2006-03-01

Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but it is not clear which is the best. It is therefore important to further study the different normalization methods in detail and the nature of microarray data in general. A methodological study of affine models for gene expression data is carried out. Focus is on two-channel comparative studies, but the findings generalize also to single- and multi-channel data. The discussion applies to spotted as well as in-situ synthesized microarray data. Existing normalization methods such as curve-fit ("lowess") normalization, parallel and perpendicular translation normalization, and quantile normalization, but also dye-swap normalization are revisited in the light of the affine model and their strengths and weaknesses are investigated in this context. As a direct result from this study, we propose a robust non-parametric multi-dimensional affine normalization method, which can be applied to any number of microarrays with any number of channels either individually or all at once. A high-quality cDNA microarray data set with spike-in controls is used to demonstrate the power of the affine model and the proposed normalization method. We find that an affine model can explain non-linear intensity-dependent systematic effects in observed log-ratios. Affine normalization removes such artifacts for non-differentially expressed genes and assures that symmetry between negative and positive log-ratios is obtained, which is fundamental when identifying differentially expressed genes. In addition, affine normalization makes the empirical distributions in different channels more equal, which is the purpose of quantile normalization, and may also explain why dye-swap normalization works or fails. All methods are made available in the aroma package, which is a platform-independent package for R.

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data.

PubMed

Glez-Peña, Daniel; Alvarez, Rodrigo; Díaz, Fernando; Fdez-Riverola, Florentino

2009-01-29

Expression profiling assays done by using DNA microarray technology generate enormous data sets that are not amenable to simple analysis. The greatest challenge in maximizing the use of this huge amount of data is to develop algorithms to interpret and interconnect results from different genes under different conditions. In this context, fuzzy logic can provide a systematic and unbiased way to both (i) find biologically significant insights relating to meaningful genes, thereby removing the need for expert knowledge in preliminary steps of microarray data analyses and (ii) reduce the cost and complexity of later applied machine learning techniques being able to achieve interpretable models. DFP is a new Bioconductor R package that implements a method for discretizing and selecting differentially expressed genes based on the application of fuzzy logic. DFP takes advantage of fuzzy membership functions to assign linguistic labels to gene expression levels. The technique builds a reduced set of relevant genes (FP, Fuzzy Pattern) able to summarize and represent each underlying class (pathology). A last step constructs a biased set of genes (DFP, Discriminant Fuzzy Pattern) by intersecting existing fuzzy patterns in order to detect discriminative elements. In addition, the software provides new functions and visualisation tools that summarize achieved results and aid in the interpretation of differentially expressed genes from multiple microarray experiments. DFP integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It has the advantage that its parameters are highly configurable, facilitating the discovery of biologically relevant connections between sets of genes belonging to different pathologies. This information makes it possible to automatically filter irrelevant genes thereby reducing the large volume of data supplied by microarray experiments. Based on these contributions GENECBR, a successful tool for cancer diagnosis using microarray datasets, has recently been released.

Revisiting the global surface energy budgets with maximum-entropy-production model of surface heat fluxes

NASA Astrophysics Data System (ADS)

Huang, Shih-Yu; Deng, Yi; Wang, Jingfeng

2017-09-01

The maximum-entropy-production (MEP) model of surface heat fluxes, based on contemporary non-equilibrium thermodynamics, information theory, and atmospheric turbulence theory, is used to re-estimate the global surface heat fluxes. The MEP model predicted surface fluxes automatically balance the surface energy budgets at all time and space scales without the explicit use of near-surface temperature and moisture gradient, wind speed and surface roughness data. The new MEP-based global annual mean fluxes over the land surface, using input data of surface radiation, temperature data from National Aeronautics and Space Administration-Clouds and the Earth's Radiant Energy System (NASA CERES) supplemented by surface specific humidity data from the Modern-Era Retrospective Analysis for Research and Applications (MERRA), agree closely with previous estimates. The new estimate of ocean evaporation, not using the MERRA reanalysis data as model inputs, is lower than previous estimates, while the new estimate of ocean sensible heat flux is higher than previously reported. The MEP model also produces the first global map of ocean surface heat flux that is not available from existing global reanalysis products.

Enabling Research Tools for Sustained Climate Assessment

NASA Technical Reports Server (NTRS)

Leidner, Allison K.; Bosilovich, Michael G.; Jasinski, Michael F.; Nemani, Ramakrishna R.; Waliser, Duane Edward; Lee, Tsengdar J.

2016-01-01

The U.S. Global Change Research Program Sustained Assessment process benefits from long-term investments in Earth science research that enable the scientific community to conduct assessment-relevant science. To this end, NASA initiated several research programs over the past five years to support the Earth observation community in developing indicators, datasets, research products, and tools to support ongoing and future National Climate Assessments. These activities complement NASA's ongoing Earth science research programs. One aspect of the assessment portfolio funds four "enabling tools" projects at NASA research centers. Each tool leverages existing capacity within the center, but has developed tailored applications and products for National Climate Assessments. The four projects build on the capabilities of a global atmospheric reanalysis (MERRA-2), a continental U.S. land surface reanalysis (NCA-LDAS), the NASA Earth Exchange (NEX), and a Regional Climate Model Evaluation System (RCMES). Here, we provide a brief overview of each enabling tool, highlighting the ways in which it has advanced assessment science to date. We also discuss how the assessment community can access and utilize these tools for National Climate Assessments and other sustained assessment activities.

Rainy Days in the New Arctic: A Comprehensive Look at Precipitation from 8 Reanalysis

NASA Astrophysics Data System (ADS)

Boisvert, L.; Webster, M.; Petty, A.; Markus, T.

2017-12-01

Precipitation in the Arctic plays an important role in the fresh water budget, and is the primary control of snow accumulation on sea ice. However, Arctic precipitation from reanalysis is highly uncertain due to differences in the atmospheric physics and use/approaches of data assimilation and sea ice concentrations across the different products. More specifically, yearly cumulative precipitation in some regions can vary by 100-150 mm across reanalyses. This creates problems for those modeling snow depth on sea ice, specifically for use in deriving sea ice thickness from satellite altimetry. In recent years, this new Arctic has become warmer and wetter, and evaporation from the ice-free ocean has been increasing, which leads to the question: is more precipitation falling and is more of this precipitation rain? This could pose a big problem for model and remote sensing applications and studies those modeling snow accumulation because rain events will can melt the existing snow pack, reduce surface albedo, and modify the ocean-to-atmosphere heat flux via snow densification. In this work we compare precipitation (both snow and rain) from 8 different reanalysis: MERRA, MERRA2, NCEP-R1, NCEP-R2, ERA-Interim, ERA-5, ASR and JRA-55. We examine the annual, seasonal, and regional differences and compare with buoy data to assess discrepancies between products during observed snowfall and rainfall events. Magnitudes and frequencies of these precipitation events are evaluated, as well as the "residual drizzle" between reanalyzes. Lastly, we will look at whether the frequency and magnitude of "rainy days" in the Arctic have been changing over recent decades.

A comprehensive transcript index of the human genome generated using microarrays and computational approaches

PubMed Central

Schadt, Eric E; Edwards, Stephen W; GuhaThakurta, Debraj; Holder, Dan; Ying, Lisa; Svetnik, Vladimir; Leonardson, Amy; Hart, Kyle W; Russell, Archie; Li, Guoya; Cavet, Guy; Castle, John; McDonagh, Paul; Kan, Zhengyan; Chen, Ronghua; Kasarskis, Andrew; Margarint, Mihai; Caceres, Ramon M; Johnson, Jason M; Armour, Christopher D; Garrett-Engele, Philip W; Tsinoremas, Nicholas F; Shoemaker, Daniel D

2004-01-01

Background Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. Results The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. Conclusions These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized. PMID:15461792

Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification

PubMed Central

Wang, Yun; Huang, Fangzhou

2018-01-01

The selection of feature genes with high recognition ability from the gene expression profiles has gained great significance in biology. However, most of the existing methods have a high time complexity and poor classification performance. Motivated by this, an effective feature selection method, called supervised locally linear embedding and Spearman's rank correlation coefficient (SLLE-SC2), is proposed which is based on the concept of locally linear embedding and correlation coefficient algorithms. Supervised locally linear embedding takes into account class label information and improves the classification performance. Furthermore, Spearman's rank correlation coefficient is used to remove the coexpression genes. The experiment results obtained on four public tumor microarray datasets illustrate that our method is valid and feasible. PMID:29666661

Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification.

PubMed

Xu, Jiucheng; Mu, Huiyu; Wang, Yun; Huang, Fangzhou

2018-01-01

The selection of feature genes with high recognition ability from the gene expression profiles has gained great significance in biology. However, most of the existing methods have a high time complexity and poor classification performance. Motivated by this, an effective feature selection method, called supervised locally linear embedding and Spearman's rank correlation coefficient (SLLE-SC 2 ), is proposed which is based on the concept of locally linear embedding and correlation coefficient algorithms. Supervised locally linear embedding takes into account class label information and improves the classification performance. Furthermore, Spearman's rank correlation coefficient is used to remove the coexpression genes. The experiment results obtained on four public tumor microarray datasets illustrate that our method is valid and feasible.

Using in vitro models for expression profiling studies on ethanol and drugs of abuse.

PubMed

Thibault, Christelle; Hassan, Sajida; Miles, Michael

2005-03-01

The use of expression profiling with microarrays offers great potential for studying the mechanisms of action of drugs of abuse. Studies with the intact nervous system seem likely to be most relevant to understanding the mechanisms of drug abuse-related behaviours. However, the use of expression profiling with in vitro culture models offers significant advantages for identifying details of cellular signalling actions and toxicity for drugs of abuse. This study discusses general issues of the use of microarrays and cell culture models for studies on drugs of abuse. Specific results from existing studies are also discussed, providing clear examples of relevance for in vitro studies on ethanol, nicotine, opiates, cannabinoids and hallucinogens such as LSD. In addition to providing details on signalling mechanisms relevant to the neurobiology of drugs of abuse, microarray studies on a variety of cell culture systems have also provided important information on mechanisms of cellular/organ toxicity with drugs of abuse. Efforts to integrate genomic studies on drugs of abuse with both in vivo and in vitro models offer the potential for novel mechanistic rigor and physiological relevance.

A comparison of bootstrap methods and an adjusted bootstrap approach for estimating the prediction error in microarray classification.

PubMed

Jiang, Wenyu; Simon, Richard

2007-12-20

This paper first provides a critical review on some existing methods for estimating the prediction error in classifying microarray data where the number of genes greatly exceeds the number of specimens. Special attention is given to the bootstrap-related methods. When the sample size n is small, we find that all the reviewed methods suffer from either substantial bias or variability. We introduce a repeated leave-one-out bootstrap (RLOOB) method that predicts for each specimen in the sample using bootstrap learning sets of size ln. We then propose an adjusted bootstrap (ABS) method that fits a learning curve to the RLOOB estimates calculated with different bootstrap learning set sizes. The ABS method is robust across the situations we investigate and provides a slightly conservative estimate for the prediction error. Even with small samples, it does not suffer from large upward bias as the leave-one-out bootstrap and the 0.632+ bootstrap, and it does not suffer from large variability as the leave-one-out cross-validation in microarray applications. Copyright (c) 2007 John Wiley & Sons, Ltd.

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies

PubMed Central

Nilsson, Björn; Håkansson, Petra; Johansson, Mikael; Nelander, Sven; Fioretos, Thoas

2007-01-01

Ontological analysis facilitates the interpretation of microarray data. Here we describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enhanced approach. PMID:17488501

Analysis of Atmosphere-Ocean Surface Flux Feedbacks in Recent Satellite and Model Reanalysis Products

NASA Technical Reports Server (NTRS)

Roberts, J. Brent; Robertson, F. R.; Clayson, C. A.

2010-01-01

Recent investigations have examined observations in an attempt to determine when and how the ocean forces the atmosphere, and vice versa. These studies focus primarily on relationships between sea surface temperature anomalies and the turbulent and radiative surface heat fluxes. It has been found that both positive and negative feedbacks, which enhance or reduce sea surface temperature anomaly amplitudes, can be generated through changes in the surface boundary layer. Consequent changes in sea surface temperature act to change boundary layer characteristics through changes in static stability or turbulent fluxes. Previous studies over the global oceans have used coarse-resolution observational and model products such as ICOADS and the NCEP Reanalysis. This study focuses on documenting the atmosphere ocean feedbacks that exist in recently produced higher resolution products, namely the SeaFlux v1.0 product and the NASA Modern Era Retrospective-Analysis for Research and Applications (MERRA). It has been noted in recent studies that evidence of oceanic forcing of the atmosphere exists on smaller scales than the usually more dominant atmospheric forcing of the ocean, particularly in higher latitudes. It is expected that use of these higher resolution products will allow for a more comprehensive description of these small-scale ocean-atmosphere feedbacks. The SeaFlux intercomparisons have revealed large scatter between various surface flux climatologies. This study also investigates the uncertainty in surface flux feedbacks based on several of these recent satellite based climatologies

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Genotyping microarray (gene chip) for the ABCR (ABCA4) gene.

PubMed

Jaakson, K; Zernant, J; Külm, M; Hutchinson, A; Tonisson, N; Glavac, D; Ravnik-Glavac, M; Hawlina, M; Meltzer, M R; Caruso, R C; Testa, F; Maugeri, A; Hoyng, C B; Gouras, P; Simonelli, F; Lewis, R A; Lupski, J R; Cremers, F P M; Allikmets, R

2003-11-01

Genetic variation in the ABCR (ABCA4) gene has been associated with five distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), and age-related macular degeneration (AMD). Comparative genetic analyses of ABCR variation and diagnostics have been complicated by substantial allelic heterogeneity and by differences in screening methods. To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants. The ABCR genotyping microarray (the ABCR400 chip) was constructed by the arrayed primer extension (APEX) technology. Each sequence change in ABCR was included on the chip by synthesis and application of sequence-specific oligonucleotides. We validated the chip by screening 136 confirmed STGD patients and 96 healthy controls, each of whom we had analyzed previously by single strand conformation polymorphism (SSCP) technology and/or heteroduplex analysis. The microarray was >98% effective in determining the existing genetic variation and was comparable to direct sequencing in that it yielded many sequence changes undetected by SSCP. In STGD patient cohorts, the efficiency of the array to detect disease-associated alleles was between 54% and 78%, depending on the ethnic composition and degree of clinical and molecular characterization of a cohort. In addition, chip analysis suggested a high carrier frequency (up to 1:10) of ABCR variants in the general population. The ABCR genotyping microarray is a robust, cost-effective, and comprehensive screening tool for variation in one gene in which mutations are responsible for a substantial fraction of retinal disease. The ABCR chip is a prototype for the next generation of screening and diagnostic tools in ophthalmic genetics, bridging clinical and scientific research. Copyright 2003 Wiley-Liss, Inc.

Linking microarray reporters with protein functions

PubMed Central

Gaj, Stan; van Erk, Arie; van Haaften, Rachel IM; Evelo, Chris TA

2007-01-01

Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/. PMID:17897448

Analysis of population structure and genetic history of cattle breeds based on high-density SNP data

USDA-ARS?s Scientific Manuscript database

Advances in single nucleotide polymorphism (SNP) genotyping microarrays have facilitated a new understanding of population structure and evolutionary history for several species. Most existing studies in livestock were based on low density SNP arrays. The first wave of low density SNP studies on cat...

A reanalysis dataset of the South China Sea.

PubMed

Zeng, Xuezhi; Peng, Shiqiu; Li, Zhijin; Qi, Yiquan; Chen, Rongyu

2014-01-01

Ocean reanalysis provides a temporally continuous and spatially gridded four-dimensional estimate of the ocean state for a better understanding of the ocean dynamics and its spatial/temporal variability. Here we present a 19-year (1992-2010) high-resolution ocean reanalysis dataset of the upper ocean in the South China Sea (SCS) produced from an ocean data assimilation system. A wide variety of observations, including in-situ temperature/salinity profiles, ship-measured and satellite-derived sea surface temperatures, and sea surface height anomalies from satellite altimetry, are assimilated into the outputs of an ocean general circulation model using a multi-scale incremental three-dimensional variational data assimilation scheme, yielding a daily high-resolution reanalysis dataset of the SCS. Comparisons between the reanalysis and independent observations support the reliability of the dataset. The presented dataset provides the research community of the SCS an important data source for studying the thermodynamic processes of the ocean circulation and meso-scale features in the SCS, including their spatial and temporal variability.

A reanalysis dataset of the South China Sea

PubMed Central

Zeng, Xuezhi; Peng, Shiqiu; Li, Zhijin; Qi, Yiquan; Chen, Rongyu

2014-01-01

Ocean reanalysis provides a temporally continuous and spatially gridded four-dimensional estimate of the ocean state for a better understanding of the ocean dynamics and its spatial/temporal variability. Here we present a 19-year (1992–2010) high-resolution ocean reanalysis dataset of the upper ocean in the South China Sea (SCS) produced from an ocean data assimilation system. A wide variety of observations, including in-situ temperature/salinity profiles, ship-measured and satellite-derived sea surface temperatures, and sea surface height anomalies from satellite altimetry, are assimilated into the outputs of an ocean general circulation model using a multi-scale incremental three-dimensional variational data assimilation scheme, yielding a daily high-resolution reanalysis dataset of the SCS. Comparisons between the reanalysis and independent observations support the reliability of the dataset. The presented dataset provides the research community of the SCS an important data source for studying the thermodynamic processes of the ocean circulation and meso-scale features in the SCS, including their spatial and temporal variability. PMID:25977803

Web-based Reanalysis Intercomparison Tools (WRIT): Comparing Reanalyses and Observational data.

NASA Astrophysics Data System (ADS)

Compo, G. P.; Smith, C. A.; Hooper, D. K.

2014-12-01

While atmospheric reanalysis datasets are widely used in climate science, many technical issues hinder comparing them to each other and to observations. The reanalysis fields are stored in diverse file architectures, data formats, and resolutions, with metadata, such as variable name and units, that also differ. Individual users have to download the fields, convert them to a common format, store them locally, change variable names, re-grid if needed, and convert units. Comparing reanalyses with observational datasets is difficult for similar reasons. Even if a dataset can be read via Open-source Project for a Network Data Access Protocol (OPeNDAP) or a similar protocol, most of this work is still needed. All of these tasks take time, effort, and money. To overcome some of the obstacles in reanalysis intercomparison, our group at the Cooperative Institute for Research in the Environmental Sciences (CIRES) at the University of Colorado and affiliated colleagues at National Oceanic and Atmospheric Administration's (NOAA's) Earth System Research Laboratory Physical Sciences Division (ESRL/PSD) have created a set of Web-based Reanalysis Intercomparison Tools (WRIT) at http://www.esrl.noaa.gov/psd/data/writ/. WRIT allows users to easily plot and compare reanalysis and observational datasets, and to test hypotheses. Currently, there are tools to plot monthly mean maps and vertical cross-sections, timeseries, and trajectories for standard pressure level and surface variables. Users can refine dates, statistics, and plotting options. Reanalysis datasets currently available include the NCEP/NCAR R1, NCEP/DOE R2, MERRA, ERA-Interim, NCEP CFSR and the 20CR. Observational datasets include those containing precipitation (e.g. GPCP), temperature (e.g. GHCNCAMS), winds (e.g. WASWinds), precipitable water (e.g. NASA NVAP), SLP (HadSLP2), and SST (NOAA ERSST). WRIT also facilitates the mission of the Reanalyses.org website as a convenient toolkit for studying the reanalysis datasets.

Uncertainties in Decadal Model Evaluation due to the Choice of Different Reanalysis Products

NASA Astrophysics Data System (ADS)

Illing, Sebastian; Kadow, Christopher; Kunst, Oliver; Cubasch, Ulrich

2014-05-01

In recent years decadal predictions have become very popular in the climate science community. A major task is the evaluation and validation of a decadal prediction system. Therefore hindcast experiments are performed and evaluated against observation based or reanalysis data-sets. That is, various metrics and skill scores like the anomaly correlation or the mean squared error skill score (MSSS) are calculated to estimate potential prediction skill of the model system. Our results will mostly feature the Baseline 1 hindcast experiments from the MiKlip decadal prediction system. MiKlip (www.fona-miklip.de) is a project for medium-term climate prediction funded by the Federal Ministry of Education and Research in Germany (BMBF) and has the aim to create a model system that can provide reliable decadal forecasts on climate and weather. There are various reanalysis and observation based products covering at least the last forty years which can be used for model evaluation, for instance the 20th Century Reanalysis from NOAA-CIRES, the Climate Forecast System Reanalysis from NCEP or the Interim Reanalysis from ECMWF. Each of them is based on different climate models and observations. We will show that the choice of the reanalysis product has a huge impact on the value of various skill metrics. In some cases this may actually lead to a change in the interpretation of the results, e.g. when one tries to compare two model versions and the anomaly correlation difference changes its sign for two different reanalysis products. We will also show first results of our studies investigating the influence and effect of this source of uncertainty for decadal model evaluation. Furthermore we point out regions which are most affected by this uncertainty and where one has to cautious interpreting skill scores. In addition we introduce some strategies to overcome or at least reduce this source of uncertainty.

Missing value imputation for microarray data: a comprehensive comparison study and a web tool

PubMed Central

2013-01-01

Background Microarray data are usually peppered with missing values due to various reasons. However, most of the downstream analyses for microarray data require complete datasets. Therefore, accurate algorithms for missing value estimation are needed for improving the performance of microarray data analyses. Although many algorithms have been developed, there are many debates on the selection of the optimal algorithm. The studies about the performance comparison of different algorithms are still incomprehensive, especially in the number of benchmark datasets used, the number of algorithms compared, the rounds of simulation conducted, and the performance measures used. Results In this paper, we performed a comprehensive comparison by using (I) thirteen datasets, (II) nine algorithms, (III) 110 independent runs of simulation, and (IV) three types of measures to evaluate the performance of each imputation algorithm fairly. First, the effects of different types of microarray datasets on the performance of each imputation algorithm were evaluated. Second, we discussed whether the datasets from different species have different impact on the performance of different algorithms. To assess the performance of each algorithm fairly, all evaluations were performed using three types of measures. Our results indicate that the performance of an imputation algorithm mainly depends on the type of a dataset but not on the species where the samples come from. In addition to the statistical measure, two other measures with biological meanings are useful to reflect the impact of missing value imputation on the downstream data analyses. Our study suggests that local-least-squares-based methods are good choices to handle missing values for most of the microarray datasets. Conclusions In this work, we carried out a comprehensive comparison of the algorithms for microarray missing value imputation. Based on such a comprehensive comparison, researchers could choose the optimal algorithm for their datasets easily. Moreover, new imputation algorithms could be compared with the existing algorithms using this comparison strategy as a standard protocol. In addition, to assist researchers in dealing with missing values easily, we built a web-based and easy-to-use imputation tool, MissVIA (http://cosbi.ee.ncku.edu.tw/MissVIA), which supports many imputation algorithms. Once users upload a real microarray dataset and choose the imputation algorithms, MissVIA will determine the optimal algorithm for the users' data through a series of simulations, and then the imputed results can be downloaded for the downstream data analyses. PMID:24565220

Climatology and trend of wind power resources in China and its surrounding regions: a revisit using Climate Forecast System Reanalysis data

Treesearch

Lejiang Yu; Shiyuan Zhong; Xindi Bian; Warren E. Heilman

2015-01-01

The mean climatology, seasonal and interannual variability and trend of wind speeds at the hub height (80 m) of modern wind turbines over China and its surrounding regions are revisited using 33-year (1979–2011) wind data from the Climate Forecast System Reanalysis (CFSR) that has many improvements including higher spatial resolution over previous global reanalysis...

Maintaining Atmospheric Mass and Water Balance Within Reanalysis

NASA Technical Reports Server (NTRS)

Takacs, Lawrence L.; Suarez, Max; Todling, Ricardo

2015-01-01

This report describes the modifications implemented into the Goddard Earth Observing System Version-5 (GEOS-5) Atmospheric Data Assimilation System (ADAS) to maintain global conservation of dry atmospheric mass as well as to preserve the model balance of globally integrated precipitation and surface evaporation during reanalysis. Section 1 begins with a review of these global quantities from four current reanalysis efforts. Section 2 introduces the modifications necessary to preserve these constraints within the atmospheric general circulation model (AGCM), the Gridpoint Statistical Interpolation (GSI) analysis procedure, and the Incremental Analysis Update (IAU) algorithm. Section 3 presents experiments quantifying the impact of the new procedure. Section 4 shows preliminary results from its use within the GMAO MERRA-2 Reanalysis project. Section 5 concludes with a summary.

The Hadley circulation: assessing NCEP/NCAR reanalysis and sparse in-situ estimates

NASA Astrophysics Data System (ADS)

Waliser, D. E.; Shi, Zhixiong; Lanzante, J. R.; Oort, A. H.

We present a comparison of the zonal mean meridional circulations derived from monthly in situ data (i.e. radiosondes and ship reports) and from the NCEP/NCAR reanalysis product. To facilitate the interpretation of the results, a third estimate of the mean meridional circulation is produced by subsampling the reanalysis at the locations where radiosonde and surface ship data are available for the in situ calculation. This third estimate, known as the subsampled estimate, is compared to the complete reanalysis estimate to assess biases in conventional, in situ estimates of the Hadley circulation associated with the sparseness of the data sources (i.e., radiosonde network). The subsampled estimate is also compared to the in situ estimate to assess the biases introduced into the reanalysis product by the numerical model, initialization process and/or indirect data sources such as satellite retrievals. The comparisons suggest that a number of qualitative differences between the in situ and reanalysis estimates are mainly associated with the sparse sampling and simplified interpolation schemes associated with in situ estimates. These differences include: (1) a southern Hadley cell that consistently extends up to 200 hPa in the reanalysis, whereas the bulk of the circulation for the in situ and subsampled estimates tends to be confined to the lower half of the troposphere, (2) more well-defined and consistent poleward limits of the Hadley cells in the reanalysis compared to the in-situ and subsampled estimates, and (3) considerably less variability in magnitude and latitudinal extent of the Ferrel cells and southern polar cell exhibited in the reanalysis estimate compared to the in situ and subsampled estimates. Quantitative comparison shows that the subsampled estimate, relative to the reanalysis estimate, produces a stronger northern Hadley cell ( 20%), a weaker southern Hadley cell ( 20-60%), and weaker Ferrel cells in both hemispheres. These differences stem from poorly measured oceanic regions which necessitate significant interpolation over broad regions. Moreover, they help to pinpoint specific shortcomings in the present and previous in situ estimates of the Hadley circulation. Comparisons between the subsampled and in situ estimates suggest that the subsampled estimate produces a slightly stronger Hadley circulation in both hemispheres, with the relative differences in some seasons as large as 20-30%. 6These differences suggest that the mean meridional circulation associated with the NCEP/NCAR reanalysis is more energetic than observations suggest. Examination of ENSO-related changes to the Hadley circulation suggest that the in situ and subsampled estimates significantly overestimate the effects of ENSO on the Hadley circulation due to the reliance on sparsely distributed data. While all three estimates capture the large-scale region of low-level equatorial convergence near the dateline that occurs during El Nino, the in situ and subsampled estimates fail to effectively reproduce the large-scale areas of equatorial mass divergence to the west and east of this convergence area, leading to an overestimate of the effects of ENSO on the zonal mean circulation.

Arctic sea ice in the global eddy-permitting ocean reanalysis ORAP5

NASA Astrophysics Data System (ADS)

Tietsche, Steffen; Balmaseda, Magdalena A.; Zuo, Hao; Mogensen, Kristian

2017-08-01

We discuss the state of Arctic sea ice in the global eddy-permitting ocean reanalysis Ocean ReAnalysis Pilot 5 (ORAP5). Among other innovations, ORAP5 now assimilates observations of sea ice concentration using a univariate 3DVar-FGAT scheme. We focus on the period 1993-2012 and emphasize the evaluation of model performance with respect to recent observations of sea ice thickness. We find that sea ice concentration in ORAP5 is close to assimilated observations, with root mean square analysis residuals of less than 5 % in most regions. However, larger discrepancies exist for the Labrador Sea and east of Greenland during winter owing to biases in the free-running model. Sea ice thickness is evaluated against three different observational data sets that have sufficient spatial and temporal coverage: ICESat, IceBridge and SMOSIce. Large-scale features like the gradient between the thickest ice in the Canadian Arctic and thinner ice in the Siberian Arctic are simulated well by ORAP5. However, some biases remain. Of special note is the model's tendency to accumulate too thick ice in the Beaufort Gyre. The root mean square error of ORAP5 sea ice thickness with respect to ICESat observations is 1.0 m, which is on par with the well-established PIOMAS model sea ice reconstruction. Interannual variability and trend of sea ice volume in ORAP5 also compare well with PIOMAS and ICESat estimates. We conclude that, notwithstanding a relatively simple sea ice data assimilation scheme, the overall state of Arctic sea ice in ORAP5 is in good agreement with observations and will provide useful initial conditions for predictions.

Diagnosing Possible Anthropogenic Contributions to Heavy Colorado Rainfall in September 2013

NASA Astrophysics Data System (ADS)

Pall, Pardeep; Patricola, Christina; Wehner, Michael; Stone, Dáithí; Paciorek, Christopher; Collins, William

2015-04-01

Unusually heavy rainfall occurred over the Colorado Front Range during early September 2013, with record or near-record totals recorded in several locations. It was associated predominantly with a stationary large-scale weather pattern (akin to the North American Monsoon, which occurs earlier in the year) that drove a strong plume of deep moisture inland from the Gulf of Mexico against the Front Range foothills. The resulting floods across the South Platte River basin impacted several thousands of people and many homes, roads, and businesses. To diagnose possible anthropogenic contributions to the odds of such heavy rainfall, we adapt an existing event attribution paradigm of modelling an 'event that was' for September 2013 and comparing it to a modelled 'event that might have been' for that same time but for the absence of historical anthropogenic drivers of climate. Specifically, we first perform 'event that was' simulations with the regional Weather Research and Forecasting (WRF) model at 12 km resolution over North America, driven by NCEP2 re-analysis. We then re-simulate, having adjusted the re-analysis to 'event that might have been conditions' by modifying atmospheric greenhouse gas and other pollutant concentrations, temperature, humidity, and winds, as well as sea ice coverage, and sea-surface temperatures - all according to estimates from global climate model simulations. Thus our findings are highly conditional on the driving re-analysis and adjustments therein, but the setup allows us to elucidate possible mechanisms responsible for heavy Colorado rainfall in September 2013. Our model results suggests that, given an insignificant change in the pattern of large-scale driving weather, there is an increase in atmospheric water vapour under anthropogenic climate warming leading to a substantial increase in the probability of heavy rainfall occurring over the South Platte River basin in September 2013.

Diagnosing Possible Anthropogenic Contributions to Heavy Colorado Rainfall in September 2013

NASA Astrophysics Data System (ADS)

Pall, P.; Patricola, C. M.; Wehner, M. F.; Stone, D. A.; Paciorek, C. J.; Collins, W.

2014-12-01

Unusually heavy rainfall occurred over the Colorado Front Range during early September 2013, with record or near-record totals recorded in several locations. It was associated predominantly with a stationary large-scale weather pattern (akin to the North American Monsoon, which occurs earlier in the year) that drove a strong plume of deep moisture inland from the Gulf of Mexico against the Front Range foothills. The resulting floods impacted several thousands of people and many homes, roads, and businesses. To diagnose possible anthropogenic contributions to the odds of such heavy rainfall, we adapt an existing event attribution paradigm of modelling a 'world that was' for September 2013 and comparing it to a modelled 'world that might have been' for that same time but for the absence of historical anthropogenic drivers of climate. Specifically, we first perform 'world that was' simulations with the regional WRF model at 12 km resolution over North America, driven by NCEP2 re-analysis. We then re-simulate, having adjusted the re-analysis to 'world that might have been conditions' by modifying atmospheric greenhouse gas and other pollutant concentrations, temperature, humidity, and winds, as well as sea ice coverage, and sea-surface temperatures - all according to estimates from global climate model simulations. Thus our findings are highly conditional on the driving re-analysis and adjustments therein, but the setup allows us to elucidate possible mechanisms responsible for heavy Colorado rainfall in September 2013. For example, preliminary analysis suggests that, given no change in the pattern of large-scale driving weather, there is an increase in atmospheric water vapour under anthropogenic climate warming leading to a substantial increase in the odds of heavy rainfall over the Front Range.

Status and Plans for Reanalysis at NASA/GMAO

NASA Technical Reports Server (NTRS)

Gelaro, Ron

2017-01-01

Reanalysis plays a critical role in GMAOs goal to enhance NASA's program of Earth observations, providing vital data sets for climate research and the development of future missions. As the breadth of NASAs observations expands to include multiple components of the Earth system, so does the need to assimilate observations from currently uncoupled components of the system in a more physically consistent manner. GMAOs most recent reanalysis of the satellite era, MERRA-2, has completed the period 1980-present, and is now running as a continuing global climate analysis with two- to three-week latency. MERRA-2 assimilates meteorological and aerosol observations as a weakly coupled assimilation system as a first step toward GMAOs longer term goal of developing an integrated Earth system analysis (IESA) capability that will couple assimilation systems for the atmosphere, ocean, land and chemistry. The GMAO strategy is to progress incrementally toward an IESA through an evolving combination of coupled systems and offline component reanalyses driven by, for example, MERRA-2 atmospheric forcing. Most recently, the GMAO has implemented a weakly coupled assimilation scheme for analyzing ocean skin temperature within the existing atmospheric analysis. The scheme uses background fields from a near-surface ocean diurnal layer model to assimilate surface-sensitive radiances plus in-situ observations along with all other observations in the atmospheric assimilation system. In addition, MERRA-2-driven simulations of the ocean (plus sea ice) and atmospheric chemistry (for the EOS period) are currently underway, as is the development of a coupled atmosphere-ocean assimilation system. This talk will describe the status of these ongoing efforts and the planned steps toward an IESA capability for climate research.

Groundwater Variability in a Sandstone Catchment and Linkages with Large-scale Climatic Circulatio

NASA Astrophysics Data System (ADS)

Hannah, D. M.; Lavers, D. A.; Bradley, C.

2015-12-01

Groundwater is a crucial water resource that sustains river ecosystems and provides public water supply. Furthermore, during periods of prolonged high rainfall, groundwater-dominated catchments can be subject to protracted flooding. Climate change and associated projected increases in the frequency and intensity of hydrological extremes have implications for groundwater levels. This study builds on previous research undertaken on a Chalk catchment by investigating groundwater variability in a UK sandstone catchment: the Tern in Shropshire. In contrast to the Chalk, sandstone is characterised by a more lagged response to precipitation inputs; and, as such, it is important to determine the groundwater behaviour and its links with the large-scale climatic circulation to improve process understanding of recharge, groundwater level and river flow responses to hydroclimatological drivers. Precipitation, river discharge and groundwater levels for borehole sites in the Tern basin over 1974-2010 are analysed as the target variables; and we use monthly gridded reanalysis data from the Twentieth Century Reanalysis Project (20CR). First, groundwater variability is evaluated and associations with precipitation / discharge are explored using monthly concurrent and lagged correlation analyses. Second, gridded 20CR reanalysis data are used in composite and correlation analyses to identify the regions of strongest climate-groundwater association. Results show that reasonably strong climate-groundwater connections exist in the Tern basin, with a several months lag. These lags are associated primarily with the time taken for recharge waters to percolate through to the groundwater table. The uncovered patterns improve knowledge of large-scale climate forcing of groundwater variability and may provide a basis to inform seasonal prediction of groundwater levels, which would be useful for strategic water resource planning.

Overview of the reanalysis of the Harvard Six Cities Study and American Cancer Society Study of Particulate Air Pollution and Mortality.

PubMed

Krewski, Daniel; Burnett, Richard T; Goldberg, Mark S; Hoover, B Kristin; Siemiatycki, Jack; Jerrett, Michael; Abrahamowicz, Michal; White, Warren H

This article provides an overview of the Reanalysis Study of the Harvard Six Cities and the American Cancer Society (ACS) studies of particulate air pollution and mortality. The previous findings of the studies have been subject to debate. In response, a reanalysis team, comprised of Canadian and American researchers, was invited to participate in an independent reanalysis project to address the concerns. Phase I of the reanalysis involved the design of data audits to determine whether each study conformed to the consistency and accuracy of their data. Phase II of the reanalysis involved conducting a series of comprehensive analyses using alternative statistical methods. Alternative models were also used to identify covariates that may confound or modify the association of particulate air pollution as well as identify sensitive population subgroups. The audit demonstrated that the data in the original analyses were of high quality, as were the risk estimates reported by the original investigators. The sensitivity analysis illustrated that the mortality risk estimates reported in both studies were found to be robust against alternative Cox models. Detailed investigation of the covariate effects found a significant modifying effect of education and a relative risk of mortality associated with fine particles and declining education levels. The study team applied spatial analytic methods to the ACS data, resulting in various levels of spatial autocorrelations supporting the reported association for fine particles mortality of the original investigators as well as demonstrating a significant association between sulfur dioxide and mortality. Collectively, our reanalysis suggest that mortality may be attributable to more than one component of the complex mixture of ambient air pollutants for U.S. urban areas.

Decadal reanalysis of biogeochemical indicators and fluxes in the North West European shelf-sea ecosystem

NASA Astrophysics Data System (ADS)

Ciavatta, S.; Kay, S.; Saux-Picart, S.; Butenschön, M.; Allen, J. I.

2016-03-01

This paper presents the first decadal reanalysis simulation of the biogeochemistry of the North West European shelf, along with a full evaluation of its skill, confidence, and value. An error-characterized satellite product for chlorophyll was assimilated into a physical-biogeochemical model of the North East Atlantic, applying a localized Ensemble Kalman filter. The results showed that the reanalysis improved the model simulation of assimilated chlorophyll in 60% of the study region. Model validation metrics showed that the reanalysis had skill in matching a large data set of in situ observations for 10 ecosystem variables. Spearman rank correlations were significant and higher than 0.7 for physical-chemical variables (temperature, salinity, and oxygen), ˜0.6 for chlorophyll and nutrients (phosphate, nitrate, and silicate), and significant, though lower in value, for partial pressure of dissolved carbon dioxide (˜0.4). The reanalysis captured the magnitude of pH and ammonia observations, but not their variability. The value of the reanalysis for assessing environmental status and variability has been exemplified in two case studies. The first shows that between 325,000 and 365,000 km2 of shelf bottom waters were vulnerable to oxygen deficiency potentially threatening bottom fishes and benthos. The second application confirmed that the shelf is a net sink of atmospheric carbon dioxide, but the total amount of uptake varies between 36 and 46 Tg C yr-1 at a 90% confidence level. These results indicate that the reanalysis output data set can inform the management of the North West European shelf ecosystem, in relation to eutrophication, fishery, and variability of the carbon cycle.

Toward a chemical reanalysis in a coupled chemistry-climate model: An evaluation of MOPITT CO assimilation and its impact on tropospheric composition

NASA Astrophysics Data System (ADS)

Gaubert, B.; Arellano, A. F.; Barré, J.; Worden, H. M.; Emmons, L. K.; Tilmes, S.; Buchholz, R. R.; Vitt, F.; Raeder, K.; Collins, N.; Anderson, J. L.; Wiedinmyer, C.; Martinez Alonso, S.; Edwards, D. P.; Andreae, M. O.; Hannigan, J. W.; Petri, C.; Strong, K.; Jones, N.

2016-06-01

We examine in detail a 1 year global reanalysis of carbon monoxide (CO) that is based on joint assimilation of conventional meteorological observations and Measurement of Pollution in The Troposphere (MOPITT) multispectral CO retrievals in the Community Earth System Model (CESM). Our focus is to assess the impact to the chemical system when CO distribution is constrained in a coupled full chemistry-climate model like CESM. To do this, we first evaluate the joint reanalysis (MOPITT Reanalysis) against four sets of independent observations and compare its performance against a reanalysis with no MOPITT assimilation (Control Run). We then investigate the CO burden and chemical response with the aid of tagged sectoral CO tracers. We estimate the total tropospheric CO burden in 2002 (from ensemble mean and spread) to be 371 ± 12% Tg for MOPITT Reanalysis and 291 ± 9% Tg for Control Run. Our multispecies analysis of this difference suggests that (a) direct emissions of CO and hydrocarbons are too low in the inventory used in this study and (b) chemical oxidation, transport, and deposition processes are not accurately and consistently represented in the model. Increases in CO led to net reduction of OH and subsequent longer lifetime of CH4 (Control Run: 8.7 years versus MOPITT Reanalysis: 9.3 years). Yet at the same time, this increase led to 5-10% enhancement of Northern Hemisphere O3 and overall photochemical activity via HOx recycling. Such nonlinear effects further complicate the attribution to uncertainties in direct emissions alone. This has implications to chemistry-climate modeling and inversion studies of longer-lived species.

The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing.

PubMed

Wain, Karen E; Riggs, Erin; Hanson, Karen; Savage, Melissa; Riethmaier, Darlene; Muirhead, Andrea; Mitchell, Elyse; Packard, Bethanny Smith; Faucett, W Andrew

2012-10-01

The International Standards for Cytogenomic Arrays (ISCA) Consortium is a worldwide collaborative effort dedicated to optimizing patient care by improving the quality of chromosomal microarray testing. The primary effort of the ISCA Consortium has been the development of a database of copy number variants (CNVs) identified during the course of clinical microarray testing. This database is a powerful resource for clinicians, laboratories, and researchers, and can be utilized for a variety of applications, such as facilitating standardized interpretations of certain CNVs across laboratories or providing phenotypic information for counseling purposes when published data is sparse. A recognized limitation to the clinical utility of this database, however, is the quality of clinical information available for each patient. Clinical genetic counselors are uniquely suited to facilitate the communication of this information to the laboratory by virtue of their existing clinical responsibilities, case management skills, and appreciation of the evolving nature of scientific knowledge. We intend to highlight the critical role that genetic counselors play in ensuring optimal patient care through contributing to the clinical utility of the ISCA Consortium's database, as well as the quality of individual patient microarray reports provided by contributing laboratories. Current tools, paper and electronic forms, created to maximize this collaboration are shared. In addition to making a professional commitment to providing complete clinical information, genetic counselors are invited to become ISCA members and to become involved in the discussions and initiatives within the Consortium.

Assimilation of Ocean-Color Plankton Functional Types to Improve Marine Ecosystem Simulations

NASA Astrophysics Data System (ADS)

Ciavatta, S.; Brewin, R. J. W.; Skákala, J.; Polimene, L.; de Mora, L.; Artioli, Y.; Allen, J. I.

2018-02-01

We assimilated phytoplankton functional types (PFTs) derived from ocean color into a marine ecosystem model, to improve the simulation of biogeochemical indicators and emerging properties in a shelf sea. Error-characterized chlorophyll concentrations of four PFTs (diatoms, dinoflagellates, nanoplankton, and picoplankton), as well as total chlorophyll for comparison, were assimilated into a physical-biogeochemical model of the North East Atlantic, applying a localized Ensemble Kalman filter. The reanalysis simulations spanned the years 1998-2003. The skill of the reference and reanalysis simulations in estimating ocean color and in situ biogeochemical data were compared by using robust statistics. The reanalysis outperformed both the reference and the assimilation of total chlorophyll in estimating the ocean-color PFTs (except nanoplankton), as well as the not-assimilated total chlorophyll, leading the model to simulate better the plankton community structure. Crucially, the reanalysis improved the estimates of not-assimilated in situ data of PFTs, as well as of phosphate and pCO2, impacting the simulation of the air-sea carbon flux. However, the reanalysis increased further the model overestimation of nitrate, in spite of increases in plankton nitrate uptake. The method proposed here is easily adaptable for use with other ecosystem models that simulate PFTs, for, e.g., reanalysis of carbon fluxes in the global ocean and for operational forecasts of biogeochemical indicators in shelf-sea ecosystems.

Training analysis and reanalysis in the development of the psychoanalyst.

PubMed

Meyer, Jon K

2007-01-01

A psychoanalyst faces the extraordinary demand of becoming instrumental in the psychoanalytic process. In the candidate's attempt to rise to that expectation, the first step is the training analysis. As the center-piece of psychoanalytic education, it is no ordinary analysis and bears special burdens intrinsic to its multiple functions and institutionalization. Recognizing the difficulties of both analytic education and analytic practice, Freud suggested that the analyst be periodically reanalyzed; for many, reanalysis is integral to their analytic development. Indeed, an analyst is actually never "made" but is always "in the making," developing and maturing in life and in practice. Reanalysis serves to focus elements of transference and resistance, rework defenses, facilitate more extensive regression in the service of the ego, deepen emotional integration, rework those elements of psychoanalysis itself that have been incorporated into defensive structure, and further the maturation of the analyzing instrument. If analysis is our most powerful mode of initial education, reanalysis is the most powerful form of continuing education. That remarkably little attention has been paid to reanalysis is testimony to the infantile fantasies that remain invested in our personal analyses.

ELISA microarray technology as a high-throughput system for cancer biomarker validation

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

Zangar, Richard C.; Daly, Don S.; White, Amanda M.

A large gap currently exists between the ability to discover potential biomarkers and the ability to assess the real value of these proteins for cancer screening. One major challenge in biomarker validation is the inherent variability in biomarker levels. This variability stems from the diversity across the human population and the considerable molecular heterogeneity between individual tumors, even those that originate from a single tissue. Another major challenge with cancer screening is that most cancers are rare in the general population, meaning that the specificity of an assay must be very high if the number of false positive is notmore » going to be much greater than the number of true positives. Because of these challenges with biomarker validation, it is necessary to analysis of thousands of samples before a clear idea of the utility of a screening assay can be determined. Enzyme-linked immunosorbent assay (ELISA) microarray technology can simultaneously quantify levels of multiple proteins and has the potential to accelerate biomarker validation. In this review, we discuss current ELISA microarray technology and the enabling advances needed to achieve the reproducibility and throughput that are required to evaluate cancer biomarkers.« less

Reproducibility-optimized test statistic for ranking genes in microarray studies.

PubMed

Elo, Laura L; Filén, Sanna; Lahesmaa, Riitta; Aittokallio, Tero

2008-01-01

A principal goal of microarray studies is to identify the genes showing differential expression under distinct conditions. In such studies, the selection of an optimal test statistic is a crucial challenge, which depends on the type and amount of data under analysis. While previous studies on simulated or spike-in datasets do not provide practical guidance on how to choose the best method for a given real dataset, we introduce an enhanced reproducibility-optimization procedure, which enables the selection of a suitable gene- anking statistic directly from the data. In comparison with existing ranking methods, the reproducibilityoptimized statistic shows good performance consistently under various simulated conditions and on Affymetrix spike-in dataset. Further, the feasibility of the novel statistic is confirmed in a practical research setting using data from an in-house cDNA microarray study of asthma-related gene expression changes. These results suggest that the procedure facilitates the selection of an appropriate test statistic for a given dataset without relying on a priori assumptions, which may bias the findings and their interpretation. Moreover, the general reproducibilityoptimization procedure is not limited to detecting differential expression only but could be extended to a wide range of other applications as well.

A new voxel-based model for the determination of atmospheric weighted mean temperature in GPS atmospheric sounding

NASA Astrophysics Data System (ADS)

He, Changyong; Wu, Suqin; Wang, Xiaoming; Hu, Andong; Wang, Qianxin; Zhang, Kefei

2017-06-01

The Global Positioning System (GPS) is a powerful atmospheric observing system for determining precipitable water vapour (PWV). In the detection of PWV using GPS, the atmospheric weighted mean temperature (Tm) is a crucial parameter for the conversion of zenith tropospheric delay (ZTD) to PWV since the quality of PWV is affected by the accuracy of Tm. In this study, an improved voxel-based Tm model, named GWMT-D, was developed using global reanalysis data over a 4-year period from 2010 to 2013 provided by the United States National Centers for Environmental Prediction (NCEP). The performance of GWMT-D was assessed against three existing empirical Tm models - GTm-III, GWMT-IV, and GTmN - using different data sources in 2014 - the NCEP reanalysis data, surface Tm data provided by Global Geodetic Observing System and radiosonde measurements. The results show that the new GWMT-D model outperforms all the other three models with a root-mean-square error of less than 5.0 K at different altitudes over the globe. The new GWMT-D model can provide a practical alternative Tm determination method in real-time GPS-PWV remote sensing systems.

Evaluation of atmospheric precipitable water from reanalysis products using homogenized radiosonde observations over China

NASA Astrophysics Data System (ADS)

Zhao, Tianbao; Wang, Juanhuai; Dai, Aiguo

2015-10-01

Many multidecadal atmospheric reanalysis products are available now, but their consistencies and reliability are far from perfect. In this study, atmospheric precipitable water (PW) from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR), NCEP/Department of Energy (DOE), Modern Era Retrospective-Analysis for Research and Applications (MERRA), Japanese 55 year Reanalysis (JRA-55), JRA-25, ERA-Interim, ERA-40, Climate Forecast System Reanalysis (CFSR), and 20th Century Reanalysis version 2 is evaluated against homogenized radiosonde observations over China during 1979-2012 (1979-2001 for ERA-40). Results suggest that the PW biases in the reanalyses are within ˜20% for most of northern and eastern China, but the reanalyses underestimate the observed PW by 20%-40% over western China and by ˜60% over the southwestern Tibetan Plateau. The newer-generation reanalyses (e.g., JRA25, JRA55, CFSR, and ERA-Interim) have smaller root-mean-square error than the older-generation ones (NCEP/NCAR, NCEP/DOE, and ERA-40). Most of the reanalyses reproduce well the observed PW climatology and interannual variations over China. However, few reanalyses capture the observed long-term PW changes, primarily because they show spurious wet biases before about 2002. This deficiency results mainly from the discontinuities contained in reanalysis relative humidity fields in the middle-lower troposphere due to the wet bias in older radiosonde records that are assimilated into the reanalyses. An empirical orthogonal function (EOF) analysis revealed two leading modes that represent the long-term PW changes and El Niño-Southern Oscillation-related interannual variations with robust spatial patterns. The reanalysis products, especially the MERRA and JRA-25, roughly capture these EOF modes, which account for over 50% of the total variance. The results show that even during the post-1979 satellite era, discontinuities in radiosonde data can still induce large spurious long-term changes in reanalysis PW and other related fields. Thus, more efforts are needed to remove spurious changes in input data for future long-term reanalyses.

Japanese 25-year reanalysis (JRA-25)

NASA Astrophysics Data System (ADS)

Ohkawara, Nozomu

2006-12-01

A long term global atmospheric reanalysis Japanese 25-year Reanalysis (JRA-25) which covers from 1979 to 2004 was completed using the Japan Meteorological Agency (JMA) numerical assimilation and forecast system. This is the first long term reanalysis undertaken in Asia. JMA's latest numerical assimilation system, and observational data collected as much as possible, were used in JRA-25 to generate a consistent and high quality reanalysis dataset to contribute to climate research and operational work. One purpose of JRA-25 is to enhance to a high quality the analysis in the Asian region. 6-hourly data assimilation cycles were performed and produced 6-hourly atmospheric analysis and forecast fields with various kinds of physical variables. The global model used in JRA-25 has a spectral resolution of T106 (equivalent to a horizontal grid size of around 120km) and 40 vertical layers with the top level at 0.4hPa. For observational data, a great deal of satellite data was used in addition to conventional surface and upper air data. Atmospheric Motion Vector (AMV) data retrieved from geostationary satellites, brightness temperature (TBB) data from TIROS Operational Vertical Sounder (TOVS), precipitable water retrieved from radiance of microwave radiometer from orbital satellites and some other satellite data were assimilated with 3-dimensional variational method (3DVAR). Many advantages have been found in the JRA-25 reanalysis. Firstly, forecast 6-hour global total precipitation in JRA-25 performs well, distribution and amount are properly represented both in space and time. JRA-25 has the best performance compared to other reanalysis with respect to time series of global precipitation over many years, with few unrealistic variations caused by degraded quality of satellite data due to volcanic eruptions. Secondly, JRA-25 is the first reanalysis which assimilated wind profiles surrounding tropical cyclones retrieved from historical best track information; tropical cyclones were analyzed correctly in all the global regions. Additionally, low-level cloud along the subtropical western coast of continents is forecast very accurately, and snow depth analysis is also good.

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.

Developing a high-resolution regional atmospheric reanalysis for Australia

NASA Astrophysics Data System (ADS)

White, Christopher; Fox-Hughes, Paul; Su, Chun-Hsu; Jakob, Dörte; Kociuba, Greg; Eisenberg, Nathan; Steinle, Peter; Harris, Rebecca; Corney, Stuart; Love, Peter; Remenyi, Tomas; Chladil, Mark; Bally, John; Bindoff, Nathan

2017-04-01

A dynamically consistent, long-term atmospheric reanalysis can be used to support high-quality assessments of environmental risk and likelihood of extreme events. Most reanalyses are presently based on coarse-scale global systems that are not suitable for regional assessments in fire risk, water and natural resources, amongst others. The Australian Bureau of Meteorology is currently working to close this gap by producing a high-resolution reanalysis over the Australian and New Zealand region to construct a sequence of atmospheric conditions at sub-hourly intervals over the past 25 years from 1990. The Australia reanalysis consists of a convective-scale analysis nested within a 12 km regional-scale reanalysis, which is bounded by a coarse-scale ERA-Interim reanalysis that provides the required boundary and initial conditions. We use an unchanging atmospheric modelling suite based on the UERRA system used at the UK Met Office and the more recent version of the Bureau of Meteorology's operational numerical prediction model used in ACCESS-R (Australian Community Climate and Earth-System Simulator-Regional system). An advanced (4-dimensional variational) data assimilation scheme is used to optimally combine model physics with multiple observations from aircrafts, sondes, surface observations and satellites to create a best estimate of state of the atmosphere over a 6-hour moving window. This analysis is in turn used to drive a higher-resolution (1.5 km) downscaling model over selected subdomains within Australia, currently eastern New South Wales and Tasmania, with the capability to support this anywhere in the Australia-New Zealand domain. The temporal resolution of the gridded analysis fields for both the regional and higher-resolution subdomains are generally one hour, with many fields such as 10 m winds and 2 m temperatures available every 10 minutes. The reanalysis also produces many other variables that include wind, temperature, moisture, pressure, cloud cover, precipitation, evaporation, soil water, and energy fluxes. In this presentation, we report on the implementation of the Australia regional reanalysis and results from first stages of the project, with a focus on the Tasmanian subdomain. An initial benchmarking 1.5 km data set - referred to as the 'Initial Analysis' - has been constructed over the subdomains consisting of regridded and harmonised analysis and short-term forecast fields from the operational ACCESS-C model using the past 5 years (2011-2015) of archived data. Evaluation of the Initial Analysis against surface observations from automatic weather stations indicate changes in model skills over time that may be attributed to changes in NWP and assimilation systems, and model cycling frequency. Preliminary evaluations of the reanalysis across Tasmania and its inter-comparisons with the Initial Analysis and the ERA-Interim reanalysis products will be presented, including some features across the Tasmanian subdomain such as means and extremes of analysed weather variables. Finally, we describe a number of applications across Tasmania of the reanalysis of immediate interest to meteorologists, fire and landscape managers and other members of the emergency management community, including the use of the data to create post-processed fields such as soil dryness, tornados and fire danger indices for forest fire danger risk assessment, including a climatology of Continuous Haines Index.

NVAP

Atmospheric Science Data Center

2013-09-05

... of creating stable, community accepted Earth System Data Records (ESDRs) for a variety of geophysical time series. A reanalysis and ... of creating stable, community accepted Earth System Data Records (ESDRs) for a variety of geophysical time series. A reanalysis and ...

Dynamical Downscaling of Typhoon Vera (1959) and related Storm Surge based on JRA-55 Reanalysis

NASA Astrophysics Data System (ADS)

Ninomiya, J.; Takemi, T.; Mori, N.; Shibutani, Y.; Kim, S.

2015-12-01

Typhoon Vera in 1959 is historical extreme typhoon that caused severest typhoon damage mainly due to the storm surge up to 389 cm in Japan. Vera developed 895 hPa on offshore and landed with 929.2 hPa. There are many studies of the dynamical downscaling of Vera but it is difficult to simulate accurately because of the lack of the accuracy of global reanalysis data. This study carried out dynamical downscaling experiment of Vera using WRF downscaling forced by JRA-55 that are latest atmospheric model and reanalysis data. In this study, the reproducibility of five global reanalysis data for Typhoon Vera were compered. Comparison shows that reanalysis data doesn't have strong typhoon information except for JRA-55, so that downscaling with conventional reanalysis data goes wrong. The dynamical downscaling method for storm surge is studied very much (e.g. choice of physical model, nudging, 4D-VAR, bogus and so on). In this study, domain size and resolution of the coarse domain were considered. The coarse domain size influences the typhoon route and central pressure, and larger domain restrains the typhoon strength. The results of simulations with different domain size show that the threshold of developing restrain is whether the coarse domain fully includes the area of wind speed more than 15 m/s around the typhoon. The results of simulations with different resolution show that the resolution doesn't affect the typhoon route, and higher resolution gives stronger typhoon simulation.

Detection of Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia in primary endodontic infections in a Chinese population.

PubMed

Cao, H; Qi, Z; Jiang, H; Zhao, J; Liu, Z; Tang, Z

2012-08-01

To assess the prevalence of three black-pigmented bacterial species (Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia) using microarray technology in root canals of teeth associated with primary endodontic infections in a Chinese population. Microbial samples were taken from root canals of 80 teeth with pulp necrosis and primary endodontic infections in a Chinese population. DNA extracted from the samples was amplified by PCR with universal bacterial primers based on 16S rRNA gene sequences, and the products hybridized with the microarrays in which the specific oligonucleotide probes were added. The results of hybridization were screened by a confocal laser scanner. Pearson chi-square test and the two-sided Fisher exact test were used to analyse whether a significant association existed between the species and symptoms as well as in co-existence of two target organisms by a statistical software package (SAS 8.02). The 16S rRNA gene microarray detected at least one of the three test species in 76% of the study teeth. P. endodontalis, P. gingivalis and P. intermedia were found in 50%, 33% and 45%, respectively. A significant association was found in the presence of the pair P. endodontalis / P. gingivalis (P < 0.005). Both P. endodontalis (P <0.05) and P. gingivalis (P <0.005) had a statistically significant association with the presence of a sinus tract. The simultaneous presence of P. endodontalis and P. gingivalis was also associated with the presence of a sinus tract (P<0.005) and abscess formation (P<0.05). The three black-pigmented bacteria were prevalent in teeth with pulp necrosis and primary endodontic infections in a Chinese population. P. gingivalis and P. endodontalis were associated with the presence of sinus tract and abscess formation. © 2012 International Endodontic Journal.

Novel harmonic regularization approach for variable selection in Cox's proportional hazards model.

PubMed

Chu, Ge-Jin; Liang, Yong; Wang, Jia-Xuan

2014-01-01

Variable selection is an important issue in regression and a number of variable selection methods have been proposed involving nonconvex penalty functions. In this paper, we investigate a novel harmonic regularization method, which can approximate nonconvex Lq  (1/2 < q < 1) regularizations, to select key risk factors in the Cox's proportional hazards model using microarray gene expression data. The harmonic regularization method can be efficiently solved using our proposed direct path seeking approach, which can produce solutions that closely approximate those for the convex loss function and the nonconvex regularization. Simulation results based on the artificial datasets and four real microarray gene expression datasets, such as real diffuse large B-cell lymphoma (DCBCL), the lung cancer, and the AML datasets, show that the harmonic regularization method can be more accurate for variable selection than existing Lasso series methods.

Prediction of clinical behaviour and treatment for cancers.

PubMed

Futschik, Matthias E; Sullivan, Mike; Reeve, Anthony; Kasabov, Nikola

2003-01-01

Prediction of clinical behaviour and treatment for cancers is based on the integration of clinical and pathological parameters. Recent reports have demonstrated that gene expression profiling provides a powerful new approach for determining disease outcome. If clinical and microarray data each contain independent information then it should be possible to combine these datasets to gain more accurate prognostic information. Here, we have used existing clinical information and microarray data to generate a combined prognostic model for outcome prediction for diffuse large B-cell lymphoma (DLBCL). A prediction accuracy of 87.5% was achieved. This constitutes a significant improvement compared to the previously most accurate prognostic model with an accuracy of 77.6%. The model introduced here may be generally applicable to the combination of various types of molecular and clinical data for improving medical decision support systems and individualising patient care.

"Set in Stone" or "Ray of Hope": Parents' Beliefs about Cause and Prognosis after Genomic Testing of Children Diagnosed with ASD

ERIC Educational Resources Information Center

Reiff, Marian; Bugos, Eva; Giarelli, Ellen; Bernhardt, Barbara A.; Spinner, Nancy B.; Sankar, Pamela L.; Mulchandani, Surabhi

2017-01-01

Despite increasing utilization of chromosomal microarray analysis (CMA) for autism spectrum disorders (ASD), limited information exists about how results influence parents' beliefs about etiology and prognosis. We conducted in-depth interviews and surveys with 57 parents of children with ASD who received CMA results categorized as pathogenic,…

An 8-Year, High-Resolution Reanalysis of Atmospheric CO2 Mixing Ratios Based on OCO-2 and GOSAT-ACOS Retrievals

NASA Technical Reports Server (NTRS)

Weir, B.; Chatterjee, A.; Ott, L. E.; Pawson, S.

2017-01-01

The NASA GMAO (Global Modeling and Assimilation Office) reanalysis blends OCO-2 (Orbiting Carbon Observatory 2) and GOSAT-ACOS (Greenhouse Gases Observing Satellite-Atmospheric Carbon Observations from Space) retrievals (top) with GEOS (Goddard Earth Observing System) model predictions (bottom) to estimate the full 3D (three-dimensional) state of CO2 every 3 hours (middle). This poster describes monthly atmospheric growth rates derived from the reanalysis and an application to aircraft data with the potential to aid bias correction.

GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms.

PubMed

Jani, Saurin D; Argraves, Gary L; Barth, Jeremy L; Argraves, W Scott

2010-04-01

An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases. Here we describe GeneMesh, a web-based program that facilitates analysis of DNA microarray gene expression data. GeneMesh relates genes in a query set to categories available in the Medical Subject Headings (MeSH) hierarchical index. The interface enables hypothesis driven relational analysis to a specific MeSH subcategory (e.g., Cardiovascular System, Genetic Processes, Immune System Diseases etc.) or unbiased relational analysis to broader MeSH categories (e.g., Anatomy, Biological Sciences, Disease etc.). Genes found associated with a given MeSH category are dynamically linked to facilitate tabular and graphical depiction of Entrez Gene information, Gene Ontology information, KEGG metabolic pathway diagrams and intermolecular interaction information. Expression intensity values of groups of genes that cluster in relation to a given MeSH category, gene ontology or pathway can be displayed as heat maps of Z score-normalized values. GeneMesh operates on gene expression data derived from a number of commercial microarray platforms including Affymetrix, Agilent and Illumina. GeneMesh is a versatile web-based tool for testing and developing new hypotheses through relating genes in a query set (e.g., differentially expressed genes from a DNA microarray experiment) to descriptors making up the hierarchical structure of the National Library of Medicine controlled vocabulary thesaurus, MeSH. The system further enhances the discovery process by providing links between sets of genes associated with a given MeSH category to a rich set of html linked tabular and graphic information including Entrez Gene summaries, gene ontologies, intermolecular interactions, overlays of genes onto KEGG pathway diagrams and heatmaps of expression intensity values. GeneMesh is freely available online at http://proteogenomics.musc.edu/genemesh/.

Toward a 35-years North American Precipitation and Surface Reanalysis

NASA Astrophysics Data System (ADS)

Gasset, N.; Fortin, V.

2017-12-01

In support of the International Watersheds Initiative (IWI) of the International Joint Commission (IJC), a 35-years precipitation and surface reanalysis covering North America at a 3-hours and 15-km resolution is currently being developed at the Canadian Meteorological Centre (CMC). A deterministic reforecast / dynamical downscaling approach is followed where a global reanalysis (ERA-Interim) is used as initial condition of the Global Environmental Multi-scale model (GEM). Moreover, the latter is coupled with precipitation and surface data assimilation systems, i.e. the Canadian Precipitation Analysis (CaPA) and the Canadian Land Data Assimilation System (CaLDAS). While optimized to be more computationally efficient in the context of a reforecast experiment, all systems used are closely related to model versions and configurations currently run operationally at CMC, meaning they have undergone a strict and thorough validation procedure.As a proof of concept and in order to identify the optimal set-up before achieving the 35-years reanalysis, several configurations of the approach are evaluated for the years 2010-2014 using both standard CMC validation methodology as well as more dedicated scores such as comparison against the currently available products (North American Regional Reanalysis, MERRA-Land and the newly released ERA5 reanalysis). A special attention is dedicated to the evaluation of analysed variables, i.e. precipitation, snow depth, surface/ground temperature and moisture over the whole domain of interest. Results from these preliminary samples are very encouraging and the optimal set-up is identified. The coupled approach, i.e. GEM+CaPA/CaLDAS, always shows clear improvements over classical reforecast and dynamical downscaling where surface observations are present. Furthermore, results are inline or better than currently available products and the reference CMC operational approach that was operated from 2012 to 2016 (GEM 3.3, 10-km resolution). This reanalysis will allow for bias correction of current estimates and forecasts, and help decision maker understand and communicate by how much the current forecasted state of the system differs from the recent past.

Steps towards a consistent Climate Forecast System Reanalysis wave hindcast (1979-2016)

NASA Astrophysics Data System (ADS)

Stopa, Justin E.; Ardhuin, Fabrice; Huchet, Marion; Accensi, Mickael

2017-04-01

Surface gravity waves are being increasingly recognized as playing an important role within the climate system. Wave hindcasts and reanalysis products of long time series (>30 years) have been instrumental in understanding and describing the wave climate for the past several decades and have allowed a better understanding of extreme waves and inter-annual variability. Wave hindcasts have the advantage of covering the oceans in higher space-time resolution than possible with conventional observations from satellites and buoys. Wave reanalysis systems like ECWMF's ERA-Interim directly included a wave model that is coupled to the ocean and atmosphere, otherwise reanalysis wind fields are used to drive a wave model to reproduce the wave field in long time series. The ERA Interim dataset is consistent in time, but cannot adequately resolve extreme waves. On the other hand, the NCEP Climate Forecast System (CFSR) wind field better resolves the extreme wind speeds, but suffers from discontinuous features in time which are due to the quantity and quality of the remote sensing data incorporated into the product. Therefore, a consistent hindcast that resolves the extreme waves still alludes us limiting our understanding of the wave climate. In this study, we systematically correct the CFSR wind field to reproduce a homogeneous wave field in time. To verify the homogeneity of our hindcast we compute error metrics on a monthly basis using the observations from a merged altimeter wave database which has been calibrated and quality controlled from 1985-2016. Before 1985 only few wave observations exist and are limited to a select number of wave buoys mostly in the North Hemisphere. Therefore we supplement our wave observations with seismic data which responds to nonlinear wave interactions created by opposing waves with nearly equal wavenumbers. Within the CFSR wave hindcast, we find both spatial and temporal discontinuities in the error metrics. The Southern Hemisphere often has wind speed biases larger than the Northern Hemisphere and we propose a simple correction to reduce these features by applying a taper shaped by a half-Hanning window. The discontinuous features in time are corrected by scaling the entire wind field by percentages ranging typically ranging from 1-3%. Our analysis is performed on monthly time series and we expect the monthly statistics to be more adequate for climate studies.

Projecting Wind Energy Potential Under Climate Change with Ensemble of Climate Model Simulations

NASA Astrophysics Data System (ADS)

Jain, A.; Shashikanth, K.; Ghosh, S.; Mukherjee, P. P.

2013-12-01

Recent years have witnessed an increasing global concern over energy sustainability and security, triggered by a number of issues, such as (though not limited to): fossil fuel depletion, energy resource geopolitics, economic efficiency versus population growth debate, environmental concerns and climate change. Wind energy is a renewable and sustainable form of energy in which wind turbines convert the kinetic energy of wind into electrical energy. Global warming and differential surface heating may significantly impact the wind velocity and hence the wind energy potential. Sustainable design of wind mills requires understanding the impacts of climate change on wind energy potential, which we evaluate here with multiple General Circulation Models (GCMs). GCMs simulate the climate variables globally considering the greenhouse emission scenarios provided as Representation Concentration path ways (RCPs). Here we use new generation climate model outputs obtained from Coupled model Intercomparison Project 5(CMIP5). We first compute the wind energy potential with reanalysis data (NCEP/ NCAR), at a spatial resolution of 2.50, where the gridded data is fitted to Weibull distribution and with the Weibull parameters, the wind energy densities are computed at different grids. The same methodology is then used, to CMIP5 outputs (resultant of U-wind and V-wind) of MRI, CMCC, BCC, CanESM, and INMCM4 for historical runs. This is performed separately for four seasons globally, MAM, JJA, SON and DJF. We observe the muti-model average of wind energy density for historic period has significant bias with respect to that of reanalysis product. Here we develop a quantile based superensemble approach where GCM quantiles corresponding to selected CDF values are regressed to reanalysis data. It is observed that this regression approach takes care of both, bias in GCMs and combination of GCMs. With superensemble, we observe that the historical wind energy density resembles quite well with reanalysis/ observed output. We apply the same for future under RCP scenarios. We observe spatially and temporally varying global change of wind energy density. The underlying assumption is that the regression relationship will also hold good for future. The results highlight the needs to change the design standards of wind mills at different locations, considering climate change and at the same time the requirement of height modifications for existing mills to produce same energy in future.

Atmospheric response to Saharan dust deduced from ECMWF reanalysis increments

NASA Astrophysics Data System (ADS)

Kishcha, P.; Alpert, P.; Barkan, J.; Kirchner, I.; Machenhauer, B.

2003-04-01

This study focuses on the atmospheric temperature response to dust deduced from a new source of data - the European Reanalysis (ERA) increments. These increments are the systematic errors of global climate models, generated in reanalysis procedure. The model errors result not only from the lack of desert dust but also from a complex combination of many kinds of model errors. Over the Sahara desert the dust radiative effect is believed to be a predominant model defect which should significantly affect the increments. This dust effect was examined by considering correlation between the increments and remotely-sensed dust. Comparisons were made between April temporal variations of the ERA analysis increments and the variations of the Total Ozone Mapping Spectrometer aerosol index (AI) between 1979 and 1993. The distinctive structure was identified in the distribution of correlation composed of three nested areas with high positive correlation (> 0.5), low correlation, and high negative correlation (<-0.5). The innermost positive correlation area (PCA) is a large area near the center of the Sahara desert. For some local maxima inside this area the correlation even exceeds 0.8. The outermost negative correlation area (NCA) is not uniform. It consists of some areas over the eastern and western parts of North Africa with a relatively small amount of dust. Inside those areas both positive and negative high correlations exist at pressure levels ranging from 850 to 700 hPa, with the peak values near 775 hPa. Dust-forced heating (cooling) inside the PCA (NCA) is accompanied by changes in the static stability of the atmosphere above the dust layer. The reanalysis data of the European Center for Medium Range Weather Forecast(ECMWF) suggests that the PCA (NCA) corresponds mainly to anticyclonic (cyclonic) flow, negative (positive) vorticity, and downward (upward) airflow. These facts indicate an interaction between dust-forced heating /cooling and atmospheric circulation. The April correlation results are supported by the analysis of vertical distribution of dust concentration, derived from the 24-hour dust prediction system at Tel Aviv University (website: http://earth.nasa.proj.ac.il/dust/current/). For other months the analysis is more complicated because of the essential increasing of humidity along with the northward progress of the ITCZ and the significant impact on the increments.

A novel feature extraction approach for microarray data based on multi-algorithm fusion

PubMed Central

Jiang, Zhu; Xu, Rong

2015-01-01

Feature extraction is one of the most important and effective method to reduce dimension in data mining, with emerging of high dimensional data such as microarray gene expression data. Feature extraction for gene selection, mainly serves two purposes. One is to identify certain disease-related genes. The other is to find a compact set of discriminative genes to build a pattern classifier with reduced complexity and improved generalization capabilities. Depending on the purpose of gene selection, two types of feature extraction algorithms including ranking-based feature extraction and set-based feature extraction are employed in microarray gene expression data analysis. In ranking-based feature extraction, features are evaluated on an individual basis, without considering inter-relationship between features in general, while set-based feature extraction evaluates features based on their role in a feature set by taking into account dependency between features. Just as learning methods, feature extraction has a problem in its generalization ability, which is robustness. However, the issue of robustness is often overlooked in feature extraction. In order to improve the accuracy and robustness of feature extraction for microarray data, a novel approach based on multi-algorithm fusion is proposed. By fusing different types of feature extraction algorithms to select the feature from the samples set, the proposed approach is able to improve feature extraction performance. The new approach is tested against gene expression dataset including Colon cancer data, CNS data, DLBCL data, and Leukemia data. The testing results show that the performance of this algorithm is better than existing solutions. PMID:25780277

A novel feature extraction approach for microarray data based on multi-algorithm fusion.

PubMed

Jiang, Zhu; Xu, Rong

2015-01-01

Feature extraction is one of the most important and effective method to reduce dimension in data mining, with emerging of high dimensional data such as microarray gene expression data. Feature extraction for gene selection, mainly serves two purposes. One is to identify certain disease-related genes. The other is to find a compact set of discriminative genes to build a pattern classifier with reduced complexity and improved generalization capabilities. Depending on the purpose of gene selection, two types of feature extraction algorithms including ranking-based feature extraction and set-based feature extraction are employed in microarray gene expression data analysis. In ranking-based feature extraction, features are evaluated on an individual basis, without considering inter-relationship between features in general, while set-based feature extraction evaluates features based on their role in a feature set by taking into account dependency between features. Just as learning methods, feature extraction has a problem in its generalization ability, which is robustness. However, the issue of robustness is often overlooked in feature extraction. In order to improve the accuracy and robustness of feature extraction for microarray data, a novel approach based on multi-algorithm fusion is proposed. By fusing different types of feature extraction algorithms to select the feature from the samples set, the proposed approach is able to improve feature extraction performance. The new approach is tested against gene expression dataset including Colon cancer data, CNS data, DLBCL data, and Leukemia data. The testing results show that the performance of this algorithm is better than existing solutions.

Transcriptome-Wide Mega-Analyses Reveal Joint Dysregulation of Immunologic Genes and Transcription Regulators in Brain and Blood in Schizophrenia

PubMed Central

Hess, Jonathan L.; Tylee, Daniel S.; Barve, Rahul; de Jong, Simone; Ophoff, Roel A.; Kumarasinghe, Nishantha; Tooney, Paul; Schall, Ulrich; Gardiner, Erin; Beveridge, Natalie Jane; Scott, Rodney J.; Yasawardene, Surangi; Perera, Antionette; Mendis, Jayan; Carr, Vaughan; Kelly, Brian; Cairns, Murray; Tsuang, Ming T.; Glatt, Stephen J.

2016-01-01

The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n = 315) and from ex-vivo blood tissues (n = 578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia. PMID:27450777

Transcriptome-wide mega-analyses reveal joint dysregulation of immunologic genes and transcription regulators in brain and blood in schizophrenia.

PubMed

Hess, Jonathan L; Tylee, Daniel S; Barve, Rahul; de Jong, Simone; Ophoff, Roel A; Kumarasinghe, Nishantha; Tooney, Paul; Schall, Ulrich; Gardiner, Erin; Beveridge, Natalie Jane; Scott, Rodney J; Yasawardene, Surangi; Perera, Antionette; Mendis, Jayan; Carr, Vaughan; Kelly, Brian; Cairns, Murray; Tsuang, Ming T; Glatt, Stephen J

2016-10-01

The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n=315) and from ex-vivo blood tissues (n=578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia. Published by Elsevier B.V.

Supervised group Lasso with applications to microarray data analysis

PubMed Central

Ma, Shuangge; Song, Xiao; Huang, Jian

2007-01-01

Background A tremendous amount of efforts have been devoted to identifying genes for diagnosis and prognosis of diseases using microarray gene expression data. It has been demonstrated that gene expression data have cluster structure, where the clusters consist of co-regulated genes which tend to have coordinated functions. However, most available statistical methods for gene selection do not take into consideration the cluster structure. Results We propose a supervised group Lasso approach that takes into account the cluster structure in gene expression data for gene selection and predictive model building. For gene expression data without biological cluster information, we first divide genes into clusters using the K-means approach and determine the optimal number of clusters using the Gap method. The supervised group Lasso consists of two steps. In the first step, we identify important genes within each cluster using the Lasso method. In the second step, we select important clusters using the group Lasso. Tuning parameters are determined using V-fold cross validation at both steps to allow for further flexibility. Prediction performance is evaluated using leave-one-out cross validation. We apply the proposed method to disease classification and survival analysis with microarray data. Conclusion We analyze four microarray data sets using the proposed approach: two cancer data sets with binary cancer occurrence as outcomes and two lymphoma data sets with survival outcomes. The results show that the proposed approach is capable of identifying a small number of influential gene clusters and important genes within those clusters, and has better prediction performance than existing methods. PMID:17316436

Testing forward model against OCO-2 and TANSO-FTS/GOSAT observed spectra in near infrared range

NASA Astrophysics Data System (ADS)

Zadvornykh, Ilya V.; Gribanov, Konstantin G.

2015-11-01

An existing software package FIRE-ARMS (Fine InfraRed Explorer for Atmospheric Remote MeasurementS) was modified by embedding vector radiative transfer model VLIDORT. Thus the program tool includes both thermal (TIR) and near infrared (NIR) regions. We performed forward simulation of near infrared spectra on the top of the atmosphere for outgoing radiation accounting multiple scattering in cloudless atmosphere. Simulated spectra are compared with spectra measured by TANSO-FTS/GOSAT and OCO-2 in the condition of cloudless atmosphere over Western Siberia. NCEP/NCAR reanalysis data were used to complete model atmosphere.

Impact of bias-corrected reanalysis-derived lateral boundary conditions on WRF simulations

NASA Astrophysics Data System (ADS)

Moalafhi, Ditiro Benson; Sharma, Ashish; Evans, Jason Peter; Mehrotra, Rajeshwar; Rocheta, Eytan

2017-08-01

Lateral and lower boundary conditions derived from a suitable global reanalysis data set form the basis for deriving a dynamically consistent finer resolution downscaled product for climate and hydrological assessment studies. A problem with this, however, is that systematic biases have been noted to be present in the global reanalysis data sets that form these boundaries, biases which can be carried into the downscaled simulations thereby reducing their accuracy or efficacy. In this work, three Weather Research and Forecasting (WRF) model downscaling experiments are undertaken to investigate the impact of bias correcting European Centre for Medium range Weather Forecasting Reanalysis ERA-Interim (ERA-I) atmospheric temperature and relative humidity using Atmospheric Infrared Sounder (AIRS) satellite data. The downscaling is performed over a domain centered over southern Africa between the years 2003 and 2012. The sample mean and the mean as well as standard deviation at each grid cell for each variable are used for bias correction. The resultant WRF simulations of near-surface temperature and precipitation are evaluated seasonally and annually against global gridded observational data sets and compared with ERA-I reanalysis driving field. The study reveals inconsistencies between the impact of the bias correction prior to downscaling and the resultant model simulations after downscaling. Mean and standard deviation bias-corrected WRF simulations are, however, found to be marginally better than mean only bias-corrected WRF simulations and raw ERA-I reanalysis-driven WRF simulations. Performances, however, differ when assessing different attributes in the downscaled field. This raises questions about the efficacy of the correction procedures adopted.

Severe Weather Environments in Atmospheric Reanalyses

NASA Astrophysics Data System (ADS)

King, A. T.; Kennedy, A. D.

2017-12-01

Atmospheric reanalyses combine historical observation data using a fixed assimilation scheme to achieve a dynamically coherent representation of the atmosphere. How well these reanalyses represent severe weather environments via proxies is poorly defined. To quantify the performance of reanalyses, a database of proximity soundings near severe storms from the Rapid Update Cycle 2 (RUC-2) model will be compared to a suite of reanalyses including: North American Reanalysis (NARR), European Interim Reanalysis (ERA-Interim), 2nd Modern-Era Retrospective Reanalysis for Research and Applications (MERRA-2), Japanese 55-year Reanalysis (JRA-55), 20th Century Reanalysis (20CR), and Climate Forecast System Reanalysis (CFSR). A variety of severe weather parameters will be calculated from these soundings including: convective available potential energy (CAPE), storm relative helicity (SRH), supercell composite parameter (SCP), and significant tornado parameter (STP). These soundings will be generated using the SHARPpy python module, which is an open source tool used to calculate severe weather parameters. Preliminary results indicate that the NARR and JRA55 are significantly more skilled at producing accurate severe weather environments than the other reanalyses. The primary difference between these two reanalyses and the remaining reanalyses is a significant negative bias for thermodynamic parameters. To facilitate climatological studies, the scope of work will be expanded to compute these parameters for the entire domain and duration of select renalyses. Preliminary results from this effort will be presented and compared to observations at select locations. This dataset will be made pubically available to the larger scientific community, and details of this product will be provided.

REMO poor man's reanalysis

NASA Astrophysics Data System (ADS)

Ries, H.; Moseley, C.; Haensler, A.

2012-04-01

Reanalyses depict the state of the atmosphere as a best fit in space and time of many atmospheric observations in a physically consistent way. By essentially solving the data assimilation problem in a very accurate manner, reanalysis results can be used as reference for model evaluation procedures and as forcing data sets for different model applications. However, the spatial resolution of the most common and accepted reanalysis data sets (e.g. JRA25, ERA-Interim) ranges from approximately 124 km to 80 km. This resolution is too coarse to simulate certain small scale processes often associated with extreme events. In addition, many models need higher resolved forcing data ( e.g. land-surface models, tools for identifying and assessing hydrological extremes). Therefore we downscaled the ERA-Interim reanalysis over the EURO-CORDEX-Domain for the time period 1989 to 2008 to a horizontal resolution of approximately 12 km. The downscaling is performed by nudging REMO-simulations to lower and lateral boundary conditions of the reanalysis, and by re-initializing the model every 24 hours ("REMO in forecast mode"). In this study the three following questions will be addressed: 1.) Does the REMO poor man's reanalysis meet the needs (accuracy, extreme value distribution) in validation and forcing? 2.) What lessons can be learned about the model used for downscaling? As REMO is used as a pure downscaling procedure, any systematic deviations from ERA-Interim result from poor process modelling but not from predictability limitations. 3.) How much small scale information generated by the downscaling model is lost with frequent initializations? A comparison to a simulation that is performed in climate mode will be presented.

Development of the NHM-LETKF regional reanalysis system assimilating conventional observations only

NASA Astrophysics Data System (ADS)

Fukui, S.; Iwasaki, T.; Saito, K. K.; Seko, H.; Kunii, M.

2016-12-01

The information about long-term high-resolution atmospheric fields is very useful for studying meso-scale responses to climate change or analyzing extreme events. We are developing a NHM-LETKF (the local ensemble transform Kalman filter with the nonhydrostatic model of the Japan Meteorological Agency (JMA)) regional reanalysis system assimilating only conventional observations that are available over about 60 years such as surface observations at observatories and upper air observations with radiosondes. The domain covers Japan and its surroundings. Before the long-term reanalysis is performed, an experiment using the system was conducted over August in 2014 in order to identify effectiveness and problems of the regional reanalysis system. In this study, we investigated the six-hour accumulated precipitations obtained by integration from the analysis fields. The reproduced precipitation was compared with the JMA's Radar/Rain-gauge Analyzed Precipitation data over Japan islands and the precipitation of JRA-55, which is used as lateral boundary conditions. The comparisons reveal the underestimation of the precipitation in the regional reanalysis. The underestimation is improved by extending the forecast time. In the regional reanalysis system, the analysis fields are derived using the ensemble mean fields, where the conflicting components among ensemble members are filtered out. Therefore, it is important to tune the inflation factor and lateral boundary perturbations not to smooth the analysis fields excessively and to consider more time to spin-up the fields. In the extended run, the underestimation still remains. This implies that the underestimation is attributed to the forecast model itself as well as the analysis scheme.

Impact of DYNAMO observations on NASA GEOS-5 reanalyses and the representation of MJO initiation

NASA Astrophysics Data System (ADS)

Achuthavarier, D.; Wang, H.; Schubert, S. D.; Sienkiewicz, M.

2017-01-01

This study examines the impact of the Dynamics of the Madden-Julian Oscillation (DYNAMO) campaign in situ observations on NASA Goddard Earth Observing System version 5 (GEOS-5) reanalyses and the improvements gained thereby in the representation of the Madden-Julian Oscillation (MJO) initiation processes. To this end, we produced a global, high-resolution (1/4° spatially) reanalysis that assimilates the level-4, quality-controlled DYNAMO upper air soundings from about 87 stations in the equatorial Indian Ocean region along with a companion data-denied control reanalysis. The DYNAMO reanalysis produces a more realistic vertical structure of the temperature and moisture in the central tropical Indian Ocean by correcting the model biases, namely, the cold and dry biases in the lower troposphere and warm bias in the upper troposphere. The reanalysis horizontal winds are substantially improved, in that, the westerly acceleration and vertical shear of the zonal wind are enhanced. The DYNAMO reanalysis shows enhanced low-level diabatic heating, moisture anomalies and vertical velocity during the MJO initiation. Due to the warmer lower troposphere, the deep convection is invigorated, which is evident in convective cloud fraction. The GEOS-5 atmospheric general circulation model (AGCM) employed in the reanalysis is overall successful in assimilating the additional DYNAMO observations, except for an erroneous model response for medium rain rates, between 700 and 600 hPa, reminiscent of a bias in earlier versions of the AGCM. The moist heating profile shows a sharp decrease there due to the excessive convective rain re-evaporation, which is partly offset by the temperature increment produced by the analysis.

Importing MAGE-ML format microarray data into BioConductor.

PubMed

Durinck, Steffen; Allemeersch, Joke; Carey, Vincent J; Moreau, Yves; De Moor, Bart

2004-12-12

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. http://www.bioconductor.org. Open Source.

Can Atmospheric Reanalysis Data Sets Be Used to Reproduce Flooding Over Large Scales?

NASA Astrophysics Data System (ADS)

Andreadis, Konstantinos M.; Schumann, Guy J.-P.; Stampoulis, Dimitrios; Bates, Paul D.; Brakenridge, G. Robert; Kettner, Albert J.

2017-10-01

Floods are costly to global economies and can be exceptionally lethal. The ability to produce consistent flood hazard maps over large areas could provide a significant contribution to reducing such losses, as the lack of knowledge concerning flood risk is a major factor in the transformation of river floods into flood disasters. In order to accurately reproduce flooding in river channels and floodplains, high spatial resolution hydrodynamic models are needed. Despite being computationally expensive, recent advances have made their continental to global implementation feasible, although inputs for long-term simulations may require the use of reanalysis meteorological products especially in data-poor regions. We employ a coupled hydrologic/hydrodynamic model cascade forced by the 20CRv2 reanalysis data set and evaluate its ability to reproduce flood inundation area and volume for Australia during the 1973-2012 period. Ensemble simulations using the reanalysis data were performed to account for uncertainty in the meteorology and compared with a validated benchmark simulation. Results show that the reanalysis ensemble capture the inundated areas and volumes relatively well, with correlations for the ensemble mean of 0.82 and 0.85 for area and volume, respectively, although the meteorological ensemble spread propagates in large uncertainty of the simulated flood characteristics.

Providing Access to a Diverse Set of Global Reanalysis Dataset Collections

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2015-12-01

The National Center for Atmospheric Research (NCAR) Research Data Archive (RDA, http://rda.ucar.edu) provides open access to a variety of global reanalysis dataset collections to support atmospheric and related sciences research worldwide. These include products from the European Centre for Medium-Range Weather Forecasts (ECMWF), Japan Meteorological Agency (JMA), National Centers for Environmental Prediction (NCEP), National Oceanic and Atmospheric Administration (NOAA), and NCAR.All RDA hosted reanalysis collections are freely accessible to registered users through a variety of methods. Standard access methods include traditional browser and scripted HTTP file download. Enhanced downloads are available through the Globus GridFTP "fire and forget" data transfer service, which provides an efficient, reliable, and preferred alternative to traditional HTTP-based methods. For those that favor interoperable access using compatible tools, the Unidata THREDDS Data server provides remote access to complete reanalysis collections by virtual dataset aggregation "files". Finally, users can request data subsets and format conversions to be prepared for them through web interface form requests or web service API batch requests. This approach uses NCAR HPC and central file systems to effectively prepare products from the high-resolution and very large reanalyses archives. The presentation will include a detailed inventory of all RDA reanalysis dataset collection holdings, and highlight access capabilities to these collections through use case examples.

Mutual information estimation reveals global associations between stimuli and biological processes

PubMed Central

Suzuki, Taiji; Sugiyama, Masashi; Kanamori, Takafumi; Sese, Jun

2009-01-01

Background Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each group with biological functions are often used methods. However, such methods only detect partial changes within cell processes. Herein, we propose a method for discovering global changes within a cell by associating observed conditions of gene expression with gene functions. Results To elucidate the association, we introduce a novel feature selection method called Least-Squares Mutual Information (LSMI), which computes mutual information without density estimaion, and therefore LSMI can detect nonlinear associations within a cell. We demonstrate the effectiveness of LSMI through comparison with existing methods. The results of the application to yeast microarray datasets reveal that non-natural stimuli affect various biological processes, whereas others are no significant relation to specific cell processes. Furthermore, we discover that biological processes can be categorized into four types according to the responses of various stimuli: DNA/RNA metabolism, gene expression, protein metabolism, and protein localization. Conclusion We proposed a novel feature selection method called LSMI, and applied LSMI to mining the association between conditions of yeast and biological processes through microarray datasets. In fact, LSMI allows us to elucidate the global organization of cellular process control. PMID:19208155

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at . PMID:15910681

Shrinkage covariance matrix approach based on robust trimmed mean in gene sets detection

NASA Astrophysics Data System (ADS)

Karjanto, Suryaefiza; Ramli, Norazan Mohamed; Ghani, Nor Azura Md; Aripin, Rasimah; Yusop, Noorezatty Mohd

2015-02-01

Microarray involves of placing an orderly arrangement of thousands of gene sequences in a grid on a suitable surface. The technology has made a novelty discovery since its development and obtained an increasing attention among researchers. The widespread of microarray technology is largely due to its ability to perform simultaneous analysis of thousands of genes in a massively parallel manner in one experiment. Hence, it provides valuable knowledge on gene interaction and function. The microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints. Therefore, the sample covariance matrix in Hotelling's T2 statistic is not positive definite and become singular, thus it cannot be inverted. In this research, the Hotelling's T2 statistic is combined with a shrinkage approach as an alternative estimation to estimate the covariance matrix to detect significant gene sets. The use of shrinkage covariance matrix overcomes the singularity problem by converting an unbiased to an improved biased estimator of covariance matrix. Robust trimmed mean is integrated into the shrinkage matrix to reduce the influence of outliers and consequently increases its efficiency. The performance of the proposed method is measured using several simulation designs. The results are expected to outperform existing techniques in many tested conditions.

An Interview with Matthew P. Greving, PhD. Interview by Vicki Glaser.

PubMed

Greving, Matthew P

2011-10-01

Matthew P. Greving is Chief Scientific Officer at Nextval Inc., a company founded in early 2010 that has developed a discovery platform called MassInsight™.. He received his PhD in Biochemistry from Arizona State University, and prior to that he spent nearly 7 years working as a software engineer. This experience in solving complex computational problems fueled his interest in developing technologies and algorithms related to acquisition and analysis of high-dimensional biochemical data. To address the existing problems associated with label-based microarray readouts, he beganwork on a technique for label-free mass spectrometry (MS) microarray readout compatible with both matrix-assisted laser/desorption ionization (MALDI) and matrix-free nanostructure initiator mass spectrometry (NIMS). This is the core of Nextval’s MassInsight technology, which utilizes picoliter noncontact deposition of high-density arrays on mass-readout substrates along with computational algorithms for high-dimensional data processingand reduction.

Novel Harmonic Regularization Approach for Variable Selection in Cox's Proportional Hazards Model

PubMed Central

Chu, Ge-Jin; Liang, Yong; Wang, Jia-Xuan

2014-01-01

Variable selection is an important issue in regression and a number of variable selection methods have been proposed involving nonconvex penalty functions. In this paper, we investigate a novel harmonic regularization method, which can approximate nonconvex Lq  (1/2 < q < 1) regularizations, to select key risk factors in the Cox's proportional hazards model using microarray gene expression data. The harmonic regularization method can be efficiently solved using our proposed direct path seeking approach, which can produce solutions that closely approximate those for the convex loss function and the nonconvex regularization. Simulation results based on the artificial datasets and four real microarray gene expression datasets, such as real diffuse large B-cell lymphoma (DCBCL), the lung cancer, and the AML datasets, show that the harmonic regularization method can be more accurate for variable selection than existing Lasso series methods. PMID:25506389

Direct multiplexed measurement of gene expression with color-coded probe pairs.

PubMed

Geiss, Gary K; Bumgarner, Roger E; Birditt, Brian; Dahl, Timothy; Dowidar, Naeem; Dunaway, Dwayne L; Fell, H Perry; Ferree, Sean; George, Renee D; Grogan, Tammy; James, Jeffrey J; Maysuria, Malini; Mitton, Jeffrey D; Oliveri, Paola; Osborn, Jennifer L; Peng, Tao; Ratcliffe, Amber L; Webster, Philippa J; Davidson, Eric H; Hood, Leroy; Dimitrov, Krassen

2008-03-01

We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.

Probe classification of on-off type DNA microarray images with a nonlinear matching measure

NASA Astrophysics Data System (ADS)

Ryu, Munho; Kim, Jong Dae; Min, Byoung Goo; Kim, Jongwon; Kim, Y. Y.

2006-01-01

We propose a nonlinear matching measure, called counting measure, as a signal detection measure that is defined as the number of on pixels in the spot area. It is applied to classify probes for an on-off type DNA microarray, where each probe spot is classified as hybridized or not. The counting measure also incorporates the maximum response search method, where the expected signal is obtained by taking the maximum among the measured responses of the various positions and sizes of the spot template. The counting measure was compared to existing signal detection measures such as the normalized covariance and the median for 2390 patient samples tested on the human papillomavirus (HPV) DNA chip. The counting measure performed the best regardless of whether or not the maximum response search method was used. The experimental results showed that the counting measure combined with the positional search was the most preferable.

The Mediterranean interannual variability in MEDRYS, a Mediterranean Sea reanalysis over 1992-2013

NASA Astrophysics Data System (ADS)

Beuvier, Jonathan; Hamon, Mathieu; Lellouche, Jean-Michel; Greiner, Eric; Alias, Antoinette; Arsouze, Thomas; Benkiran, Mounir; Béranger, Karine; Drillet, Yann; Sevault, Florence; Somot, Samuel

2015-04-01

The French research community on the Mediterranean Sea and the French operational ocean forecasting center Mercator Océan are gathering their skills and expertises in physical oceanography, ocean modelling, atmospheric forcings and data assimilation, to carry out a MEDiterranean Sea ReanalYsiS (MEDRYS) at high resolution for the period 1992-2013. The reanalysis is used to have a realistic description of the ocean state over the recent decades and it will help to understand the long-term water cycle over the Mediterranean basin in terms of variability and trends, contributing thus to the HyMeX international program. The ocean model used is NEMOMED12 [Lebeaupin Brossier et al., 2011, Oc. Mod., 2012, Oc. Mod.; Beuvier et al., 2012a, JGR, 2012b, Mercator Newsl.], a Mediterranean configuration of NEMO [Madec and the NEMO Team, 2008], with a 1/12° (about 7 km) horizontal resolution and 75 vertical z-levels with partial steps. It is forced by the 3-hourly atmospheric fluxes coming from an ALADIN-Climate simulation at 12 km of resolution [Herrmann et al., 2011, NHESS], driven by the ERA-Interim atmospheric reanalysis. The exchanges with the Atlantic Ocean are performed through a buffer zone, with a damping on 3D theta-S and on sea level towards the ORA-S4 oceanic reanalysis [Balmaseda et al., 2012, QJRMS]. This model configuration is used to carry a 34-year free simulation over the period 1979-2013. This free simulation is the initial state of the reanalysis in October 1992. It is also used to compute anomalies from which the data assimilation scheme derives required characteristic covariances of the ocean model. MEDRYS1 uses the current Mercator Océan operational data assimilation system [Lellouche et al., 2013, Oc.Sci.]. It uses a reduced order Kalman filter with a 3D multivariate modal decomposition of the forecast error. A 3D-Var scheme corrects biases in temperature and salinity for the slowly evolving large-scale. In addition, some modifications dedicated to the Mediterranean area (more specific Post-Glacial-Rebound corrections, new model-equivalent for the Sea Level Anomaly for example) have been introduced. Temperature and salinity vertical profiles from the newly released CORA4 database, altimeter data and satellite SST and are jointly assimilated. Thus, the reanalysis benefits from the intensive observational field campaigns carried out during the HyMeX Special Observation Periods (SOPs) in fall 2012 and winter 2013 in the north-western Mediterranean Sea. We assess here the ability of a MEDRYS1 to reproduce the general circulation and the water masses in the Mediterranean Sea. We present the misfit between the reanalysis and the assimilated observations, as well as differences between the reanalysis and its twin free simulation. We show diagnostics on the surface circulation variability, heat and salt contents and deep water formation over the whole period of the reanalysis, with also a focus on the impact of the HyMeX data during the SOPs time period.

Analyzing the most frequent disease loci in targeted patient categories optimizes disease gene identification and test accuracy worldwide.

PubMed

Lebo, Roger V; Tonk, Vijay S

2015-01-21

Our genomewide studies support targeted testing the most frequent genetic diseases by patient category: (1) pregnant patients, (2) at-risk conceptuses, (3) affected children, and (4) abnormal adults. This approach not only identifies most reported disease causing sequences accurately, but also minimizes incorrectly identified additional disease causing loci. Diseases were grouped in descending order of occurrence from four data sets: (1) GeneTests 534 listed population prevalences, (2) 4129 high risk prenatal karyotypes, (3) 1265 affected patient microarrays, and (4) reanalysis of 25,452 asymptomatic patient results screened prenatally for 108 genetic diseases. These most frequent diseases are categorized by transmission: (A) autosomal recessive, (B) X-linked, (C) autosomal dominant, (D) microscopic chromosome rearrangements, (E) submicroscopic copy number changes, and (F) frequent ethnic diseases. Among affected and carrier patients worldwide, most reported mutant genes would be identified correctly according to one of four patient categories from at-risk couples with <64 tested genes to affected adults with 314 tested loci. Three clinically reported patient series confirmed this approach. First, only 54 targeted chromosomal sites would have detected all 938 microscopically visible unbalanced karyotypes among 4129 karyotyped POC, CVS, and amniocentesis samples. Second, 37 of 48 reported aneuploid regions were found among our 1265 clinical microarrays confirming the locations of 8 schizophrenia loci and 20 aneuploidies altering intellectual ability, while also identifying 9 of the most frequent deletion syndromes. Third, testing 15 frequent genes would have identified 124 couples with a 1 in 4 risk of a fetus with a recessive disease compared to the 127 couples identified by testing all 108 genes, while testing all mutations in 15 genes could have identified more couples. Testing the most frequent disease causing abnormalities in 1 of 8 reported disease loci [~1 of 84 total genes] will identify ~ 7 of 8 reported abnormal Caucasian newborn genotypes. This would eliminate ~8 to 10 of ~10 Caucasian newborn gene sequences selected as abnormal that are actually normal variants identified when testing all ~2500 diseases looking for the remaining 1 of 8 disease causing genes. This approach enables more accurate testing within available laboratory and reimbursement resources.

Using a Coupled Lake Model with WRF for Dynamical Downscaling

EPA Science Inventory

The Weather Research and Forecasting (WRF) model is used to downscale a coarse reanalysis (National Centers for Environmental Prediction–Department of Energy Atmospheric Model Intercomparison Project reanalysis, hereafter R2) as a proxy for a global climate model (GCM) to examine...

Meta-analysis of gene expression patterns in animal models of prenatal alcohol exposure suggests role for protein synthesis inhibition and chromatin remodeling

PubMed Central

Rogic, Sanja; Wong, Albertina; Pavlidis, Paul

2017-01-01

Background Prenatal alcohol exposure (PAE) can result in an array of morphological, behavioural and neurobiological deficits that can range in their severity. Despite extensive research in the field and a significant progress made, especially in understanding the range of possible malformations and neurobehavioral abnormalities, the molecular mechanisms of alcohol responses in development are still not well understood. There have been multiple transcriptomic studies looking at the changes in gene expression after PAE in animal models, however there is a limited apparent consensus among the reported findings. In an effort to address this issue, we performed a comprehensive re-analysis and meta-analysis of all suitable, publically available expression data sets. Methods We assembled ten microarray data sets of gene expression after PAE in mouse and rat models consisting of samples from a total of 63 ethanol-exposed and 80 control animals. We re-analyzed each data set for differential expression and then used the results to perform meta-analyses considering all data sets together or grouping them by time or duration of exposure (pre- and post-natal, acute and chronic, respectively). We performed network and Gene Ontology enrichment analysis to further characterize the identified signatures. Results For each sub-analysis we identified signatures of differential expressed genes that show support from multiple studies. Overall, the changes in gene expression were more extensive after acute ethanol treatment during prenatal development than in other models. Considering the analysis of all the data together, we identified a robust core signature of 104 genes down-regulated after PAE, with no up-regulated genes. Functional analysis reveals over-representation of genes involved in protein synthesis, mRNA splicing and chromatin organization. Conclusions Our meta-analysis shows that existing studies, despite superficial dissimilarity in findings, share features that allow us to identify a common core signature set of transcriptome changes in PAE. This is an important step to identifying the biological processes that underlie the etiology of FASD. PMID:26996386

On-Chip, Amplification-Free Quantification of Nucleic Acid for Point-of-Care Diagnosis

NASA Astrophysics Data System (ADS)

Yen, Tony Minghung

This dissertation demonstrates three physical device concepts to overcome limitations in point-of-care quantification of nucleic acids. Enabling sensitive, high throughput nucleic acid quantification on a chip, outside of hospital and centralized laboratory setting, is crucial for improving pathogen detection and cancer diagnosis and prognosis. Among existing platforms, microarray have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, this dissertation presents theoretical and experimental progress to develop a platform nucleic acid quantification technology that is drastically more sensitive than current microarrays while compatible with microarray architecture. The first device concept explores on-chip nucleic acid enrichment by natural evaporation of nucleic acid solution droplet. Using a micro-patterned super-hydrophobic black silicon array device, evaporative enrichment is coupled with nano-liter droplet self-assembly workflow to produce a 50 aM concentration sensitivity, 6 orders of dynamic range, and rapid hybridization time at under 5 minutes. The second device concept focuses on improving target copy number sensitivity, instead of concentration sensitivity. A comprehensive microarray physical model taking into account of molecular transport, electrostatic intermolecular interactions, and reaction kinetics is considered to guide device optimization. Device pattern size and target copy number are optimized based on model prediction to achieve maximal hybridization efficiency. At a 100-mum pattern size, a quantum leap in detection limit of 570 copies is achieved using black silicon array device with self-assembled pico-liter droplet workflow. Despite its merits, evaporative enrichment on black silicon device suffers from coffee-ring effect at 100-mum pattern size, and thus not compatible with clinical patient samples. The third device concept utilizes an integrated optomechanical laser system and a Cytop microarray device to reverse coffee-ring effect during evaporative enrichment at 100-mum pattern size. This method, named "laser-induced differential evaporation" is expected to enable 570 copies detection limit for clinical samples in near future. While the work is ongoing as of the writing of this dissertation, a clear research plan is in place to implement this method on microarray platform toward clinical sample testing for disease applications and future commercialization.

Tropical cyclone genesis potential index over the western North Pacific simulated by CMIP5 models

NASA Astrophysics Data System (ADS)

Song, Yajuan; Wang, Lei; Lei, Xiaoyan; Wang, Xidong

2015-11-01

Tropical cyclone (TC) genesis over the western North Pacific (WNP) is analyzed using 23 CMIP5 (Coupled Model Intercomparison Project Phase 5) models and reanalysis datasets. The models are evaluated according to TC genesis potential index (GPI). The spatial and temporal variations of the GPI are first calculated using three atmospheric reanalysis datasets (ERA-Interim, NCEP/NCAR Reanalysis-1, and NCEP/DOE Reanalysis-2). Spatial distributions of July-October-mean TC frequency based on the GPI from ERA-interim are more consistent with observed ones derived from IBTrACS global TC data. So, the ERA-interim reanalysis dataset is used to examine the CMIP5 models in terms of reproducing GPI during the period 1982-2005. Although most models possess deficiencies in reproducing the spatial distribution of the GPI, their multimodel ensemble (MME) mean shows a reasonable climatological GPI pattern characterized by a high GPI zone along 20°N in the WNP. There was an upward trend of TC genesis frequency during 1982 to 1998, followed by a downward trend. Both MME results and reanalysis data can represent a robust increasing trend during 1982-1998, but the models cannot simulate the downward trend after 2000. Analysis based on future projection experiments shows that the GPI exhibits no significant change in the first half of the 21st century, and then starts to decrease at the end of the 21st century under the representative concentration pathway (RCP) 2.6 scenario. Under the RCP8.5 scenario, the GPI shows an increasing trend in the vicinity of 20°N, indicating more TCs could possibly be expected over the WNP under future global warming.

Evaluation of representativeness of near-surface winds in station measurements, global and regional reanalysis for Germany

NASA Astrophysics Data System (ADS)

Kaspar, Frank; Kaiser-Weiss, Andrea K.; Heene, Vera; Borsche, Michael; Keller, Jan

2015-04-01

Within the preparation activities for a European COPERNICUS Climate Change Service (C3S) several ongoing research projects analyse the potential of global and regional model-based climate reanalyses for applications. A user survey in the FP7-project CORE-CLIMAX revealed that surface wind (10 m) is among the most frequently used parameters of global reanalysis products. The FP7 project UERRA (Uncertainties in Ensembles of Regional Re-Analysis) has the focus on regional European reanalysis and the associated uncertainties, also from a user perspective. Especially in the field of renewable energy planning and production there is a need for climatological information across all spatial scales, i.e., from climatology at a certain site to the spatial scale of national or continental renewable energy production. Here, we focus on a comparison of wind measurements of the Germany's meteorological service (Deutscher Wetterdienst, DWD) with global reanalyses of ECWMF and a regional reanalysis for Europe based on DWD's NWP-model COSMO (performed by the Hans-Ertel-Center for Weather Research, University of Bonn). Reanalyses can provide valuable additional information on larger scale variability, e.g. multi-annual variation over Germany. However, changes in the observing system, model errors and biases have to be carefully considered. On the other hand, the ground-based observation networks partly suffer from change of the station distribution, changes in instrumentation, measurements procedures and quality control as well as local changes which might modify their spatial representativeness. All these effects might often been unknown or hard to characterize, although plenty of the meta-data information has been recorded for the German stations. One focus of the presentation will be the added-value of the regional reanalysis.

Report of the 4th World Climate Research Programme International Conference on Reanalyses

NASA Technical Reports Server (NTRS)

Bosilovich, Michael G.; Rixen, Michel; van Oevelen, Peter; Asrar, Ghassem; Compo, Gilbert; Onogi, Kazutoshi; Simmons, Adrian; Trenberth, Kevin; Behringer, Dave; Bhuiyan, Tanvir Hossain;

Evaluation of four global reanalysis products using in situ observations in the Amundsen Sea Embayment, Antarctica

NASA Astrophysics Data System (ADS)

Jones, R. W.; Renfrew, I. A.; Orr, A.; Webber, B. G. M.; Holland, D. M.; Lazzara, M. A.

2016-06-01

The glaciers within the Amundsen Sea Embayment (ASE), West Antarctica, are amongst the most rapidly retreating in Antarctica. Meteorological reanalysis products are widely used to help understand and simulate the processes causing this retreat. Here we provide an evaluation against observations of four of the latest global reanalysis products within the ASE region—the European Centre for Medium-Range Weather Forecasts Interim Reanalysis (ERA-I), Japanese 55-year Reanalysis (JRA-55), Climate Forecast System Reanalysis (CFSR), and Modern Era Retrospective-Analysis for Research and Applications (MERRA). The observations comprise data from four automatic weather stations (AWSs), three research vessel cruises, and a new set of 38 radiosondes all within the period 2009-2014. All four reanalyses produce 2 m temperature fields that are colder than AWS observations, with the biases varying from approximately -1.8°C (ERA-I) to -6.8°C (MERRA). Over the Amundsen Sea, spatially averaged summertime biases are between -0.4°C (JRA-55) and -2.1°C (MERRA) with notably larger cold biases close to the continent (up to -6°C) in all reanalyses. All four reanalyses underestimate near-surface wind speed at high wind speeds (>15 m s-1) and exhibit dry biases and relatively large root-mean-square errors (RMSE) in specific humidity. A comparison to the radiosonde soundings shows that the cold, dry bias at the surface extends into the lower troposphere; here ERA-I and CFSR reanalyses provide the most accurate profiles. The reanalyses generally contain larger temperature and humidity biases, (and RMSE) when a temperature inversion is observed, and contain larger wind speed biases (~2 to 3 m s-1), when a low-level jet is observed.

Water Cycle Variability over the Global Oceans Estimated Using Homogenized Reanalysis Fluxes

NASA Astrophysics Data System (ADS)

Robertson, F. R.; Bosilovich, M. G.; Roberts, J. B.

2017-12-01

Establishing consistent records of the global water cycle fluxes and their variations is particularly difficult over oceans where the density of in situ observations varies enormously with time, satellite retrievals of flux processes are sparse, and reanalyses are uncertain. The latter have the positive attribute of assimilating diverse observations to provide boundary fluxes and transports but are hindered by at least two factors: (1) the physical parameterizations are imperfect and, (2) the forcing data availability and quality vary greatly in time and, thus, can induce time-dependent, false signals of climate variability. Here we examine the prospects for homogenization of reanalysis records, that is, identifying and greatly minimizing non-physical signals. Our analysis focuses on the satellite era, 1980 to near present. The strategy involves three atmospheric reanalysis systems: (1) the NASA MERRA-2, (2) the newest reanalysis produced by the Japanese Meteorological Agency, JRA-55, and (3) the European Centre for Medium Range Weather Forecasts 20th Century reanalysis, ERA-20C. MERRA-2 and ERA-20C are also accompanied by 10-member AMIP integrations, and JRA-55 by a reanalysis using only conventional observations, JRA-55C. Differencing these latter integrations from the more comprehensive reanalyses helps provide a clearer picture of the impact of satellite observations by removing the effects of SST forcing. This facilitates the use of principal component analysis as a tool to identify and remove non-physical signals. We then use these homogenized E, P and moisture transports to examine the consistency of diagnostics of thermodynamic and hydrologic scaling, especially the P-E pattern amplification or the "wet-get-wetter, dry-get-drier" response. Prospects for further validation by new turbulent flux retrievals by satellite are discussed.

Precipitation climatology over India: validation with observations and reanalysis datasets and spatial trends

NASA Astrophysics Data System (ADS)

Kishore, P.; Jyothi, S.; Basha, Ghouse; Rao, S. V. B.; Rajeevan, M.; Velicogna, Isabella; Sutterley, Tyler C.

2016-01-01

Changing rainfall patterns have significant effect on water resources, agriculture output in many countries, especially the country like India where the economy depends on rain-fed agriculture. Rainfall over India has large spatial as well as temporal variability. To understand the variability in rainfall, spatial-temporal analyses of rainfall have been studied by using 107 (1901-2007) years of daily gridded India Meteorological Department (IMD) rainfall datasets. Further, the validation of IMD precipitation data is carried out with different observational and different reanalysis datasets during the period from 1989 to 2007. The Global Precipitation Climatology Project data shows similar features as that of IMD with high degree of comparison, whereas Asian Precipitation-Highly-Resolved Observational Data Integration Towards Evaluation data show similar features but with large differences, especially over northwest, west coast and western Himalayas. Spatially, large deviation is observed in the interior peninsula during the monsoon season with National Aeronautics Space Administration-Modern Era Retrospective-analysis for Research and Applications (NASA-MERRA), pre-monsoon with Japanese 25 years Re Analysis (JRA-25), and post-monsoon with climate forecast system reanalysis (CFSR) reanalysis datasets. Among the reanalysis datasets, European Centre for Medium-Range Weather Forecasts Interim Re-Analysis (ERA-Interim) shows good comparison followed by CFSR, NASA-MERRA, and JRA-25. Further, for the first time, with high resolution and long-term IMD data, the spatial distribution of trends is estimated using robust regression analysis technique on the annual and seasonal rainfall data with respect to different regions of India. Significant positive and negative trends are noticed in the whole time series of data during the monsoon season. The northeast and west coast of the Indian region shows significant positive trends and negative trends over western Himalayas and north central Indian region.

Sensitivity of Statistical Downscaling Techniques to Reanalysis Choice and Implications for Regional Climate Change Scenarios

NASA Astrophysics Data System (ADS)

Manzanas, R., Sr.; Brands, S.; San Martin, D., Sr.; Gutiérrez, J. M., Sr.

2014-12-01

This work shows that local-scale climate projections obtained by means of statistical downscaling are sensitive to the choice of reanalysis used for calibration. To this aim, a Generalized Linear Model (GLM) approach is applied to downscale daily precipitation in the Philippines. First, the GLMs are trained and tested -under a cross-validation scheme- separately for two distinct reanalyses (ERA-Interim and JRA-25) for the period 1981-2000. When the observed and downscaled time-series are compared, the attained performance is found to be sensitive to the reanalysis considered if climate change signal bearing variables (temperature and/or specific humidity) are included in the predictor field. Moreover, performance differences are shown to be in correspondence with the disagreement found between the raw predictors from the two reanalyses. Second, the regression coefficients calibrated either with ERA-Interim or JRA-25 are subsequently applied to the output of a Global Climate Model (MPI-ECHAM5) in order to assess the sensitivity of local-scale climate change projections (up to 2100) to reanalysis choice. In this case, the differences detected in present climate conditions are considerably amplified, leading to "delta-change" estimates differing by up to a 35% (on average for the entire country) depending on the reanalysis used for calibration. Therefore, reanalysis choice is shown to importantly contribute to the uncertainty of local-scale climate change projections, and, consequently, should be treated with equal care as other, well-known, sources of uncertainty -e.g., the choice of the GCM and/or downscaling method.- Implications of the results for the entire tropics, as well as for the Model Output Statistics downscaling approach are also briefly discussed.

Multidecadal Changes in the UTLS Ozone from the MERRA-2 Reanalysis and the GMI Chemistry Model

NASA Technical Reports Server (NTRS)

Wargan, Krzysztof; Orbe, Clara; Pawson, Steven; Ziemke, Jerald R.; Oman, Luke; Olsen, Mark; Coy, Lawrence; Knowland, Emma

2018-01-01

Long-term changes of ozone in the UTLS (Upper Troposphere / Lower Stratosphere) reflect the response to decreases in the stratospheric concentrations of ozone-depleting substances as well as changes in the stratospheric circulation induced by climate change. To date, studies of UTLS ozone changes and variability have relied mainly on satellite and in-situ observations as well as chemistry-climate model simulations. By comparison, the potential of reanalysis ozone data remains relatively untapped. This is despite evidence from recent studies, including detailed analyses conducted under SPARC (Scalable Processor Architecture) Reanalysis Intercomparison Project (S-RIP), that demonstrate that stratospheric ozone fields from modern atmospheric reanalyses exhibit good agreement with independent data while delineating issues related to inhomogeneities in the assimilated observations. In this presentation, we will explore the possibility of inferring long-term geographically and vertically resolved behavior of the lower stratospheric (LS) ozone from NASA's MERRA-2 (Modern-Era Retrospective Analysis for Research and Applications -2) reanalysis after accounting for the few known discontinuities and gaps in its assimilated input data. This work builds upon previous studies that have documented excellent agreement between MERRA-2 ozone and ozonesonde observations in the LS. Of particular importance is a relatively good vertical resolution of MERRA-2 allowing precise separation of tropospheric and stratospheric ozone contents. We also compare the MERRA-2 LS ozone results with the recently completed 37-year simulation produced using Goddard Earth Observing System in "replay"� mode coupled with the GMI (Global Modeling Initiative) chemistry mechanism. Replay mode dynamically constrains the model with the MERRA-2 reanalysis winds, temperature, and pressure. We will emphasize the areas of agreement of the reanalysis and replay and interpret differences between them in the context of our increasing understanding of model transport driven by assimilated winds.

Spatiotemporal Evaluation of Reanalysis and In-situ Surface Air Temperature over Ethiopia

NASA Astrophysics Data System (ADS)

Tesfaye, T.

2017-12-01

Tewodros Woldemariam Tesfaye*1, C.T. Dhanya 2,and A.K. Gosain3 1Research Scholar, Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India 2Assistant Professor, Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India 3 Professor, Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India, *e-mail: tewodros2002@gmail.com Abstract: Water resources management and modelling studies are often constrained by the scarcity of observed data, especially of the two major variables i.e., precipitation and temperature. Modellers, hence, rely on reanalysis datasets as a substitute; though its performance heavily vary depending on the data availability and regional characteristics. The present study aims at examining the ability of frequently used reanalysis datasets in capturing the spatiotemporal characteristics of maximum and minimum surface temperatures over Ethiopia and to highlight the biases, if any, in these over Ethiopian region. We considered ERA-Interim, NCEP 2, MERRA and CFSR reanalysis datasets and compared these with temperature observations from 15 synoptic stations spread over Ethiopia. In addition to the long term averages and annual cycle, a critical comparison of various extreme indices such as diurnal temperature range, warm days, warm nights, cool days, cool nights, summer days and tropical nights are also undertaken. Our results indicate that, the performance of CFSR followed by NCEP 2 is better in capturing majority of the aspects. ERA-Interim suffers a huge additive bias in the simulation of various aspects of minimum temperature in all the stations considered; while its performance is better for maximum temperature. The inferior performance of ERA-Interim is noted to be only because of the difficulty in simulating minimum temperature. Key words: ERA Interim; NCEP Reanalysis; MERRA; CFSR; Diurnal temperature range; reanalysis performance.

Assessing the Suitability of Historical PM(2.5) Element Measurements for Trend Analysis.

PubMed

Hyslop, Nicole P; Trzepla, Krystyna; White, Warren H

2015-08-04

The IMPROVE (Interagency Monitoring of Protected Visual Environments) network has characterized fine particulate matter composition at locations throughout the United States since 1988. A main objective of the network is to evaluate long-term trends in aerosol concentrations. Measurements inevitably advance over time, but changes in measurement technique have the potential to confound the interpretation of long-term trends. Problems of interpretation typically arise from changing biases, and changes in bias can be difficult to identify without comparison data that are consistent throughout the measurement series, which rarely exist. We created a consistent measurement series for exactly this purpose by reanalyzing the 15-year archives (1995-2009) of aerosol samples from three sites - Great Smoky Mountains National Park, Mount Rainier National Park, and Point Reyes National Seashore-as single batches using consistent analytical methods. In most cases, trend estimates based on the original and reanalysis measurements are statistically different for elements that were not measured above the detection limit consistently over the years (e.g., Na, Cl, Si, Ti, V, Mn). The original trends are more reliable for elements consistently measured above the detection limit. All but one of the 23 site-element series with detection rates >80% had statistically indistinguishable original and reanalysis trends (overlapping 95% confidence intervals).

MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes.

PubMed

Huerta, Mario; Munyi, Marc; Expósito, David; Querol, Enric; Cedano, Juan

2014-06-15

The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories. Marker-gene database tool: http://ibb.uab.es/mgdb © The Author 2014. Published by Oxford University Press.

2008 Microarray Research Group (MARG Survey): Sensing the State of Microarray Technology

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution and transformation, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. Th...

Masculine and Feminine Stereotypes and Adjustment: A Reanalysis.

ERIC Educational Resources Information Center

Gilbert, Lucia A.; And Others

1981-01-01

Presents a reanalysis of earlier data from a study of self-perceptions of stereotypic masculine and feminine attributes, Rogerian-type conflict, and personal adjustment. Reanalyses demonstrated the advantage of distinguishing between androgynous and undifferentiated individuals rather than grouping them together into a single "balanced"…

Chemistry Simulations using the MERRA-2 Reanalysis with the GMI CTM and Replay in Support of the Atmospheric Composition Community

NASA Technical Reports Server (NTRS)

Oman, Luke D.; Strahan, Susan E.

2017-01-01

Simulations using reanalysis meteorological fields have long been used to understand the causes of atmospheric composition change in the recent past. Using the new MERRA-2 reanalysis, we are conducting chemistry simulations to create products covering 1980-2016 for the atmospheric composition community. These simulations use the Global Modeling Initiative (GMI) chemical mechanism in two different models: the GMI Chemical Transport Model (CTM) and the GEOS-5 model in Replay mode. Replay mode means an integration of the GEOS-5 general circulation model that is incrementally adjusted each time step toward the MERRA-2 reanalysis. The GMI CTM is a 1 deg x 1.25 deg simulation and the MERRA-2 GMI Replay simulation uses the native MERRA-2 grid of approximately 1/2 deg horizontal resolution on the cubed sphere. A specialized set of transport diagnostics is included in both runs to better understand trace gas transport and its variability in the recent past.

Northern Hemisphere climate trends in reanalysis and forecast model predictions: The 500 hPa annual means

NASA Astrophysics Data System (ADS)

Bordi, I.; Fraedrich, K.; Sutera, A.

2010-06-01

The lead time dependent climates of the ECMWF weather prediction model, initialized with ERA-40 reanalysis, are analysed using 44 years of day-1 to day-10 forecasts of the northern hemispheric 500-hPa geopotential height fields. The study addresses the question whether short-term tendencies have an impact on long-term trends. Comparing climate trends of ERA-40 with those of the forecasts, it seems that the forecast model rapidly loses the memory of initial conditions creating its own climate. All forecast trends show a high degree of consistency. Comparison results suggest that: (i) Only centers characterized by an upward trend are statistical significant when increasing the lead time. (ii) In midilatitudes an upward trend larger than the one observed in the reanalysis characterizes the forecasts, while in the tropics there is a good agreement. (iii) The downward trend in reanalysis at high latitudes characterizes also the day-1 forecast which, however, increasing lead time approaches zero.

Cross-evaluation of ground-based, multi-satellite and reanalysis precipitation products: Applicability of the Triple Collocation method across Mainland China

NASA Astrophysics Data System (ADS)

Li, Changming; Tang, Guoqiang; Hong, Yang

2018-07-01

Evaluating the reliability of satellite and reanalysis precipitation products is critical but challenging over ungauged or poorly gauged regions. The Triple Collocation (TC) method is a reliable approach to estimate the accuracy of any three independent inputs in the absence of truth values. This study assesses the uncertainty of three types of independent precipitation products, i.e., satellite-based, ground-based and model reanalysis over Mainland China using the TC method. The ground-based data set is Gauge Based Daily Precipitation Analysis (CGDPA). The reanalysis data set is European Reanalysis Agency Reanalysis Product (ERA-interim). The satellite-based products include five mainstream satellite products. The comparison and evaluation are conducted at 0.25° and daily resolutions from 2013 to 2015. First, the effectiveness of the TC method is evaluated in South China with dense gauge network. The results demonstrate that the TC method is reliable because the correlation coefficient (CC) and root mean square error (RMSE) derived from TC are close to those derived from ground observations, with only 9% and 7% mean relative differences, respectively. Then, the TC method is applied in Mainland China, with special attention paid to the Tibetan Plateau (TP) known as the Earth's third pole with few ground stations. Results indicate that (1) The overall performance of IMERG is better than the other satellite products over Mainland China, followed by 3B42V7, CMORPH-CRT and PERSIANN-CDR. (2) In the TP, CGDPA shows the best overall performance over gauged grid cells, however, over ungauged regions, IMERG and ERA-interim slightly outperform CGDPA with similar RMSE but higher mean CC (0.63, 0.61, and 0.58, respectively). It highlights the strengths and potentiality of remote sensing and reanalysis data over the TP and reconfirms the cons of the inherent uncertainty of CGDPA due to interpolation from sparsely gauged data. The study concludes that the TC method provides not only reliable cross-validation results over Mainland China but also a new perspective for comparatively assessing multi-source precipitation products, particularly over poorly gauged regions such as the TP.

How well do Reanalysis represent polar lows?

NASA Astrophysics Data System (ADS)

Zappa, G.; Shaffrey, L.; Hodges, K.

2013-12-01

Polar lows are intense maritime mesocyclones forming at high latitudes during polar air outbreaks. The associated high surface winds can be an important cause of coastal damage.They also seem to play a relevant role in the climate system by modulating the oceanic surface heat fluxes. This creates strong interest in understanding whether modern reanalysis datasets are able to represent polar lows, as well as how their representation may be sensitive to the model resolution. In this talk we investigate how ERA-Interim reanalysis represents the polar lows identified by the Norwegian meteorological services and listed in the STARS (Combination of Sea Surface Temperature and AltimeteR Synergy) dataset for the period 2002-2011. The sensitivity to resolution is explored by comparing ERA-Interim to the ECMWF operational analyses (2008-2011), which have three times higher horizontal resolution compared to ERA-Interim. We show that ERAI-Interim has excellent ability to capture the observed polar lows events with up to 90% of the observed events being found in the reanalysis. However, ERA-Interim tends to have polar lows of weaker dynamical intensity, in terms of both winds and vorticity, and with less spatial structure than in the ECMWF operational analyses (See Fig 1). Furthermore, we apply an objective feature tracking algorithm to the 3 hourly vorticity at 850 hPa with constraints on vorticity intensity and atmospheric static stability to objectively identify polar lows in the ERA-Interim reanalysis. We show that for the stronger polar lows the objective climatology shows good agreement with the STARS dataset over the 2002-2011 period. This allows us to extend the polar lows climatology over the whole ERA Interim period. Differences with another reanalysis product (NCEP-CFSR) will be also discussed. Fig 1: Composite of the tangential wind speed at 925 hPa for 34 polar lows observed in the Norwegian sea between 2008-2010 as represented by the ERA-Interim reanalysis (left) and by the ECMWF Operational analysis (right). Positive values indicate cyclonic circulation. The composite is centered on the polar low vorticity maxima and it is presented for a radial cap of 5 degrees of radius on the sphere (~550Km).

An 11-year global gridded aerosol optical thickness reanalysis (v1.0) for atmospheric and climate sciences

NASA Astrophysics Data System (ADS)

Lynch, Peng; Reid, Jeffrey S.; Westphal, Douglas L.; Zhang, Jianglong; Hogan, Timothy F.; Hyer, Edward J.; Curtis, Cynthia A.; Hegg, Dean A.; Shi, Yingxi; Campbell, James R.; Rubin, Juli I.; Sessions, Walter R.; Turk, F. Joseph; Walker, Annette L.

2016-04-01

While stand alone satellite and model aerosol products see wide utilization, there is a significant need in numerous atmospheric and climate applications for a fused product on a regular grid. Aerosol data assimilation is an operational reality at numerous centers, and like meteorological reanalyses, aerosol reanalyses will see significant use in the near future. Here we present a standardized 2003-2013 global 1 × 1° and 6-hourly modal aerosol optical thickness (AOT) reanalysis product. This data set can be applied to basic and applied Earth system science studies of significant aerosol events, aerosol impacts on numerical weather prediction, and electro-optical propagation and sensor performance, among other uses. This paper describes the science of how to develop and score an aerosol reanalysis product. This reanalysis utilizes a modified Navy Aerosol Analysis and Prediction System (NAAPS) at its core and assimilates quality controlled retrievals of AOT from the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua and the Multi-angle Imaging SpectroRadiometer (MISR) on Terra. The aerosol source functions, including dust and smoke, were regionally tuned to obtain the best match between the model fine- and coarse-mode AOTs and the Aerosol Robotic Network (AERONET) AOTs. Other model processes, including deposition, were tuned to minimize the AOT difference between the model and satellite AOT. Aerosol wet deposition in the tropics is driven with satellite-retrieved precipitation, rather than the model field. The final reanalyzed fine- and coarse-mode AOT at 550 nm is shown to have good agreement with AERONET observations, with global mean root mean square error around 0.1 for both fine- and coarse-mode AOTs. This paper includes a discussion of issues particular to aerosol reanalyses that make them distinct from standard meteorological reanalyses, considerations for extending such a reanalysis outside of the NASA A-Train era, and examples of how the aerosol reanalysis can be applied or fused with other model or remote sensing products. Finally, the reanalysis is evaluated in comparison with other available studies of aerosol trends, and the implications of this comparison are discussed.

Development studies towards an 11-year global gridded aerosol optical thickness reanalysis for climate and applied applications

NASA Astrophysics Data System (ADS)

Lynch, P.; Reid, J. S.; Westphal, D. L.; Zhang, J.; Hogan, T. F.; Hyer, E. J.; Curtis, C. A.; Hegg, D. A.; Shi, Y.; Campbell, J. R.; Rubin, J. I.; Sessions, W. R.; Turk, F. J.; Walker, A. L.

2015-12-01

While standalone satellite and model aerosol products see wide utilization, there is a significant need in numerous climate and applied applications for a fused product on a regular grid. Aerosol data assimilation is an operational reality at numerous centers, and like meteorological reanalyses, aerosol reanalyses will see significant use in the near future. Here we present a standardized 2003-2013 global 1° × 1° and 6 hourly modal aerosol optical thickness (AOT) reanalysis product. This dataset can be applied to basic and applied earth system science studies of significant aerosol events, aerosol impacts on numerical weather prediction, and electro-optical propagation and sensor performance, among other uses. This paper describes the science of how to develop and score an aerosol reanalysis product. This reanalysis utilizes a modified Navy Aerosol Analysis and Prediction System (NAAPS) at its core and assimilates quality controlled retrievals of AOT from the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua and the Multi-angle Imaging SpectroRadiometer (MISR) on Terra. The aerosol source functions, including dust and smoke, were regionally tuned to obtain the best match between the model fine and coarse mode AOTs and the Aerosol Robotic Network (AERONET) AOTs. Other model processes, including deposition, were tuned to minimize the AOT difference between the model and satellite AOT. Aerosol wet deposition in the tropics is driven with satellite retrieved precipitation, rather than the model field. The final reanalyzed fine and coarse mode AOT at 550 nm is shown to have good agreement with AERONET observations, with global mean root mean square error around 0.1 for both fine and coarse mode AOTs. This paper includes a discussion of issues particular to aerosol reanalyses that make them distinct from standard meteorological reanalyses, considerations for extending such a reanalysis outside of the NASA A-Train era, and examples of how the aerosol reanalysis can be applied or fused with other model or remote sensing products. Finally, the reanalysis is evaluated in comparison with other available studies of aerosol trends, and the implications of this comparison are discussed.

THE ABRF-MARG MICROARRAY SURVEY 2004: TAKING THE PULSE OF THE MICROARRAY FIELD

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. The goal of the surve...

Contributions to Statistical Problems Related to Microarray Data

ERIC Educational Resources Information Center

Hong, Feng

2009-01-01

Microarray is a high throughput technology to measure the gene expression. Analysis of microarray data brings many interesting and challenging problems. This thesis consists three studies related to microarray data. First, we propose a Bayesian model for microarray data and use Bayes Factors to identify differentially expressed genes. Second, we…

Parallel, confocal, and complete spectrum imager for fluorescent detection of high-density microarray

NASA Astrophysics Data System (ADS)

Bogdanov, Valery L.; Boyce-Jacino, Michael

1999-05-01

Confined arrays of biochemical probes deposited on a solid support surface (analytical microarray or 'chip') provide an opportunity to analysis multiple reactions simultaneously. Microarrays are increasingly used in genetics, medicine and environment scanning as research and analytical instruments. A power of microarray technology comes from its parallelism which grows with array miniaturization, minimization of reagent volume per reaction site and reaction multiplexing. An optical detector of microarray signals should combine high sensitivity, spatial and spectral resolution. Additionally, low-cost and a high processing rate are needed to transfer microarray technology into biomedical practice. We designed an imager that provides confocal and complete spectrum detection of entire fluorescently-labeled microarray in parallel. Imager uses microlens array, non-slit spectral decomposer, and high- sensitive detector (cooled CCD). Two imaging channels provide a simultaneous detection of localization, integrated and spectral intensities for each reaction site in microarray. A dimensional matching between microarray and imager's optics eliminates all in moving parts in instrumentation, enabling highly informative, fast and low-cost microarray detection. We report theory of confocal hyperspectral imaging with microlenses array and experimental data for implementation of developed imager to detect fluorescently labeled microarray with a density approximately 103 sites per cm2.

MicroRNA-integrated and network-embedded gene selection with diffusion distance.

PubMed

Huang, Di; Zhou, Xiaobo; Lyon, Christopher J; Hsueh, Willa A; Wong, Stephen T C

2010-10-29

Gene network information has been used to improve gene selection in microarray-based studies by selecting marker genes based both on their expression and the coordinate expression of genes within their gene network under a given condition. Here we propose a new network-embedded gene selection model. In this model, we first address the limitations of microarray data. Microarray data, although widely used for gene selection, measures only mRNA abundance, which does not always reflect the ultimate gene phenotype, since it does not account for post-transcriptional effects. To overcome this important (critical in certain cases) but ignored-in-almost-all-existing-studies limitation, we design a new strategy to integrate together microarray data with the information of microRNA, the major post-transcriptional regulatory factor. We also handle the challenges led by gene collaboration mechanism. To incorporate the biological facts that genes without direct interactions may work closely due to signal transduction and that two genes may be functionally connected through multi paths, we adopt the concept of diffusion distance. This concept permits us to simulate biological signal propagation and therefore to estimate the collaboration probability for all gene pairs, directly or indirectly-connected, according to multi paths connecting them. We demonstrate, using type 2 diabetes (DM2) as an example, that the proposed strategies can enhance the identification of functional gene partners, which is the key issue in a network-embedded gene selection model. More importantly, we show that our gene selection model outperforms related ones. Genes selected by our model 1) have improved classification capability; 2) agree with biological evidence of DM2-association; and 3) are involved in many well-known DM2-associated pathways.

Microarray analysis and draft genomes of two Escherichia coli 0157:H7 lineage II cattle isolates FRIK966 and FRIK2000 investigating lack of Shiga toxin expression

USDA-ARS?s Scientific Manuscript database

The existence of two separate lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that lineage I might be more pathogenic towards human hosts than lineage II. We have previously shown that lineage I expresses higher levels of Shiga toxin 2 (Stx2). To evaluate w...

Molecular Profiles for Lung Cancer Pathogenesis and Detection in U.S. Veterans

DTIC Science & Technology

2013-10-01

All small RNA sequencing and microarray data has been deposited in GEO under the accession number GSE48798. References 1. Hwang HW, Mendell JT (2006...searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send...histologically normal airway epithelium and tumor. We have validated this approach and the data will allow us to identify novel pathways for lung

MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach.

PubMed

Abduallah, Yasser; Turki, Turki; Byron, Kevin; Du, Zongxuan; Cervantes-Cervantes, Miguel; Wang, Jason T L

2017-01-01

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here, we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.

A novel harmony search-K means hybrid algorithm for clustering gene expression data

PubMed Central

Nazeer, KA Abdul; Sebastian, MP; Kumar, SD Madhu

2013-01-01

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms. PMID:23390351

A novel harmony search-K means hybrid algorithm for clustering gene expression data.

PubMed

Nazeer, Ka Abdul; Sebastian, Mp; Kumar, Sd Madhu

2013-01-01

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms.

A measure of the signal-to-noise ratio of microarray samples and studies using gene correlations.

PubMed

Venet, David; Detours, Vincent; Bersini, Hugues

2012-01-01

The quality of gene expression data can vary dramatically from platform to platform, study to study, and sample to sample. As reliable statistical analysis rests on reliable data, determining such quality is of the utmost importance. Quality measures to spot problematic samples exist, but they are platform-specific, and cannot be used to compare studies. As a proxy for quality, we propose a signal-to-noise ratio for microarray data, the "Signal-to-Noise Applied to Gene Expression Experiments", or SNAGEE. SNAGEE is based on the consistency of gene-gene correlations. We applied SNAGEE to a compendium of 80 large datasets on 37 platforms, for a total of 24,380 samples, and assessed the signal-to-noise ratio of studies and samples. This allowed us to discover serious issues with three studies. We show that signal-to-noise ratios of both studies and samples are linked to the statistical significance of the biological results. We showed that SNAGEE is an effective way to measure data quality for most types of gene expression studies, and that it often outperforms existing techniques. Furthermore, SNAGEE is platform-independent and does not require raw data files. The SNAGEE R package is available in BioConductor.

Clustering of European winter storms: A multi-model perspective

NASA Astrophysics Data System (ADS)

Renggli, Dominik; Buettner, Annemarie; Scherb, Anke; Straub, Daniel; Zimmerli, Peter

2016-04-01

The storm series over Europe in 1990 (Daria, Vivian, Wiebke, Herta) and 1999 (Anatol, Lothar, Martin) are very well known. Such clusters of severe events strongly affect the seasonally accumulated damage statistics. The (re)insurance industry has quantified clustering by using distribution assumptions deduced from the historical storm activity of the last 30 to 40 years. The use of storm series simulated by climate models has only started recently. Climate model runs can potentially represent 100s to 1000s of years, allowing a more detailed quantification of clustering than the history of the last few decades. However, it is unknown how sensitive the representation of clustering is to systematic biases. Using a multi-model ensemble allows quantifying that uncertainty. This work uses CMIP5 decadal ensemble hindcasts to study clustering of European winter storms from a multi-model perspective. An objective identification algorithm extracts winter storms (September to April) in the gridded 6-hourly wind data. Since the skill of European storm predictions is very limited on the decadal scale, the different hindcast runs are interpreted as independent realizations. As a consequence, the available hindcast ensemble represents several 1000 simulated storm seasons. The seasonal clustering of winter storms is quantified using the dispersion coefficient. The benchmark for the decadal prediction models is the 20th Century Reanalysis. The decadal prediction models are able to reproduce typical features of the clustering characteristics observed in the reanalysis data. Clustering occurs in all analyzed models over the North Atlantic and European region, in particular over Great Britain and Scandinavia as well as over Iberia (i.e. the exit regions of the North Atlantic storm track). Clustering is generally weaker in the models compared to reanalysis, although the differences between different models are substantial. In contrast to existing studies, clustering is driven by weak and moderate events, and not by extreme storms. Thus, the decision which climate model to use to quantify clustering can have a substantial impact on the risk assessment in the (re)insurance business.

Evaluation of Vitamin D Standardization Program protocols for standardizing serum 25-hydroxyvitamin D data: a case study of the program's potential for national nutrition and health surveys12345

PubMed Central

Cashman, Kevin D; Kiely, Mairead; Kinsella, Michael; Durazo-Arvizu, Ramón A; Tian, Lu; Zhang, Yue; Lucey, Alice; Flynn, Albert; Gibney, Michael J; Vesper, Hubert W; Phinney, Karen W; Coates, Paul M; Picciano, Mary F; Sempos, Christopher T

2013-01-01

Background: The Vitamin D Standardization Program (VDSP) has developed protocols for standardizing procedures of 25-hydroxyvitamin D [25(OH)D] measurement in National Health/Nutrition Surveys to promote 25(OH)D measurements that are accurate and comparable over time, location, and laboratory procedure to improve public health practice. Objective: We applied VDSP protocols to existing ELISA-derived serum 25(OH)D data from the Irish National Adult Nutrition Survey (NANS) as a case-study survey and evaluated their effectiveness by comparison of the protocol-projected estimates with those from a reanalysis of survey serums by using liquid chromatography–tandem mass spectrometry (LC–tandem MS). Design: The VDSP reference system and protocols were applied to ELISA-based serum 25(OH)D data from the representative NANS sample (n = 1118). A reanalysis of 99 stored serums by using standardized LC–tandem MS and resulting regression equations yielded predicted standardized serum 25(OH)D values, which were then compared with LC–tandem MS reanalyzed values for all serums. Results: Year-round prevalence rates for serum 25(OH)D concentrations <30, <40, and <50 nmol/L were 6.5%, 21.9%, and 40.0%, respectively, via original ELISA measurements and 11.4%, 25.3%, and 43.7%, respectively, when VDSP protocols were applied. Differences in estimates at <30- and <40-nmol/L thresholds, but not at the <50-nmol/L threshold, were significant (P < 0.05). A reanalysis of all serums by using LC–tandem MS confirmed prevalence estimates as 11.2%, 27.2%, and 45.0%, respectively. Prevalences of serum 25(OH)D concentrations >125 nmol/L were 1.2%, 0.3%, and 0.6% by means of ELISA, VDSP protocols, and LC–tandem MS, respectively. Conclusion: VDSP protocols hold a major potential for national nutrition and health surveys in terms of the standardization of serum 25(OH)D data. PMID:23615829

Quantifying the effect of varying GHG's concentration in Regional Climate Models

NASA Astrophysics Data System (ADS)

López-Romero, Jose Maria; Jerez, Sonia; Palacios-Peña, Laura; José Gómez-Navarro, Juan; Jiménez-Guerrero, Pedro; Montavez, Juan Pedro

2017-04-01

Regional Climate Models (RCMs) are driven at the boundaries by Global Circulation Models (GCM), and in the particular case of Climate Change projections, such simulations are forced by varying greenhouse gases (GHGs) concentrations. In hindcast simulations driven by reanalysis products, the climate change signal is usually introduced in the assimilation process as well. An interesting question arising in this context is whether GHGs concentrations have to be varied within the RCMs model itself, or rather they should be kept constant. Some groups keep the GHGs concentrations constant under the assumption that information about climate change signal is given throughout the boundaries; sometimes certain radiation parameterization schemes do not permit such changes. Other approaches vary these concentrations arguing that this preserves the physical coherence respect to the driving conditions for the RCM. This work aims to shed light on this topic. For this task, various regional climate simulations with the WRF model for the 1954-2004 period have been carried out for using a Euro-CORDEX compliant domain. A series of simulations with constant and variable GHGs have been performed using both, a GCM (ECHAM6-OM) and a reanalysis product (ERA-20C) data. Results indicate that there exist noticeable differences when introducing varying GHGs concentrations within the RCM domain. The differences in 2-m temperature series between the experiments with varying or constant GHGs concentration strongly depend on the atmospheric conditions, appearing a strong interannual variability. This suggests that short-term experiments are not recommended if the aim is to assess the role of varying GHGs. In addition, and consistently in both GCM and reanalysis-driven experiments, the magnitude of temperature trends, as well as the spatial pattern represented by varying GHGs experiment, are closer to the driving dataset than in experiments keeping constant the GHGs concentration. These results point towards the need for the inclusion of varying GHGs concentration within the RCM itself when dynamically downscaling global datasets, both in GCM and hindcast simulations.

Seasonal evaluation of evapotranspiration fluxes from MODIS satellite and mesoscale model downscaled global reanalysis datasets

NASA Astrophysics Data System (ADS)

Srivastava, Prashant K.; Han, Dawei; Islam, Tanvir; Petropoulos, George P.; Gupta, Manika; Dai, Qiang

2016-04-01

Reference evapotranspiration (ETo) is an important variable in hydrological modeling, which is not always available, especially for ungauged catchments. Satellite data, such as those available from the MODerate Resolution Imaging Spectroradiometer (MODIS), and global datasets via the European Centre for Medium Range Weather Forecasts (ECMWF) reanalysis (ERA) interim and National Centers for Environmental Prediction (NCEP) reanalysis are important sources of information for ETo. This study explored the seasonal performances of MODIS (MOD16) and Weather Research and Forecasting (WRF) model downscaled global reanalysis datasets, such as ERA interim and NCEP-derived ETo, against ground-based datasets. Overall, on the basis of the statistical metrics computed, ETo derived from ERA interim and MODIS were more accurate in comparison to the estimates from NCEP for all the seasons. The pooled datasets also revealed a similar performance to the seasonal assessment with higher agreement for the ERA interim (r = 0.96, RMSE = 2.76 mm/8 days; bias = 0.24 mm/8 days), followed by MODIS (r = 0.95, RMSE = 7.66 mm/8 days; bias = -7.17 mm/8 days) and NCEP (r = 0.76, RMSE = 11.81 mm/8 days; bias = -10.20 mm/8 days). The only limitation with downscaling ERA interim reanalysis datasets using WRF is that it is time-consuming in contrast to the readily available MODIS operational product for use in mesoscale studies and practical applications.

Rapid iterative reanalysis for automated design

NASA Technical Reports Server (NTRS)

Bhatia, K. G.

1973-01-01

A method for iterative reanalysis in automated structural design is presented for a finite-element analysis using the direct stiffness approach. A basic feature of the method is that the generalized stiffness and inertia matrices are expressed as functions of structural design parameters, and these generalized matrices are expanded in Taylor series about the initial design. Only the linear terms are retained in the expansions. The method is approximate because it uses static condensation, modal reduction, and the linear Taylor series expansions. The exact linear representation of the expansions of the generalized matrices is also described and a basis for the present method is established. Results of applications of the present method to the recalculation of the natural frequencies of two simple platelike structural models are presented and compared with results obtained by using a commonly applied analysis procedure used as a reference. In general, the results are in good agreement. A comparison of the computer times required for the use of the present method and the reference method indicated that the present method required substantially less time for reanalysis. Although the results presented are for relatively small-order problems, the present method will become more efficient relative to the reference method as the problem size increases. An extension of the present method to static reanalysis is described, ana a basis for unifying the static and dynamic reanalysis procedures is presented.

Dissociating retrieval interference and reanalysis in the P600 during sentence comprehension.

PubMed

Tanner, Darren; Grey, Sarah; van Hell, Janet G

2017-02-01

We investigated the relative independence of two key processes in language comprehension, as reflected in the P600 ERP component. Numerous studies have linked the P600 to sentence- or message-level reanalysis; however, much research has shown that skilled, cue-based memory retrieval operations are also important to successful language processing. Our goal was to identify whether these cue-based retrieval operations are part of the reanalysis processes indexed by the P600. To this end, participants read sentences that were either grammatical or ungrammatical via subject-verb agreement violations, and in which there was either no possibility for retrieval interference or there was an attractor noun interfering with the computation of subject-verb agreement (e.g., "The slogan on the political poster(s) was/were …"). A stimulus onset asynchrony manipulation (fast, medium, or slow presentation rate) was designed to modulate participants' ability to engage in reanalysis processes. Results showed a reliable attraction interference effect, indexed by reduced behavioral sensitivity to ungrammaticalities and P600 amplitudes when there was an opportunity for retrieval interference, as well as an effect of presentation rate, with reduced behavioral sensitivity and smaller P600 effects at faster presentation rates. Importantly, there was no interaction between the two, suggesting that retrieval interference and sentence-level reanalysis processes indexed by the P600 can be neurocognitively distinct processes. © 2016 Society for Psychophysiological Research.

Chemiluminescence microarrays in analytical chemistry: a critical review.

PubMed

Seidel, Michael; Niessner, Reinhard

2014-09-01

Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review.

Analysis of High-Throughput ELISA Microarray Data

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

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

Filling the Silence: Reactivation, not Reconstruction

PubMed Central

Paape, Dario L. J. F.

2016-01-01

In a self-paced reading experiment, we investigated the processing of sluicing constructions (“sluices”) whose antecedent contained a known garden-path structure in German. Results showed decreased processing times for sluices with garden-path antecedents as well as a disadvantage for antecedents with non-canonical word order downstream from the ellipsis site. A post-hoc analysis showed the garden-path advantage also to be present in the region right before the ellipsis site. While no existing account of ellipsis processing explicitly predicted the results, we argue that they are best captured by combining a local antecedent mismatch effect with memory trace reactivation through reanalysis. PMID:26858674

Effects of Deficient Reporting on Meta-Analysis: A Conceptual Framework and Reanalysis

ERIC Educational Resources Information Center

Orwin, Robert G.; Cordray, David S.

1985-01-01

Identifies three sources of reporting deficiency for meta-analytic results: quality (adequacy) of publicizing; quality of macrolevel reporting, and quality of microlevel reporting. Reanalysis of 25 reports from the Smith, Glass and Miller (1980) psychotherapy meta-analysis established two sources of misinformation, interrater reliabilities and…

Differential Effects of Treatments for Chronic Depression: A Latent Growth Model Reanalysis

ERIC Educational Resources Information Center

Stulz, Niklaus; Thase, Michael E.; Klein, Daniel N.; Manber, Rachel; Crits-Christoph, Paul

2010-01-01

Objective: Psychotherapy-pharmacotherapy combinations are frequently recommended for the treatment of chronic depressive disorders. Our aim in this novel reanalysis of archival data was to identify patient subgroups on the basis of symptom trajectories and examine the clinical significance of the resultant classification on basis of differential…

The Circumplex Pattern of the Life Styles Inventory: A Reanalysis.

ERIC Educational Resources Information Center

Levin, Joseph

1991-01-01

A reanalysis of the intercorrelation matrix from a principal components analysis of the Life Styles Inventory was conducted using a Canadian sample. Using nonmetric multidimensional scaling, analyses show an almost perfect circumplex pattern. Results illustrate the inadequacy of factor analytic procedures for the analysis and representation of a…

NASA's EOSDIS Near Term Challenges

NASA Technical Reports Server (NTRS)

Behnke, Jeanne

2018-01-01

Given the long-term requirements, and the rapid pace of information technology and changing expectations of the user community, the ESDIS Project has had to evolve EOSDIS continually over the past three decades. However, many challenges remain. One near-term challenge is the enormous quantity of new data that will need to be managed by the EOSDIS. With the upcoming launch of the latest NASA missions coupled with existing operational missions and field campaigns, EOSDIS can expect to handle as much as 50 petabytes of data per year. In perspective, this is twice the size of the current existing archive, which took over 21 years to collect. Another continuing challenge is the disparate requirements of a diverse science community. Maintaining rigorous long-term data preservation, supporting ease of discovery and access, incorporating user feedback, enabling reanalysis/ reprocessing, and agile integration of new data sources, continue to be the Project's objectives.

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

PubMed Central

Weniger, Markus; Engelmann, Julia C; Schultz, Jörg

2007-01-01

Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular conditions. The data derived out of microarray experiments is highly dimensional and often noisy, and interpretation of the results can get intricate. Although programs for the statistical analysis of microarray data exist, most of them lack an integration of analysis results and biological interpretation. Results We have developed GEPAT, Genome Expression Pathway Analysis Tool, offering an analysis of gene expression data under genomic, proteomic and metabolic context. We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip. GEPAT imports various types of oligonucleotide and cDNA array data formats. Different normalization methods can be applied to the data, afterwards data annotation is performed. After import, GEPAT offers various statistical data analysis methods, as hierarchical, k-means and PCA clustering, a linear model based t-test or chromosomal profile comparison. The results of the analysis can be interpreted by enrichment of biological terms, pathway analysis or interaction networks. Different biological databases are included, to give various information for each probe on the chip. GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis. GEPAT relies on established data analysis packages, offers a modular approach for an easy extension, and can be run on a computer grid to allow a large number of users. It is freely available under the LGPL open source license for academic and commercial users at . Conclusion GEPAT is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data. An installation available for academic users can be found at . PMID:17543125

Identification of candidate genes involved in neuroblastoma progression by combining genomic and expression microarrays with survival data.

PubMed

Łastowska, M; Viprey, V; Santibanez-Koref, M; Wappler, I; Peters, H; Cullinane, C; Roberts, P; Hall, A G; Tweddle, D A; Pearson, A D J; Lewis, I; Burchill, S A; Jackson, M S

2007-11-22

Identifying genes, whose expression is consistently altered by chromosomal gains or losses, is an important step in defining genes of biological relevance in a wide variety of tumour types. However, additional criteria are needed to discriminate further among the large number of candidate genes identified. This is particularly true for neuroblastoma, where multiple genomic copy number changes of proven prognostic value exist. We have used Affymetrix microarrays and a combination of fluorescent in situ hybridization and single nucleotide polymorphism (SNP) microarrays to establish expression profiles and delineate copy number alterations in 30 primary neuroblastomas. Correlation of microarray data with patient survival and analysis of expression within rodent neuroblastoma cell lines were then used to define further genes likely to be involved in the disease process. Using this approach, we identify >1000 genes within eight recurrent genomic alterations (loss of 1p, 3p, 4p, 10q and 11q, 2p gain, 17q gain, and the MYCN amplicon) whose expression is consistently altered by copy number change. Of these, 84 correlate with patient survival, with the minimal regions of 17q gain and 4p loss being enriched significantly for such genes. These include genes involved in RNA and DNA metabolism, and apoptosis. Orthologues of all but one of these genes on 17q are overexpressed in rodent neuroblastoma cell lines. A significant excess of SNPs whose copy number correlates with survival is also observed on proximal 4p in stage 4 tumours, and we find that deletion of 4p is associated with improved outcome in an extended cohort of tumours. These results define the major impact of genomic copy number alterations upon transcription within neuroblastoma, and highlight genes on distal 17q and proximal 4p for downstream analyses. They also suggest that integration of discriminators, such as survival and comparative gene expression, with microarray data may be useful in the identification of critical genes within regions of loss or gain in many human cancers.

Cross-Study Homogeneity of Psoriasis Gene Expression in Skin across a Large Expression Range

PubMed Central

Kerkof, Keith; Timour, Martin; Russell, Christopher B.

2013-01-01

Background In psoriasis, only limited overlap between sets of genes identified as differentially expressed (psoriatic lesional vs. psoriatic non-lesional) was found using statistical and fold-change cut-offs. To provide a framework for utilizing prior psoriasis data sets we sought to understand the consistency of those sets. Methodology/Principal Findings Microarray expression profiling and qRT-PCR were used to characterize gene expression in PP and PN skin from psoriasis patients. cDNA (three new data sets) and cRNA hybridization (four existing data sets) data were compared using a common analysis pipeline. Agreement between data sets was assessed using varying qualitative and quantitative cut-offs to generate a DEG list in a source data set and then using other data sets to validate the list. Concordance increased from 67% across all probe sets to over 99% across more than 10,000 probe sets when statistical filters were employed. The fold-change behavior of individual genes tended to be consistent across the multiple data sets. We found that genes with <2-fold change values were quantitatively reproducible between pairs of data-sets. In a subset of transcripts with a role in inflammation changes detected by microarray were confirmed by qRT-PCR with high concordance. For transcripts with both PN and PP levels within the microarray dynamic range, microarray and qRT-PCR were quantitatively reproducible, including minimal fold-changes in IL13, TNFSF11, and TNFRSF11B and genes with >10-fold changes in either direction such as CHRM3, IL12B and IFNG. Conclusions/Significance Gene expression changes in psoriatic lesions were consistent across different studies, despite differences in patient selection, sample handling, and microarray platforms but between-study comparisons showed stronger agreement within than between platforms. We could use cut-offs as low as log10(ratio) = 0.1 (fold-change = 1.26), generating larger gene lists that validate on independent data sets. The reproducibility of PP signatures across data sets suggests that different sample sets can be productively compared. PMID:23308107

Comparative study of classification algorithms for immunosignaturing data

PubMed Central

2012-01-01

Background High-throughput technologies such as DNA, RNA, protein, antibody and peptide microarrays are often used to examine differences across drug treatments, diseases, transgenic animals, and others. Typically one trains a classification system by gathering large amounts of probe-level data, selecting informative features, and classifies test samples using a small number of features. As new microarrays are invented, classification systems that worked well for other array types may not be ideal. Expression microarrays, arguably one of the most prevalent array types, have been used for years to help develop classification algorithms. Many biological assumptions are built into classifiers that were designed for these types of data. One of the more problematic is the assumption of independence, both at the probe level and again at the biological level. Probes for RNA transcripts are designed to bind single transcripts. At the biological level, many genes have dependencies across transcriptional pathways where co-regulation of transcriptional units may make many genes appear as being completely dependent. Thus, algorithms that perform well for gene expression data may not be suitable when other technologies with different binding characteristics exist. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides. It relies on many-to-many binding of antibodies to the random sequence peptides. Each peptide can bind multiple antibodies and each antibody can bind multiple peptides. This technology has been shown to be highly reproducible and appears promising for diagnosing a variety of disease states. However, it is not clear what is the optimal classification algorithm for analyzing this new type of data. Results We characterized several classification algorithms to analyze immunosignaturing data. We selected several datasets that range from easy to difficult to classify, from simple monoclonal binding to complex binding patterns in asthma patients. We then classified the biological samples using 17 different classification algorithms. Using a wide variety of assessment criteria, we found ‘Naïve Bayes’ far more useful than other widely used methods due to its simplicity, robustness, speed and accuracy. Conclusions ‘Naïve Bayes’ algorithm appears to accommodate the complex patterns hidden within multilayered immunosignaturing microarray data due to its fundamental mathematical properties. PMID:22720696

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

Living Cell Microarrays: An Overview of Concepts

PubMed Central

Jonczyk, Rebecca; Kurth, Tracy; Lavrentieva, Antonina; Walter, Johanna-Gabriela; Scheper, Thomas; Stahl, Frank

2016-01-01

Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays. PMID:27600077

Assessment of Patient-Specific Surgery Effect Based on Weighted Estimation and Propensity Scoring in the Re-Analysis of the Sciatica Trial

PubMed Central

Mertens, Bart J. A.; Jacobs, Wilco C. H.; Brand, Ronald; Peul, Wilco C.

2014-01-01

We consider a re-analysis of the wait-and-see (control) arm of a recent clinical trial on sciatica. While the original randomised trial was designed to evaluate the public policy effect of a conservative wait-and-see approach versus early surgery, we investigate the impact of surgery at the individual patient level in a re-analysis of the wait-and-see group data. Both marginal structural model re-weighted estimates as well as propensity score adjusted analyses are presented. Results indicate that patients with high propensity to receive surgery may have beneficial effects at 2 years from delayed disc surgery. PMID:25353633

The NOAA-NASA CZCS Reanalysis Effort

NASA Technical Reports Server (NTRS)

Gregg, Watson W.; Conkright, Margarita E.; OReilly, John E.; Patt, Frederick S.; Wang, Meng-Hua; Yoder, James; Casey-McCabe, Nancy; Koblinsky, Chester J. (Technical Monitor)

2001-01-01

Satellite observations of global ocean chlorophyll span over two decades. However, incompatibilities between processing algorithms prevent us from quantifying natural variability. We applied a comprehensive reanalysis to the Coastal Zone Color Scanner (CZCS) archive, called the NOAA-NASA CZCS Reanalysis (NCR) Effort. NCR consisted of 1) algorithm improvement (AI), where CZCS processing algorithms were improved using modernized atmospheric correction and bio-optical algorithms, and 2) blending, where in situ data were incorporated into the CZCS AI to minimize residual errors. The results indicated major improvement over the previously available CZCS archive. Global spatial and seasonal patterns of NCR chlorophyll indicated remarkable correspondence with modern sensors, suggesting compatibility. The NCR permits quantitative analyses of interannual and interdecadal trends in global ocean chlorophyll.

ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data

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

White, Amanda M.; Collett, James L.; Seurynck-Servoss, Shannon L.

ELISA-BASE is an open-source database for capturing, organizing and analyzing protein enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Soft-ware Environment (BASE) database system, which was developed for DNA microarrays. In order to make BASE suitable for protein microarray experiments, we developed several plugins for importing and analyzing quantitative ELISA microarray data. Most notably, our Protein Microarray Analysis Tool (ProMAT) for processing quantita-tive ELISA data is now available as a plugin to the database.

Thermodynamically optimal whole-genome tiling microarray design and validation.

PubMed

Cho, Hyejin; Chou, Hui-Hsien

2016-06-13

Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics.

PubMed

Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Coatrieux, Jean-Louis; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Porro, Ivan; Beltrame, Francesco; Tollis, Ioannis; Van der Lei, Johan

2007-03-08

The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to improve collaborative progress between both domains (ref. to http://www.symbiomatics.org). As part of the project experts in both research fields will be identified and approached through a survey. To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics. This paper presents results of a systematic analysis of the scientific literature from medical informatics research and bioinformatics research. In the analysis pairs of words (bigrams) from the leading bioinformatics and medical informatics journals have been used as indication of existing and emerging technologies and topics over the period 2000-2005 ("recent") and 1990-1990 ("past"). We identified emerging topics that were equally important to bioinformatics and medical informatics in recent years such as microarray experiments, ontologies, open source, text mining and support vector machines. Emerging topics that evolved only in bioinformatics were system biology, protein interaction networks and statistical methods for microarray analyses, whereas emerging topics in medical informatics were grid technology and tissue microarrays. We conclude that although both fields have their own specific domains of interest, they share common technological developments that tend to be initiated by new developments in biotechnology and computer science.

SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics

PubMed Central

Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Coatrieux, Jean-Louis; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Porro, Ivan; Beltrame, Francesco; Tollis, Ioannis; Van der Lei, Johan

2007-01-01

Background The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to improve collaborative progress between both domains (ref. to ). As part of the project experts in both research fields will be identified and approached through a survey. To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics. Results This paper presents results of a systematic analysis of the scientific literature from medical informatics research and bioinformatics research. In the analysis pairs of words (bigrams) from the leading bioinformatics and medical informatics journals have been used as indication of existing and emerging technologies and topics over the period 2000–2005 ("recent") and 1990–1990 ("past"). We identified emerging topics that were equally important to bioinformatics and medical informatics in recent years such as microarray experiments, ontologies, open source, text mining and support vector machines. Emerging topics that evolved only in bioinformatics were system biology, protein interaction networks and statistical methods for microarray analyses, whereas emerging topics in medical informatics were grid technology and tissue microarrays. Conclusion We conclude that although both fields have their own specific domains of interest, they share common technological developments that tend to be initiated by new developments in biotechnology and computer science. PMID:17430562

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

PubMed

Swertz, Morris A; De Brock, E O; Van Hijum, Sacha A F T; De Jong, Anne; Buist, Girbe; Baerends, Richard J S; Kok, Jan; Kuipers, Oscar P; Jansen, Ritsert C

2004-09-01

Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. http://www.molgenis.nl

Classification of mislabelled microarrays using robust sparse logistic regression.

PubMed

Bootkrajang, Jakramate; Kabán, Ata

2013-04-01

Previous studies reported that labelling errors are not uncommon in microarray datasets. In such cases, the training set may become misleading, and the ability of classifiers to make reliable inferences from the data is compromised. Yet, few methods are currently available in the bioinformatics literature to deal with this problem. The few existing methods focus on data cleansing alone, without reference to classification, and their performance crucially depends on some tuning parameters. In this article, we develop a new method to detect mislabelled arrays simultaneously with learning a sparse logistic regression classifier. Our method may be seen as a label-noise robust extension of the well-known and successful Bayesian logistic regression classifier. To account for possible mislabelling, we formulate a label-flipping process as part of the classifier. The regularization parameter is automatically set using Bayesian regularization, which not only saves the computation time that cross-validation would take, but also eliminates any unwanted effects of label noise when setting the regularization parameter. Extensive experiments with both synthetic data and real microarray datasets demonstrate that our approach is able to counter the bad effects of labelling errors in terms of predictive performance, it is effective at identifying marker genes and simultaneously it detects mislabelled arrays to high accuracy. The code is available from http://cs.bham.ac.uk/∼jxb008. Supplementary data are available at Bioinformatics online.

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes

PubMed Central

Li, Ben; Sun, Zhaonan; He, Qing; Zhu, Yu; Qin, Zhaohui S.

2016-01-01

Motivation: Modern high-throughput biotechnologies such as microarray are capable of producing a massive amount of information for each sample. However, in a typical high-throughput experiment, only limited number of samples were assayed, thus the classical ‘large p, small n’ problem. On the other hand, rapid propagation of these high-throughput technologies has resulted in a substantial collection of data, often carried out on the same platform and using the same protocol. It is highly desirable to utilize the existing data when performing analysis and inference on a new dataset. Results: Utilizing existing data can be carried out in a straightforward fashion under the Bayesian framework in which the repository of historical data can be exploited to build informative priors and used in new data analysis. In this work, using microarray data, we investigate the feasibility and effectiveness of deriving informative priors from historical data and using them in the problem of detecting differentially expressed genes. Through simulation and real data analysis, we show that the proposed strategy significantly outperforms existing methods including the popular and state-of-the-art Bayesian hierarchical model-based approaches. Our work illustrates the feasibility and benefits of exploiting the increasingly available genomics big data in statistical inference and presents a promising practical strategy for dealing with the ‘large p, small n’ problem. Availability and implementation: Our method is implemented in R package IPBT, which is freely available from https://github.com/benliemory/IPBT. Contact: yuzhu@purdue.edu; zhaohui.qin@emory.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26519502

Smart Climatology System

DTIC Science & Technology

2010-09-24

12 2.1 Downscaling /Reanalysis Data ................................................................................ 12 2.2 Downscaling of...Comparison of Resolutions of Maximum Significant Wave heights for La Niña >= 8 ft >= 6 ft 12 2 Data Production Issues 2.1 Downscaling /Reanalysis...numerical weather prediction systems. The usage of satellite data , for example, is markedly different than the past practice. This played havoc with

Reanalysis of Clause Boundaries in Japanese as a Constraint-Driven Process.

ERIC Educational Resources Information Center

Miyamoto, Edson T.

2003-01-01

Reports on two experiments that focus on clause boundaries in Japanese that suggest that minimal change restriction is unnecessary to characterize reanalysis. Proposes that the data and previous observations are more naturally explained by a constraint-driven model in which revisions are performed only when required by parsing constraints.…

Does Nutrition Cause Intelligence? A Reanalysis of the Cali Experiment.

ERIC Educational Resources Information Center

Bejar, Isaac I.

1981-01-01

Recent literature suggests a causal link between malnutrition and impaired cognitive development. A selective literature review indicates that the presence or absence of such a link cannot be established. A reanalysis of an experiment indicated after four years of treatment there was no association between cognitive and nutritional status.…

Cognitive Development Among Retardates: Reanalysis of Inhelder's Data.

ERIC Educational Resources Information Center

Jordan, Valerie Barnes

A reanalysis of B. Inhelder's (1968) data concerning cognitive development among retardates was performed by selecting from the original 159 subjects a sample of 104 educable mentally retarded Ss (7-19 years old) who were diagnosed as fixated or nonfixated at three of the cognitive stages postulated by Jean Piaget. The results indicated that among…

The Value of Reanalysis: TV Viewing and Attention Problems

ERIC Educational Resources Information Center

Foster, E. Michael; Watkins, Stephanie

2010-01-01

Using data from the National Longitudinal Survey of Youth (N = 1,159), this study reexamines the link between maternal reports of television viewing at ages 1 and 3 and attention problems at age 7. This work represents a reanalysis and extension of recent research suggesting young children's television viewing causes subsequent attention problems.…

Assessment of Uncertainties in Recent Changes in the South American Low-Level Jet Based on Various Reanalyses

NASA Astrophysics Data System (ADS)

Montini, T.; Jones, C.

2017-12-01

The South American low-level jet (SALLJ) is one of the key components of the South American Monsoon System. The SALLJ transports large amounts of moisture to the subtropics, influencing the development of deep convection and heavy precipitation over southeastern South America. Previous studies have analyzed the jet using reanalysis data due to the lack of available upper-air observations over this region. The purpose of the current study is to quantify uncertainties in the climatology, variability, and changes in the SALLJ based on various reanalyses for the period 1979-2015. This is important because there are significant differences among reanalysis datasets due to variations in their data quality control, data assimilation systems, and model physics. The datasets used in this analysis are: (1) Climate Forecast System Reanalysis, (2) ERA-Interim, (3) the Japanese 55-year reanalysis, (4) the Second Modern Era Retrospective-analysis for Research and Applications (MERRA-2). Finally, significant changes in the SALLJ are discussed in relation to substantial warming over South America in recent decades and changes in the monsoon.

Surface Mass Balance of the Greenland Ice Sheet Derived from Paleoclimate Reanalysis

NASA Astrophysics Data System (ADS)

Badgeley, J.; Steig, E. J.; Hakim, G. J.; Anderson, J.; Tardif, R.

2017-12-01

Modeling past ice-sheet behavior requires independent knowledge of past surface mass balance. Though models provide useful insight into ice-sheet response to climate forcing, if past climate is unknown, then ascertaining the rate and extent of past ice-sheet change is limited to geological and geophysical constraints. We use a novel data-assimilation framework developed under the Last Millennium Reanalysis Project (Hakim et al., 2016) to reconstruct past climate over ice sheets with the intent of creating an independent surface mass balance record for paleo ice-sheet modeling. Paleoclimate data assimilation combines the physics of climate models and the time series evidence of proxy records in an offline, ensemble-based approach. This framework allows for the assimilation of numerous proxy records and archive types while maintaining spatial consistency with known climate dynamics and physics captured by the models. In our reconstruction, we use the Community Climate System Model version 4, CMIP5 last millennium simulation (Taylor et al., 2012; Landrum et al., 2013) and a nearly complete database of ice core oxygen isotope records to reconstruct Holocene surface temperature and precipitation over the Greenland Ice Sheet on a decadal timescale. By applying a seasonality to this reconstruction (from the TraCE-21ka simulation; Liu et al., 2009), our reanalysis can be used in seasonally-based surface mass balance models. Here we discuss the methods behind our reanalysis and the performance of our reconstruction through prediction of unassimilated proxy records and comparison to paleoclimate reconstructions and reanalysis products.

Reanalysis of the Indian summer monsoon: four dimensional data assimilation of AIRS retrievals in a regional data assimilation and modeling framework

NASA Astrophysics Data System (ADS)

Attada, Raju; Parekh, Anant; Chowdary, J. S.; Gnanaseelan, C.

2018-04-01

This work is the first attempt to produce a multi-year downscaled regional reanalysis of the Indian summer monsoon (ISM) using the National Centers for Environmental Prediction (NCEP) operational analyses and Atmospheric Infrared Sounder (AIRS) version 5 temperature and moisture retrievals in a regional model. Reanalysis of nine monsoon seasons (2003-2011) are produced in two parallel setups. The first set of experiments simply downscale the original NCEP operational analyses, whilst the second one assimilates the AIRS temperature and moisture profiles. The results show better representation of the key monsoon features such as low level jet, tropical easterly jet, subtropical westerly jet, monsoon trough and the spatial pattern of precipitation when AIRS profiles are assimilated (compared to those without AIRS data assimilation). The distribution of temperature, moisture and meridional gradients of dynamical and thermodynamical fields over the monsoon region are better represented in the reanalysis that assimilates AIRS profiles. The change induced by AIRS data on the moist and thermodynamic conditions results in more realistic rendering of the vertical shear associated with the monsoon, which in turn leads to a proper moisture transport and the moist convective feedback. This feedback benefits the representation of the regional monsoon characteristics, the monsoon dynamics and the moist convective processes on the seasonal time scale. This study emphasizes the use of AIRS soundings for downscaling of ISM representation in a regional reanalysis.

The Mars Analysis Correction Data Assimilation (MACDA): A reference atmospheric reanalysis

NASA Astrophysics Data System (ADS)

Montabone, Luca; Read, Peter; Lewis, Stephen; Steele, Liam; Holmes, James; Valeanu, Alexandru

2016-07-01

The Mars Analysis Correction Data Assimilation (MACDA) dataset version 1.0 contains the reanalysis of fundamental atmospheric and surface variables for the planet Mars covering a period of about three Martian years (late MY 24 to early MY 27). This has been produced by data assimilation of retrieved thermal profiles and column dust optical depths from NASA's Mars Global Surveyor/Thermal Emission Spectrometer (MGS/TES), which have been assimilated into a Mars global climate model (MGCM) using the Analysis Correction scheme developed at the UK Meteorological Office. The MACDA v1.0 reanalysis is publicly available, and the NetCDF files can be downloaded from the archive at the Centre for Environmental Data Analysis/British Atmospheric Data Centre (CEDA/BADC). The variables included in the dataset can be visualised using an ad-hoc graphical user interface (the "MACDA Plotter") at the following URL: http://macdap.physics.ox.ac.uk/ MACDA is an ongoing collaborative project, and work is currently undertaken to produce version 2.0 of the Mars atmospheric reanalysis. One of the key improvements is the extension of the reanalysis period to nine martian years (MY 24 through MY 32), with the assimilation of NASA's Mars Reconnaissance Orbiter/Mars Climate Sounder (MRO/MCS) retrievals of thermal and dust opacity profiles. MACDA 2.0 is also going to be based on an improved version of the underlying MGCM and an updated scheme to fully assimilate (radiative active) tracers, such as dust and water ice.

Trends in solar radiation in NCEP/NCAR database and measurements in northeastern Brazil

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

Silva, Vicente de Paulo Rodrigues da; Silva, Roberta Araujo e; Cavalcanti, Enilson Palmeira

2010-10-15

The database from the National Center for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) re-analysis project available for the period from 1948 to 2009 was used for obtaining long-term solar radiation for northeastern Brazil. Measurements of global solar radiation (R{sub s}) from data collection platform (DCP) for four climatic zones of northeastern Brazil were compared to the re-analysis data. Applying cluster analysis to R{sub s} from database, homogeneous sub-regions in northeastern Brazil were determined. Long times series of R{sub s} and sunshine duration measurements data for two sites, Petrolina (09 09'S, 40 22'W) and Juazeiro (09 24'S, 40 26'W), exceedingmore » 30 years, were analyzed. In order to exclude the decadal variations which are linked to the Pacific Decadal Oscillation, high-frequency cycles in the solar radiation and sunshine duration time series were eliminated by using a 14-year moving average, and the Mann-Kendall test was employed to assess the long-term variability of re-analysis and measured solar radiation. This study provides an overview of the decrease in solar radiation in a large area, which can be attributed to the global dimming effect. The global solar radiation obtained from the NCEP/NCAR re-analysis data overestimate that obtained from DCP measurements by 1.6% to 18.6%. Results show that there is a notable symmetry between R{sub s} from the re-analysis data and sunshine duration measurements. (author)« less

Met Éireann high resolution reanalysis for Ireland

NASA Astrophysics Data System (ADS)

Gleeson, Emily; Whelan, Eoin; Hanley, John

2017-03-01

The Irish Meteorological Service, Met Éireann, has carried out a 35-year very high resolution (2.5 km horizontal grid) regional climate reanalysis for Ireland using the ALADIN-HIRLAM numerical weather prediction system. This article provides an overview of the reanalysis, called MÉRA, as well as a preliminary analysis of surface parameters including screen level temperature, 10 m wind speeds, mean sea-level pressure (MSLP), soil temperatures, soil moisture and 24 h rainfall accumulations. The quality of the 3-D variational data assimilation used in the reanalysis is also assessed. Preliminary analysis shows that it takes almost 12 months to spin up the deep soil in terms of moisture, justifying the choice of running year-long spin up periods. Overall, the model performed consistently over the time period. Small biases were found in screen-level temperatures (less than -0.5 °C), MSLP (within 0.5 hPa) and 10 m wind speed (up to 0.5 m s-1) Soil temperatures are well represented by the model. 24 h accumulations of precipitation generally exhibit a small positive bias of ˜ 1 mm per day and negative biases over mountains due to a mismatch between the model orography and the geography of the region. MÉRA outperforms the ERA-Interim reanalysis, particularly in terms of standard deviations in screen-level temperatures and surface winds. This dataset is the first of its kind for Ireland that will be made publically available during spring 2017.

Large differences in reanalyses of diabatic heating in the tropical upper troposphere and lower stratosphere

NASA Astrophysics Data System (ADS)

Wright, J. S.; Fueglistaler, S.

2013-09-01

We present the time mean heat budgets of the tropical upper troposphere (UT) and lower stratosphere (LS) as simulated by five reanalysis models: the Modern-Era Retrospective Analysis for Research and Applications (MERRA), European Reanalysis (ERA-Interim), Climate Forecast System Reanalysis (CFSR), Japanese 25-yr Reanalysis and Japan Meteorological Agency Climate Data Assimilation System (JRA-25/JCDAS), and National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) Reanalysis 1. The simulated diabatic heat budget in the tropical UTLS differs significantly from model to model, with substantial implications for representations of transport and mixing. Large differences are apparent both in the net heat budget and in all comparable individual components, including latent heating, heating due to radiative transfer, and heating due to parameterised vertical mixing. We describe and discuss the most pronounced differences. Discrepancies in latent heating reflect continuing difficulties in representing moist convection in models. Although these discrepancies may be expected, their magnitude is still disturbing. We pay particular attention to discrepancies in radiative heating (which may be surprising given the strength of observational constraints on temperature and tropospheric water vapour) and discrepancies in heating due to turbulent mixing (which have received comparatively little attention). The largest differences in radiative heating in the tropical UTLS are attributable to differences in cloud radiative heating, but important systematic differences are present even in the absence of clouds. Local maxima in heating and cooling due to parameterised turbulent mixing occur in the vicinity of the tropical tropopause.

Extending Climate Analytics-As to the Earth System Grid Federation

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; McInerney, M.; Nadeau, D.; Li, J.; Strong, S.; Thompson, J. H.

2015-12-01

We are building three extensions to prior-funded work on climate analytics-as-a-service that will benefit the Earth System Grid Federation (ESGF) as it addresses the Big Data challenges of future climate research: (1) We are creating a cloud-based, high-performance Virtual Real-Time Analytics Testbed supporting a select set of climate variables from six major reanalysis data sets. This near real-time capability will enable advanced technologies like the Cloudera Impala-based Structured Query Language (SQL) query capabilities and Hadoop-based MapReduce analytics over native NetCDF files while providing a platform for community experimentation with emerging analytic technologies. (2) We are building a full-featured Reanalysis Ensemble Service comprising monthly means data from six reanalysis data sets. The service will provide a basic set of commonly used operations over the reanalysis collections. The operations will be made accessible through NASA's climate data analytics Web services and our client-side Climate Data Services (CDS) API. (3) We are establishing an Open Geospatial Consortium (OGC) WPS-compliant Web service interface to our climate data analytics service that will enable greater interoperability with next-generation ESGF capabilities. The CDS API will be extended to accommodate the new WPS Web service endpoints as well as ESGF's Web service endpoints. These activities address some of the most important technical challenges for server-side analytics and support the research community's requirements for improved interoperability and improved access to reanalysis data.

Recent Reanalysis Activities at ECMWF: Results from ERA-20C and Plans for ERA5

NASA Astrophysics Data System (ADS)

Dragani, R.; Hersbach, H.; Poli, P.; Pebeuy, C.; Hirahara, S.; Simmons, A.; Dee, D.

2015-12-01

This presentation will provide an overview of the most recent reanalysis activities performed at the European Centre for Medium-Range Weather Forecasts (ECMWF). A pilot reanalysis of the 20th-century (ERA-20C) has recently been completed. Funded through the European FP7 collaborative project ERA-CLIM, ERA-20C is part of a suite of experiments that also includes a model-only integration (ERA-20CM) and a land-surface reanalysis (ERA-20CL). Its data assimilation system is constrained by only surface observations obtained from ISPD (3.2.6) and ICOADS (2.5.1). Surface boundary conditions are provided by the Hadley Centre (HadISST2.1.0.0) and radiative forcing follows CMIP5 recommended data sets. First-guess uncertainty estimates are based on a 10-member ensemble of Data Assimilations, ERA-20C ensemble, run prior to ERA-20C using ten SST and sea-ice realizations from the Hadley Centre. In November 2014, the European Commission entrusted ECMWF to run on its behalf the Copernicus Climate Change Service (C3S) aiming at producing quality-assured information about the past, current and future states of the climate at both European and global scales. Reanalysis will be one of the main components of the C3S portfolio and the first one to be produced is a global modern era reanalysis (ERA5) covering the period from 1979 onwards. Based on a recent version of the ECMWF data assimilation system, ERA5 will replace the widely used ERA-Interim dataset. This new production will benefit from a much improved model, and better characterized and exploited observations compared to its predecessor. The first part of the presentation will focus on the ERA-20C production, provide an overview of its main characteristics and discuss some of the key results from its assessment. The second part of the talk will give an overview of ERA5, and briefly discuss some of its challenges.

Assessment of Precipitation Trends over Europe by Comparing ERA-20C with a New Homogenized Observational GPCC Dataset

NASA Astrophysics Data System (ADS)

Rustemeier, E.; Ziese, M.; Meyer-Christoffer, A.; Finger, P.; Schneider, U.; Becker, A.

2015-12-01

Reliable data is essential for robust climate analysis. The ERA-20C reanalysis was developed during the projects ERA-CLIM and ERA-CLIM2. These projects focus on multi-decadal reanalyses of the global climate system. To ensure data quality and provide end users with information about uncertainties in these products, the 4th work package of ERA_CLIM2 deals with the quality assessment of the products including quality control and error estimation.In doing so, the monthly totals of the ERA-20C reanalysis are compared to two corresponding Global Precipitation Climatology Centre (GPCC) products; the Full Data Reanalysis Version 7 and the new HOMogenized PRecipitation Analysis of European in-situ data (HOMPRA Europe).ERA-20C reanalysis was produced based on ECMWFs IFS version Cy38r1 with a spatial resolution of about 125 km. It covers the time period 1900 to 2010. Only surface observations are assimilated namely marine winds and pressure. This allows the comparison with independent, not assimilated data. The GPCC Full Data Reanalysis Version 7 comprises monthly land-surface precipitation from approximately 75,000 rain-gauges covering the time period 1901-2013. For this paper, the version with 1° resolution is utilized. For trend analysis, a monthly European subset of the ERA-20C reanalysis is investigated spanning the years 1951-2005. The European subset will be compared to a new homogenized GPCC data set HOMPRA Europe. The latter is based on a collective of 5373 homogenized monthly rain gauge time series, carefully chosen from the GPCC archive of precipitation data.For the spatial and temporal evaluation of ERA-20C, global scores on monthly, seasonal and annual time scales are calculated. These include contingency table scores, correlation, along with spatial scores such as the fractional skill score. Unsurprisingly regions with strongest deviations are those of data scarcity, mountainous regions with their luv and lee effects, and monsoon regions. They all exhibit strong biases throughout their series, and severe shifts in the means. The new HOMPRA Europe data set is useful in particular for trend analysis. Therefore it is compared to a monthly European subset of the ERA-20C reanalysis for the same period, i.e. the years 1951-2005, to study the ERA-20C capability in reproducing observed trends across Europe.

The Mars Analysis Correction Data Assimilation (MACDA): A reference atmospheric reanalysis

NASA Astrophysics Data System (ADS)

Montabone, Luca; Lewis, Stephen R.; Steele, Liam J.; Holmes, James; Read, Peter L.; Valeanu, Alexandru; Smith, Michael D.; Kass, David; Kleinboehl, Armin; LMD Team, MGS/TES Team, MRO/MCS Team

2016-10-01

The Mars Analysis Correction Data Assimilation (MACDA) dataset version 1.0 contains the reanalysis of fundamental atmospheric and surface variables for the planet Mars covering a period of about three Martian years (late MY 24 to early MY 27). This four-dimensional dataset has been produced by data assimilation of retrieved thermal profiles and column dust optical depths from NASA's Mars Global Surveyor/Thermal Emission Spectrometer (MGS/TES), which have been assimilated into a Mars global climate model (MGCM) using the Analysis Correction scheme developed at the UK Meteorological Office.The MACDA v1.0 reanalysis is publicly available, and the NetCDF files can be downloaded from the archive at the Centre for Environmental Data Analysis/British Atmospheric Data Centre (CEDA/BADC). The variables included in the dataset can be visualised using an ad-hoc graphical user interface (the "MACDA Plotter") located at the following URL: http://macdap.physics.ox.ac.uk/The first paper about MACDA reanalysis of TES retrievals appeared in 2006, although the acronym MACDA was not yet used at that time. Ten years later, MACDA v1.0 has been used by several researchers worldwide and has contributed to the advancement of the knowledge about the martian atmosphere in critical areas such as the radiative impact of water ice clouds, the solsticial pause in baroclinic wave activity, and the climatology and dynamics of polar vortices, to cite only a few. It is therefore timely to review the scientific results obtained by using such Mars reference atmospheric reanalysis, in order to understand what priorities the user community should focus on in the next decade.MACDA is an ongoing collaborative project, and work funded by NASA MDAP Programme is currently undertaken to produce version 2.0 of the Mars atmospheric reanalysis. One of the key improvements is the extension of the reanalysis period to nine martian years (MY 24 through MY 32), with the assimilation of NASA's Mars Reconnaissance Orbiter/Mars Climate Sounder (MRO/MCS) retrievals of thermal and dust opacity profiles. MACDA 2.0 is also going to be based on an improved version of the underlying MGCM and an updated scheme to fully assimilate (radiative active) tracers, such as dust.

Evaluation of reanalysis near-surface winds over northern Africa in Boreal summer

NASA Astrophysics Data System (ADS)

Engelstaedter, Sebastian; Washington, Richard

2014-05-01

The emission of dust from desert surfaces depends on the combined effects of surface properties such as surface roughness, soil moisture, soil texture and particle size (erodibility) and wind speed (erosivity). In order for dust cycle models to realistically simulate dust emissions for the right reasons, it is essential that erosivity and erodibility controlling factors are represented correctly. There has been a focus on improving dust emission schemes or input fields of soil distribution and texture even though it has been shown that the use of wind fields from different reanalysis datasets to drive the same model can result in significant differences in the dust emissions. Here we evaluate the representation of near-surface wind speed from three different reanalysis datasets (ERA-Interim, CFSR and MERRA) over the North African domain. Reanalysis 10m wind speeds are compared with observations from SYNOP and METAR reports available from the UK Meteorological Office Integrated Data Archive System (MIDAS) Land and Marine Surface Stations Dataset. We compare 6-hourly observations of 10m wind speed between 1 January 1989 and 31 December 2009 from more the 500 surface stations with the corresponding reanalysis values. A station data based mean wind speed climatology for North Africa is presented. Overall, the representation of 10m winds is relatively poor in all three reanalysis datasets with stations in the northern parts of the Sahara still being better simulated (correlation coefficients ~ 0.5) than stations in the Sahel (correlation coefficients < 0.3) which points at the reanalyses not being able to realistically capture the Sahel dynamics systems. All three reanalyses have a systematic bias towards overestimating wind speed below 3-4 m/s and underestimating wind speed above 4 m/s. This bias becomes larger with increasing wind speed but is independent of the time of day. For instance, 14 m/s observed wind speeds are underestimated on average by 6 m/s in the ERA-Interim reanalysis. Given the cubic relationship between wind speed and dust emission this large underestimation is expected to significantly impact the simulation of dust emissions. A negative relationship between observed and ERA-Interim wind speed is found for winds above 14 m/s indicating that high wind speed generating processes are not well (if at all) represented in the model.

cDNA microarray analysis of esophageal cancer: discoveries and prospects.

PubMed

Shimada, Yutaka; Sato, Fumiaki; Shimizu, Kazuharu; Tsujimoto, Gozoh; Tsukada, Kazuhiro

2009-07-01

Recent progress in molecular biology has revealed many genetic and epigenetic alterations that are involved in the development and progression of esophageal cancer. Microarray analysis has also revealed several genetic networks that are involved in esophageal cancer. However, clinical application of microarray techniques and use of microarray data have not yet occurred. In this review, we focus on the recent developments and problems with microarray analysis of esophageal cancer.

Manufacturing of microarrays.

PubMed

Petersen, David W; Kawasaki, Ernest S

2007-01-01

DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. While the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions.

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

PubMed Central

Killion, Patrick J; Sherlock, Gavin; Iyer, Vishwanath R

2003-01-01

Background The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at Conclusions Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. PMID:12930545

Development and evaluation of a high-resolution reanalysis of the East Australian Current region using the Regional Ocean Modelling System (ROMS 3.4) and Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) data assimilation

NASA Astrophysics Data System (ADS)

Kerry, Colette; Powell, Brian; Roughan, Moninya; Oke, Peter

2016-10-01

As with other Western Boundary Currents globally, the East Australian Current (EAC) is highly variable making it a challenge to model and predict. For the EAC region, we combine a high-resolution state-of-the-art numerical ocean model with a variety of traditional and newly available observations using an advanced variational data assimilation scheme. The numerical model is configured using the Regional Ocean Modelling System (ROMS 3.4) and takes boundary forcing from the BlueLink ReANalysis (BRAN3). For the data assimilation, we use an Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) scheme, which uses the model dynamics to perturb the initial conditions, atmospheric forcing, and boundary conditions, such that the modelled ocean state better fits and is in balance with the observations. This paper describes the data assimilative model configuration that achieves a significant reduction of the difference between the modelled solution and the observations to give a dynamically consistent "best estimate" of the ocean state over a 2-year period. The reanalysis is shown to represent both assimilated and non-assimilated observations well. It achieves mean spatially averaged root mean squared (rms) residuals with the observations of 7.6 cm for sea surface height (SSH) and 0.4 °C for sea surface temperature (SST) over the assimilation period. The time-mean rms residual for subsurface temperature measured by Argo floats is a maximum of 0.9 °C between water depths of 100 and 300 m and smaller throughout the rest of the water column. Velocities at several offshore and continental shelf moorings are well represented in the reanalysis with complex correlations between 0.8 and 1 for all observations in the upper 500 m. Surface radial velocities from a high-frequency radar array are assimilated and the reanalysis provides surface velocity estimates with complex correlations with observed velocities of 0.8-1 across the radar footprint. A comparison with independent (non-assimilated) shipboard conductivity temperature depth (CTD) cast observations shows a marked improvement in the representation of the subsurface ocean in the reanalysis, with the rms residual in potential density reduced to about half of the residual with the free-running model in the upper eddy-influenced part of the water column. This shows that information is successfully propagated from observed variables to unobserved regions as the assimilation system uses the model dynamics to adjust the model state estimate. This is the first study to generate a reanalysis of the region at such a high resolution, making use of an unprecedented observational data set and using an assimilation method that uses the time-evolving model physics to adjust the model in a dynamically consistent way. As such, the reanalysis potentially represents a marked improvement in our ability to capture important circulation dynamics in the EAC. The reanalysis is being used to study EAC dynamics, observation impact in state-estimation, and as forcing for a variety of downscaling studies.

[Microarray CGH: principle and use for constitutional disorders].

PubMed

Sanlaville, D; Lapierre, J M; Coquin, A; Turleau, C; Vermeesch, J; Colleaux, L; Borck, G; Vekemans, M; Aurias, A; Romana, S P

2005-10-01

Chips technology has allowed to miniaturize process making possible to realize in one step and using the same device a lot of chemical reactions. The application of this technology to molecular cytogenetics resulted in the development of comparative genomic hybridization (CGH) on microarrays technique. Using this technique it is possible to detect very small genetic imbalances anywhere in the genome. Its usefulness has been well documented in cancer and more recently in constitutional disorders. In particular it has been used to detect interstitial and subtelomeric submicroscopic imbalances, to characterize their size at the molecular level or to define the breakpoints of translocation. The challenge today is to transfer this technology in laboratory medicine. Nevertheless this technology remains expensive and the existence of numerous sequence polymorphisms makes its interpretation difficult. Finally its is unlikely that it will make karyotyping obsolete as it does not allow to detect balanced rearrangements which after meiotic segregation might result in genome imbalance in the progeny.

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

PubMed Central

Thompson, Jeffrey A.; Tan, Jie

2016-01-01

Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language. PMID:26844019

Investigating the Genome Diversity of B. cereus and Evolutionary Aspects of B. anthracis Emergence

PubMed Central

Papazisi, Leka; Rasko, David A.; Ratnayake, Shashikala; Bock, Geoff R.; Remortel, Brian G.; Appalla, Lakshmi; Liu, Jia; Dracheva, Tatiana; Braisted, John C.; Shallom, Shamira; Jarrahi, Benham; Snesrud, Erik; Ahn, Susie; Sun, Qiang; Rilstone, Jenifer; Økstad, Ole Andreas; Kolstø, Anne-Brit; Fleischmann, Robert D.; Peterson, Scott N.

2011-01-01

Here we report the use of a multi-genome DNA microarray to investigate the genome diversity of Bacillus cereus group members and elucidate the events associated with the emergence of B. anthracis the causative agent of anthrax–a lethal zoonotic disease. We initially performed directed genome sequencing of seven diverse B. cereus strains to identify novel sequences encoded in those genomes. The novel genes identified, combined with those publicly available, allowed the design of a “species” DNA microarray. Comparative genomic hybridization analyses of 41 strains indicates that substantial heterogeneity exists with respect to the genes comprising functional role categories. While the acquisition of the plasmid-encoded pathogenicity island (pXO1) and capsule genes (pXO2) represent a crucial landmark dictating the emergence of B. anthracis, the evolution of this species and its close relatives was associated with an overall a shift in the fraction of genes devoted to energy metabolism, cellular processes, transport, as well as virulence. PMID:21447378

Fast gene ontology based clustering for microarray experiments.

PubMed

Ovaska, Kristian; Laakso, Marko; Hautaniemi, Sampsa

2008-11-21

Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data.

PubMed

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Song, Jiuzhou; Liu, George E

2013-06-25

Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed.

A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities.

PubMed

Soneson, Charlotte; Fontes, Magnus

2012-01-01

Analysis of multivariate data sets from, for example, microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper, we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward comparison between any 2 lists. It can also be used to generate new more stable gene rankings incorporating more information from the experimental data. Using 2 microarray data sets, we show that the proposed method provides more robust gene rankings than existing methods with respect to sampling variations, without compromising the biological significance of the rankings.

EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments (Volume 1) (Interagency Science Discussion Draft)

EPA Science Inventory

EPA is releasing the draft report, EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments (Volume 1), that was distributed to Federal agencies and White House Offices for comment during the Science Discussion step of the On the Extraction of Components and the Applicability of the Factor Model.

ERIC Educational Resources Information Center

Dziuban, Charles D.; Harris, Chester W.

A reanalysis of Shaycroft's matrix of intercorrelations of 10 test variables plus 4 random variables is discussed. Three different procedures were used in the reanalysis: (1) Image Component Analysis, (2) Uniqueness Rescaling Factor Analysis, and (3) Alpha Factor Analysis. The results of these analyses are presented in tables. It is concluded from…

EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments (External Review Draft)

EPA Science Inventory